Contacts of the helix formed by residues 25 - 51 (chain G) in PDB entry 2Q9Q
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 25 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G GLU* 3.9 23.1 + - - +
9G LEU* 3.6 17.8 - - + +
12G GLU* 3.2 27.5 + - - +
23G ALA 3.1 2.8 + - - +
24G PHE* 1.3 71.7 - - - +
26G GLU* 1.3 61.2 + - - +
27G ASP* 3.6 7.6 + - - +
28G GLY* 2.8 29.1 + - - +
29G LEU* 3.1 20.1 + - - +
79G TYR* 2.8 22.3 + - - +
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Residues in contact with GLU 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU* 5.4 7.4 - - - +
24G PHE* 3.1 33.6 + - + +
25G ASN* 1.3 73.2 - - - +
27G ASP* 1.3 64.0 + - - +
29G LEU* 3.4 5.4 + - + +
30G ARG* 2.9 28.0 + - + +
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Residues in contact with ASP 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A HIS* 4.3 7.6 + - - -
81A GLU* 2.8 38.5 + - - +
5G LYS* 5.6 1.8 - - - +
25G ASN* 3.3 6.2 + - - +
26G GLU* 1.3 78.3 - - - +
28G GLY* 1.3 57.9 + - - +
30G ARG* 3.0 27.6 + - - +
31G GLN* 2.9 45.6 + - - +
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Residues in contact with GLY 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G LYS* 3.6 24.4 - - - +
8G GLU* 5.7 0.2 - - - -
9G LEU* 4.3 10.1 - - - -
25G ASN* 2.8 26.4 + - - -
27G ASP* 1.3 74.2 - - - +
29G LEU* 1.3 56.8 + - - +
31G GLN* 3.4 1.2 + - - +
32G VAL* 3.0 36.7 + - - +
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Residues in contact with LEU 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F VAL* 3.9 22.9 - - + +
145F ALA* 4.5 4.5 - - + -
9G LEU* 4.2 14.2 - - + +
24G PHE* 3.7 30.7 - - + -
25G ASN 3.1 18.1 + - - +
26G GLU* 3.8 6.5 - - + +
28G GLY* 1.3 75.2 - - - +
30G ARG* 1.3 62.1 + - - +
32G VAL* 3.9 2.8 - - + +
33G LEU* 3.1 46.0 + - + +
76G THR* 3.8 31.4 - - + +
79G TYR* 5.6 3.6 - - + -
80G LEU* 4.7 7.2 - - + -
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Residues in contact with ARG 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G GLU* 2.9 20.2 + - + +
27G ASP* 3.0 33.2 + - - +
29G LEU* 1.3 76.0 - - - +
31G GLN* 1.3 86.3 + - - +
33G LEU* 3.3 10.2 + - + +
34G GLU* 2.9 62.9 + - + +
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Residues in contact with GLN 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G LYS* 3.4 45.6 + - + +
27G ASP* 2.9 29.9 + - - +
28G GLY 3.8 3.8 - - - +
30G ARG* 1.3 92.3 - - - +
32G VAL* 1.3 60.4 + - - +
34G GLU* 3.2 12.7 + - - +
35G GLU* 2.9 29.0 + - - +
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Residues in contact with VAL 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G LYS* 4.0 9.0 - - + -
6G ALA* 3.6 35.0 - - + +
9G LEU* 4.3 7.9 - - + -
28G GLY 3.0 22.5 + - - +
29G LEU* 3.9 5.8 - - - +
30G ARG 3.3 0.2 - - - -
31G GLN* 1.3 74.4 - - - +
33G LEU* 1.3 59.7 + - + +
35G GLU* 3.1 10.9 + - - +
36G MET* 2.9 30.2 + - - +
72G ASN* 3.7 28.4 - - + +
76G THR* 3.6 23.6 - - - +
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Residues in contact with LEU 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F VAL 4.9 2.5 - - - +
145F ALA* 4.3 12.8 - - + +
148F HIS* 4.0 35.9 - - + +
149F MET* 3.9 33.4 - - + -
150F PRO* 5.7 0.3 - - - +
29G LEU* 3.1 40.1 + - + +
30G ARG* 3.6 8.5 - - + +
32G VAL* 1.3 78.3 - - + +
34G GLU* 1.3 61.7 + - + +
36G MET* 3.3 12.7 + - - +
37G LYS* 3.1 22.2 + - - +
76G THR* 5.4 1.3 - - - +
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Residues in contact with GLU 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G ARG* 2.9 56.1 + - + +
31G GLN* 3.2 11.9 + - - +
33G LEU* 1.3 77.9 - - + +
35G GLU* 1.3 58.2 + - - +
37G LYS* 3.5 13.6 + - + +
38G ALA* 3.1 26.5 + - - +
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Residues in contact with GLU 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET 5.3 0.7 - - - +
2G PHE* 3.2 24.7 - - + +
3G CYS* 2.8 30.2 + - - -
4G GLU 5.0 0.7 + - - -
5G LYS* 4.6 16.3 - - - +
31G GLN 2.9 12.7 + - - +
32G VAL* 3.5 9.4 - - - +
34G GLU* 1.3 75.8 - - - +
36G MET* 1.3 59.9 + - - +
37G LYS 3.2 0.2 - - - -
38G ALA* 3.8 6.5 - - + +
39G LEU* 2.9 39.0 + - + +
72G ASN* 3.5 17.0 + - - +
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Residues in contact with MET 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F MET* 3.5 42.6 - - + +
150F PRO* 3.5 18.5 - - + +
153F LEU* 4.5 7.9 - - + -
32G VAL* 2.9 19.2 + - - +
33G LEU* 3.7 20.4 - - + +
34G GLU 3.3 0.2 - - - -
35G GLU* 1.3 76.3 - - - +
37G LYS* 1.3 56.1 + - - +
39G LEU* 4.4 1.1 - - - -
40G TYR* 2.9 27.2 + - - +
69G LEU* 3.2 40.7 - - + +
72G ASN* 3.5 29.8 - - + +
73G ARG* 4.0 10.5 - - + -
76G THR* 5.0 0.7 - - - -
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Residues in contact with LYS 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F PRO* 4.5 6.0 - - + +
33G LEU 3.1 14.1 + - - +
34G GLU* 3.6 14.6 - - + +
35G GLU 3.2 0.2 - - - -
36G MET* 1.3 75.1 - - - +
38G ALA* 1.3 66.7 + - - +
40G TYR* 3.1 11.0 + - + +
41G GLU* 2.9 54.6 + - - +
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Residues in contact with ALA 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G GLU 3.1 14.6 + - - +
35G GLU* 3.8 7.6 - - + +
37G LYS* 1.3 79.1 - - - +
39G LEU* 1.3 57.5 + - + +
41G GLU* 3.3 16.5 - - - +
42G GLN* 3.0 35.5 + - - +
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Residues in contact with LEU 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G PHE* 3.5 38.1 - - + -
35G GLU* 2.9 37.4 + - + +
38G ALA* 1.3 78.0 - - + +
40G TYR* 1.3 56.8 + - - +
42G GLN* 3.8 5.6 - - - +
43G ASN* 3.0 30.3 + - - +
65G ARG* 3.6 28.5 - - + +
68G SER* 3.9 17.0 - - - -
69G LEU* 3.6 24.6 - - + +
72G ASN* 3.7 25.4 - - - +
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Residues in contact with TYR 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F PRO* 3.5 16.8 - - + -
151F PRO* 3.5 36.7 - - + +
152F ASN* 3.4 34.1 - - - -
36G MET 2.9 18.8 + - - +
37G LYS* 3.1 9.4 + - + +
39G LEU* 1.3 77.9 - - - +
41G GLU* 1.3 62.5 + - + +
43G ASN* 3.4 4.0 + - + +
44G GLN* 3.0 71.8 + - + +
69G LEU* 4.2 12.7 - - + +
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Residues in contact with GLU 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G LYS* 2.9 48.1 + - - +
38G ALA* 3.3 19.1 - - - +
40G TYR* 1.3 78.1 - - + +
42G GLN* 1.3 63.8 + - - +
43G ASN 3.1 0.7 - - - -
44G GLN* 3.3 10.4 + - - +
45G SER* 3.1 24.1 + - - -
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Residues in contact with GLN 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G PHE* 4.4 14.2 - - - -
38G ALA* 3.0 21.6 + - - +
39G LEU* 3.8 6.7 - - - +
41G GLU* 1.3 77.7 - - + +
43G ASN* 1.3 60.9 + - - +
45G SER* 3.8 6.4 + - - -
46G ASP* 3.5 15.8 + - - +
65G ARG* 3.3 46.6 + - - +
42H ARG* 5.7 6.6 + - - +
43H LEU* 5.8 0.3 - - - +
47H PHE* 6.1 3.4 - - - -
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Residues in contact with ASN 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G LEU 3.0 15.8 + - - +
40G TYR* 3.7 7.6 - - + +
41G GLU 3.1 0.2 - - - -
42G GLN* 1.3 76.9 - - - +
44G GLN* 1.3 54.0 + - - +
45G SER 3.2 0.2 - - - -
46G ASP* 3.0 2.9 + - - +
47G VAL* 2.8 43.4 + - + +
62G ILE* 3.1 44.2 + - - +
65G ARG* 2.6 41.1 + - - +
66G HIS* 4.0 15.2 + - - +
69G LEU* 4.9 5.1 - - + +
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Residues in contact with GLN 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G TYR* 3.0 63.5 + - + +
41G GLU* 3.5 10.1 - - - +
43G ASN* 1.3 75.5 - - - +
45G SER* 1.3 62.3 + - - +
47G VAL* 3.3 21.6 + - - +
48G ASN* 3.3 15.9 + - - +
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Residues in contact with SER 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G GLU 3.1 16.0 + - - -
42G GLN* 3.8 9.4 - - - -
43G ASN 3.2 0.2 - - - -
44G GLN* 1.3 78.0 - - - +
46G ASP* 1.3 64.4 + - - +
48G ASN* 4.1 4.7 + - - +
49G GLU* 3.7 22.2 + - - +
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Residues in contact with ASP 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G GLN* 3.5 6.9 + - - +
43G ASN 3.0 4.9 + - - +
45G SER* 1.3 82.0 + - - +
47G VAL* 1.3 61.8 + - - +
48G ASN 3.2 1.8 - - - -
49G GLU* 3.8 3.3 - - - +
50G ALA* 3.0 31.7 + - - +
58G LEU* 3.8 16.4 - - + +
61G THR* 4.3 0.9 - - - +
62G ILE* 4.2 10.5 - - + -
65G ARG* 2.5 37.5 + - - +
42H ARG* 2.5 44.3 + - - -
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Residues in contact with VAL 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G ASN* 2.8 31.4 + - + +
44G GLN* 3.3 14.8 + - - +
46G ASP* 1.3 77.6 - - - +
48G ASN* 1.3 56.9 + - - +
50G ALA* 4.5 0.2 - - - -
51G LYS* 2.9 54.3 + - + +
52G SER* 4.8 0.2 + - - -
62G ILE* 3.9 32.1 - - + -
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Residues in contact with ASN 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G GLN 3.3 12.2 + - - +
45G SER* 4.4 5.6 + - - +
46G ASP 3.2 0.2 - - - -
47G VAL* 1.3 77.7 - - - +
49G GLU* 1.3 58.5 + - - +
50G ALA 3.1 4.7 - - - -
52G SER* 2.9 55.0 + - - +
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Residues in contact with GLU 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G SER* 3.7 17.9 + - - +
46G ASP* 3.4 6.3 + - - +
48G ASN* 1.3 82.2 - - - +
50G ALA* 1.3 56.9 + - - +
52G SER 4.6 2.2 - - - -
53G GLY 3.0 32.2 - - - +
54G GLY* 3.4 3.5 + - - -
58G LEU* 3.3 15.7 - - + +
42H ARG* 2.9 32.1 + - - -
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Residues in contact with ALA 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ASP 3.0 18.0 + - - +
47G VAL 4.0 1.6 - - - +
49G GLU* 1.3 76.6 - - - +
51G LYS* 1.3 63.2 + - + +
52G SER 2.8 10.1 + - - -
53G GLY 3.6 0.3 + - - -
54G GLY* 3.5 25.9 + - - +
56G SER* 4.7 19.7 + - - +
58G LEU* 4.1 21.5 - - + -
59G ILE* 5.4 2.9 - - + +
62G ILE* 4.2 10.5 - - + -
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Residues in contact with LYS 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G VAL* 2.9 37.7 + - + +
50G ALA* 1.3 78.5 - - + +
52G SER* 1.3 66.1 + - - +
56G SER* 6.0 0.4 - - - -
59G ILE* 5.4 14.8 - - + +
62G ILE* 5.6 7.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il