Nginx error upstream timed out (110: Connection timed out) while SSL handshaking to upstream

Question

I have three docker containers in my project: Nginx, tornado-app, and DB. My Tornado app serves WebSocket app (URLs are /clientSocket and /gatewaySocket) and Django app (URLs are everything except WebSocket URLs).I use upstream for serving tornado app (that runs in port 8000) with Nginx. my Project just works fine in last few months with no errors until today that I got strange 504 Errors from Nginx. Here is my Nginx config file:

limit_req_zone $binary_remote_addr zone=one:10m rate=10r/s;
limit_req_zone $binary_remote_addr zone=sms:10m rate=1r/m;

upstream my_server{
    server web_instance_1:8000;  # tornado app
}

map $http_upgrade $connection_upgrade {
    default upgrade;
    ''      close;
}

server {
    listen      80;
    server_name server.com;
    return 301 https://$host$request_uri;
}

server {
    listen       443 ssl;
    server_name  server.com;
    ssl on;

    ssl_certificate /etc/nginx/ssl/chained.crt;
    ssl_certificate_key /etc/nginx/ssl/nginx.key;


    location / {
#        limit_req zone=one burst=5;
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header X-Forwarded-For $remote_addr;
        proxy_set_header Host $host;
        proxy_pass      https://my_server;
    }

    location /rest/register/gateway/phone_number {
        limit_req zone=sms burst=5;
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header X-Forwarded-For $remote_addr;
        proxy_set_header Host $host;
        proxy_pass      https://my_server;
    }

    location ~ /.well-known {
        root /var/www/acme;
        allow all;
    }

    location ~ ^/(admin|main-panel) {
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header X-Forwarded-For $remote_addr;
        proxy_set_header Host $host;
        proxy_pass      https://my_server;
    }

    location /gatewaySocket {
        proxy_set_header Upgrade $http_upgrade;
        proxy_set_header Connection $connection_upgrade;
        proxy_pass      https://my_server;
    }

    location /clientSocket {
        proxy_http_version 1.1;
        proxy_set_header Upgrade $http_upgrade;
        proxy_set_header Connection $connection_upgrade;
        proxy_pass      https://my_server;
    }
}

and here the strange upstream timeout Errors :

2018/06/12 19:23:09 [error] 5#5: *154 upstream timed out (110:Connection timed out) while reading response header from upstream,client: x.x.x.x, server: server.com, request: "GET /admin/main/serverlogs/834591/change/ HTTP/1.1", upstream:"https://172.18.0.3:8000/admin/main/serverlogs/834591/change/",host:"server.com", referrer: "https://server.com/admin/main/serverlogs/"


2018/06/12 19:23:09 [error] 5#5: *145 upstream timed out (110:Connection timed out) while reading response header from upstream,client: x.x.x.x, server: server.com, request: "GET /robots.txtHTTP/1.1", upstream:"https://172.18.0.3:8000/robots.txt",host:"server.com"


2018/06/12 19:40:51 [error] 5#5: *420 upstream timed out (110:Connection timed out) while SSL handshaking to upstream, client:x.x.x.x, server: server.com, request: "GET /gatewaySocket HTTP/1.1",upstream: "https://172.18.0.3:8000/gatewaySocket",host:"server.com:443"