Contacts of the helix formed by residues 21 - 47 (chain G) in PDB entry 4PHZ
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 LEU 21 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F THR* 4.7 17.3 - - + +
29F MET* 4.1 20.4 - - + -
19G VAL* 4.9 9.0 - - + -
20G ASP* 1.3 83.3 - - - +
22G ARG* 1.3 66.1 + - - +
23G GLY 3.2 3.1 - - - -
24G MET* 3.1 20.6 + - + +
25G TRP* 3.1 46.5 + - + +
105G VAL* 4.8 4.9 - - + -
109G GLN* 3.2 39.8 + - + +
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Residues in contact with ARG 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ASP* 3.0 40.7 + - - +
21G LEU* 1.3 79.5 - - - +
23G GLY* 1.3 57.5 + - - +
25G TRP* 3.4 35.8 - - - +
26G ILE* 2.9 44.0 + - + +
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Residues in contact with GLY 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ASP* 5.6 1.6 - - - +
21G LEU 3.2 1.4 - - - +
22G ARG* 1.3 79.3 - - - +
24G MET* 1.3 61.0 + - - +
26G ILE* 3.5 12.6 - - - +
27G GLY* 3.1 17.0 + - - -
109G GLN* 4.3 1.6 + - - -
302G PGT 3.6 40.8 - - - +
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Residues in contact with MET 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F MET* 3.9 34.5 - - + -
21G LEU* 3.1 19.6 + - + +
23G GLY* 1.3 73.4 - - - +
25G TRP* 1.3 95.6 + - + +
27G GLY* 3.0 2.9 + - - -
28G LEU* 2.7 48.5 + - + +
109G GLN* 3.6 25.8 + - + +
112G VAL* 3.7 26.7 - - + -
113G VAL* 4.2 2.3 - - + +
302G PGT 4.2 9.4 - - - -
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Residues in contact with TRP 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G LEU* 3.1 33.0 + - + +
22G ARG* 3.4 38.3 - - - +
24G MET* 1.3 103.1 - - + +
26G ILE* 1.3 66.1 + - + +
28G LEU* 4.1 20.0 - - + -
29G VAL* 2.8 35.9 + - + +
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Residues in contact with ILE 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G ARG* 2.9 36.3 + - + +
23G GLY* 3.5 9.9 - - - +
25G TRP* 1.3 74.5 - - + +
27G GLY* 1.3 53.4 + - - +
29G VAL* 3.7 4.5 - - - +
30G LEU* 2.8 61.9 + - + +
302G PGT 6.3 1.6 - - + -
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Residues in contact with GLY 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G GLY 3.1 8.1 + - - -
24G MET 3.0 6.0 + - - -
26G ILE* 1.3 78.9 - - - +
28G LEU* 1.3 63.2 + - - +
30G LEU* 3.2 4.7 + - - +
31G LEU* 3.0 27.1 + - - +
113G VAL* 4.3 6.7 - - - -
302G PGT 3.9 32.9 - - - +
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Residues in contact with LEU 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G MET* 2.7 33.2 + - + +
25G TRP* 3.7 28.9 - - + +
27G GLY* 1.3 70.3 - - - +
29G VAL* 1.3 64.3 + - + +
31G LEU* 3.9 2.5 - - + +
32G ASN* 2.9 40.2 + - - +
112G VAL* 4.4 10.3 - - + -
113G VAL* 3.9 19.3 - - + +
116G ILE* 4.1 40.4 - - + -
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Residues in contact with VAL 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G TRP* 2.8 29.4 + - + +
26G ILE* 3.7 4.5 - - - +
28G LEU* 1.3 73.6 - - + +
30G LEU* 1.3 61.0 + - + +
31G LEU 2.9 6.8 + - - -
32G ASN* 4.9 2.2 - - - +
33G VAL* 3.0 41.6 + - + +
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Residues in contact with LEU 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G ILE* 2.8 46.6 + - + +
27G GLY* 3.2 7.6 + - - +
29G VAL* 1.3 75.5 - - + +
31G LEU* 1.3 56.6 + - - +
33G VAL* 4.9 2.9 - - - +
34G PHE* 3.4 11.4 + - - +
302G PGT 3.3 49.5 - - + +
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Residues in contact with LEU 31 (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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27G GLY 3.0 14.5 + - - +
28G LEU* 3.9 3.8 - - + +
30G LEU* 1.3 77.0 - - - +
32G ASN* 1.3 67.9 + - - +
33G VAL 3.2 1.3 - - - -
34G PHE* 2.9 7.0 + - + +
35G TYR* 2.8 45.4 + - + +
113G VAL* 4.6 13.9 - - + +
116G ILE* 3.5 28.0 - - + -
117G ALA* 3.9 24.0 - - + +
156G ILE* 4.2 17.5 - - + -
160G ILE* 4.8 0.4 - - + -
302G PGT 3.8 34.8 - - + -
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Residues in contact with ASN 32 (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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28G LEU* 2.9 36.2 + - - +
29G VAL* 4.3 2.2 - - - +
31G LEU* 1.3 77.2 - - - +
33G VAL* 1.3 58.7 + - + +
35G TYR* 3.4 1.7 + - - +
36G LEU* 2.9 41.2 + - + +
116G ILE* 4.0 12.7 - - - +
120G TRP* 3.3 34.0 + - + +
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Residues in contact with VAL 33 (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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29G VAL* 3.0 32.4 + - + +
30G LEU* 4.8 2.7 - - - +
32G ASN* 1.3 76.6 - - + +
34G PHE* 1.3 67.6 + - - +
36G LEU* 3.0 8.6 + - - +
37G ILE* 2.9 39.3 + - + +
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Residues in contact with PHE 34 (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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30G LEU 3.4 20.3 + - - +
31G LEU* 2.9 10.1 + - + +
33G VAL* 1.3 77.7 - - - +
35G TYR* 1.3 73.7 + + - +
37G ILE* 3.3 18.7 + - + +
38G VAL* 3.0 52.3 + - + +
152G MET* 3.8 27.4 - - + -
156G ILE* 4.1 13.0 - - + -
302G PGT 3.8 28.9 - - + -
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Residues in contact with TYR 35 (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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31G LEU* 2.8 38.4 + - + +
32G ASN 3.9 0.7 - - - +
34G PHE* 1.3 84.6 - + - +
36G LEU* 1.3 57.8 + - - +
38G VAL* 3.2 3.5 + - + +
39G ARG* 2.7 36.4 + - - +
117G ALA* 5.1 4.0 + - - -
120G TRP* 3.2 63.6 - + + +
125G PHE* 3.5 17.0 - + + -
152G MET* 3.1 31.0 - - + -
153G SER* 3.2 29.3 + - - -
156G ILE* 3.5 22.7 - - + +
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Residues in contact with LEU 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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32G ASN* 2.9 27.0 + - + +
33G VAL* 3.3 7.9 - - - +
35G TYR* 1.3 73.6 - - - +
37G ILE* 1.3 67.2 + - + +
39G ARG* 3.2 6.4 + - + +
40G ILE* 2.8 53.1 + - + +
120G TRP* 4.6 15.7 - - + -
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Residues in contact with ILE 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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33G VAL* 2.9 38.2 + - + +
34G PHE* 3.3 18.2 - - + +
36G LEU* 1.3 76.0 - - + +
38G VAL* 1.3 56.9 + - + +
40G ILE* 3.3 9.4 + - + +
41G TYR* 2.7 44.7 + - + +
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Residues in contact with VAL 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 PHE* 3.0 51.2 + - + +
35G TYR* 3.2 9.2 + - - +
37G ILE* 1.3 78.9 - - + +
39G ARG* 1.3 57.6 + - - +
41G TYR* 3.3 10.7 + - + +
42G GLU* 2.9 28.2 + - - +
62G TRP* 6.2 0.2 - - + -
125G PHE* 4.2 6.5 - - + -
148G ILE* 3.9 43.3 - - + -
152G MET* 4.0 9.4 - - + -
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Residues in contact with ARG 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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111F VAL* 3.0 34.9 + - + +
112F ASN* 3.0 15.1 + - - -
115F GLY 3.9 0.8 - - - -
116F TRP* 3.4 24.7 - - - +
35G TYR 2.7 20.0 + - - +
36G LEU* 3.7 6.3 - - + +
38G VAL* 1.3 69.8 - - - +
40G ILE* 1.3 67.1 + - + +
42G GLU* 3.1 24.7 - - - +
43G GLN* 2.8 49.6 + - - +
120G TRP* 5.2 2.2 - - + -
124G PHE* 3.8 21.8 - - + -
125G PHE* 4.7 1.1 - - + -
128G GLN* 3.7 7.2 - - - +
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Residues in contact with ILE 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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36G LEU* 2.8 47.6 + - + +
37G ILE* 3.6 7.2 - - - +
39G ARG* 1.3 73.7 - - + +
41G TYR* 1.3 65.9 + - - +
43G GLN* 3.1 23.3 + - + +
44G VAL* 3.2 15.3 + - + +
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Residues in contact with TYR 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 ILE* 2.7 29.2 + - + +
38G VAL* 3.5 9.4 - - + +
40G ILE* 1.3 76.0 - - + +
42G GLU* 1.3 59.1 + - - +
44G VAL* 3.1 8.1 + - - +
45G PHE* 2.9 55.0 + + + -
61G TYR* 2.7 41.5 + + - +
62G TRP* 3.8 29.4 - + - -
64G SER* 5.1 1.2 + - - -
65G ILE* 3.8 17.4 - - + +
148G ILE* 6.3 0.2 - - + -
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Residues in contact with GLU 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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116F TRP* 2.9 28.8 + - + -
38G VAL 2.9 16.4 + - - +
39G ARG* 3.1 34.3 - - - +
41G TYR* 1.3 73.5 - - - +
43G GLN* 1.3 60.4 + - - +
46G GLY* 2.9 22.7 + - - -
62G TRP* 3.4 26.5 - - + -
125G PHE* 3.3 13.1 - - - -
128G GLN* 2.8 40.3 + - - +
144G PRO 4.8 2.3 - - - +
145G SER* 5.2 0.3 - - - -
148G ILE* 3.6 22.7 - - - +
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Residues in contact with GLN 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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115F GLY 3.3 20.2 + - - +
116F TRP* 3.6 20.1 + - - +
118F TYR* 3.5 17.4 + - - -
39G ARG* 2.8 44.4 + - - +
40G ILE* 3.2 14.6 - - + +
42G GLU* 1.3 80.0 - - - +
44G VAL* 1.3 66.6 + - + +
46G GLY 3.9 1.9 + - - -
47G TRP* 4.0 20.6 + - - +
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Residues in contact with VAL 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 ILE* 3.2 14.5 + - + +
41G TYR* 3.1 9.9 + - - +
43G GLN* 1.3 84.5 - - + +
45G PHE* 1.3 90.1 + - + +
46G GLY 3.3 0.4 - - - -
47G TRP 3.1 19.6 - - - +
48G ARG 4.3 0.9 - - - +
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Residues in contact with PHE 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 TYR* 2.9 51.6 + + + +
44G VAL* 1.3 94.7 - - + +
46G GLY* 1.3 61.8 + - - +
47G TRP 4.3 0.4 - - - -
48G ARG 4.2 2.5 - - - -
49G ALA* 2.9 26.2 - - + +
50G GLY 3.3 1.0 + - - -
61G TYR* 3.4 49.6 - + + -
62G TRP* 2.8 35.1 + - + +
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Residues in contact with GLY 46 (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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116F TRP* 4.4 4.9 - - - -
42G GLU 2.9 23.1 + - - -
45G PHE* 1.3 77.1 - - - +
47G TRP* 1.3 59.8 + - - +
48G ARG 3.5 0.9 + - - -
50G GLY* 3.2 27.3 + - - -
51G LEU* 3.9 1.7 - - - +
62G TRP* 4.1 9.0 - - - -
132G TRP* 3.6 25.4 - - - -
144G PRO* 5.1 0.9 - - - -
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Residues in contact with TRP 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E PRO* 3.8 19.2 + - + +
128E ARG* 3.5 33.9 - - - +
132E TRP* 3.6 26.7 - + + -
116F TRP* 2.3 71.3 - + - -
117F THR* 3.2 28.7 - - + -
118F TYR* 4.8 0.2 - + - -
43G GLN* 4.0 17.1 + - - +
44G VAL 3.1 14.3 - - - +
46G GLY* 1.3 70.4 - - - +
48G ARG* 1.3 79.5 + - + +
51G LEU* 4.2 14.1 - - + -
132G TRP* 4.4 4.5 - + - -
135G THR* 4.2 14.1 - - + +
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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