Contacts of the helix formed by residues 33 - 61 (chain B) in PDB entry 6N1G
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 MET 33 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LYS* 1.3 74.1 - - - +
34B VAL* 1.3 57.3 + - - +
35B ARG 3.0 4.5 - - - -
36B GLU* 2.5 26.6 + - - +
37B PHE* 2.8 12.4 + - - +
110B ARG 4.9 0.7 - - - +
111B LYS* 3.6 36.8 - - + +
114B VAL* 3.2 44.2 - - + -
115B TYR* 3.1 39.0 - - + -
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LYS* 3.3 27.1 - - + +
33B MET* 1.3 79.3 - - - +
35B ARG* 1.3 61.6 + - - +
36B GLU 3.2 0.2 - - - -
37B PHE* 4.0 16.8 - - + -
38B LEU* 3.2 28.2 + - + +
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Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LYS* 2.8 82.1 - - - +
33B MET 3.0 0.2 - - - -
34B VAL* 1.3 78.6 - - - +
36B GLU* 1.3 57.1 + - - +
38B LEU* 4.1 4.8 - - - +
39B ALA* 3.5 15.2 + - - +
88B ILE* 3.2 36.1 - - + +
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Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LYS 4.0 8.1 - - - +
33B MET* 2.5 22.6 + - - +
35B ARG* 1.3 71.7 - - - +
37B PHE* 1.3 78.8 + - - -
38B LEU 3.1 1.8 - - - -
39B ALA* 3.0 6.2 + - - +
40B GLU* 2.8 43.3 + - - +
88B ILE* 3.6 29.4 - - + +
89B SER* 3.1 11.7 - - - -
111B LYS* 5.2 1.8 - - - +
115B TYR* 2.7 58.3 - - - +
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Residues in contact with PHE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B MET* 2.8 14.5 + - + +
34B VAL* 4.2 16.4 - - + +
36B GLU* 1.3 81.6 + - - +
38B LEU* 1.3 59.8 + - - +
40B GLU* 3.0 6.6 + - - +
41B PHE* 2.8 33.4 + + + +
114B VAL* 2.7 51.4 - - + -
115B TYR* 4.9 0.2 - - - -
117B LEU* 3.5 19.5 - - + -
118B GLY* 3.0 32.2 - - - -
121B LEU* 5.0 13.7 - - + -
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 3.2 22.1 + - + +
35B ARG* 4.1 6.1 - - - +
36B GLU 3.1 0.6 - - - -
37B PHE* 1.3 83.4 - - + +
39B ALA* 1.3 56.4 - - - +
41B PHE* 3.5 13.7 + - + +
42B MET* 3.0 43.9 + - + +
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ARG 3.5 6.4 + - - +
36B GLU* 3.0 8.8 + - - +
38B LEU* 1.3 78.5 - - - +
40B GLU* 1.3 57.6 + - - +
42B MET* 3.2 17.0 - - + +
43B SER* 3.0 32.9 + - - -
85B ALA* 3.5 14.3 - - + +
88B ILE* 3.2 35.4 - - + -
89B SER* 4.6 4.5 - - - -
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Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLU* 2.8 38.2 + - - +
37B PHE* 3.0 8.9 + - - +
39B ALA* 1.3 74.9 - - - +
41B PHE* 1.3 63.2 + - - +
44B THR* 2.8 30.8 + - - -
89B SER* 3.1 21.1 - - - -
92B HIS* 3.1 27.8 + - - +
93B MET* 3.2 15.9 - - - +
115B TYR* 4.1 12.1 - - + +
118B GLY* 3.9 4.3 - - - +
119B GLN* 2.8 42.1 + - + +
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 2.8 18.8 + + + +
38B LEU* 3.5 19.5 - - + +
40B GLU* 1.3 77.0 - - - +
42B MET* 1.3 69.2 + - + +
45B TYR* 3.3 28.0 + + - +
118B GLY* 3.2 19.2 + - - +
121B LEU* 3.4 46.0 - - + -
122B GLY* 3.4 22.0 - - - -
125B LEU* 3.3 34.5 - - + -
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Residues in contact with MET 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.0 43.5 + - + +
39B ALA* 3.2 24.2 - - + +
41B PHE* 1.3 82.3 - - + +
43B SER* 1.3 65.6 + - - +
45B TYR* 3.2 7.8 - - - +
46B VAL* 3.1 31.9 + - + +
84B VAL* 4.4 22.0 - - + +
85B ALA* 4.5 4.3 - - + -
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Residues in contact with SER 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA 3.0 20.0 + - - -
41B PHE 3.4 0.2 - - - -
42B MET* 1.3 77.2 - - - +
44B THR* 1.3 60.3 + - - +
46B VAL* 3.7 4.1 + - - +
47B MET* 3.6 18.2 + - - +
81B GLY* 2.6 37.7 + - - -
84B VAL* 4.0 8.5 - - - -
85B ALA* 3.6 11.7 - - - -
91B ALA* 5.4 0.3 - - - -
93B MET* 3.1 25.8 - - - +
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Residues in contact with THR 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLU 2.8 14.1 + - - -
41B PHE 4.3 1.8 - - - -
43B SER* 1.3 71.9 - - - +
45B TYR* 1.3 62.4 + - - +
47B MET* 3.0 34.6 - - + +
48B MET* 3.2 10.9 + - - +
93B MET* 2.6 33.6 - - - +
119B GLN* 3.5 25.0 - - + +
122B GLY 4.5 0.2 - - - -
123B SER* 2.9 31.6 + - - +
226B ASN* 4.4 10.5 - - - +
228B SER* 4.2 6.3 - - - +
229B ARG* 5.3 1.3 - - - +
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Residues in contact with TYR 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 3.3 21.5 + + - +
42B MET* 3.2 13.5 - - - +
44B THR* 1.3 74.8 - - - +
46B VAL* 1.3 68.8 + - + +
48B MET* 2.8 4.0 + - - +
49B VAL* 2.8 46.2 + - + +
122B GLY* 3.0 24.3 + - - -
125B LEU* 2.6 26.2 + - + +
126B ALA* 3.1 30.5 - - + -
129B THR* 2.1 42.2 + - + +
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B MET* 3.1 16.7 + - + +
43B SER* 3.7 8.0 + - - +
44B THR 3.5 0.4 - - - -
45B TYR* 1.3 78.7 - - + +
47B MET* 1.3 61.3 + - - +
49B VAL* 3.5 9.2 - - + -
50B PHE* 3.0 58.2 + - + +
77B GLY 4.0 12.1 - - - +
80B MET* 4.0 11.4 - - + -
81B GLY* 4.4 4.3 - - - +
84B VAL* 4.8 14.4 - - + -
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Residues in contact with MET 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B SER 3.6 4.6 + - - +
44B THR* 3.0 33.9 - - + +
45B TYR 3.1 0.6 - - - -
46B VAL* 1.3 79.8 - - - +
48B MET* 1.3 57.3 + - + +
50B PHE* 4.2 1.0 - - - +
51B GLY* 2.7 27.4 + - - -
74B PHE* 4.1 18.0 - - + +
77B GLY* 4.3 10.9 - - - +
78B VAL* 3.7 51.8 - - + +
81B GLY* 5.2 1.6 - - - -
93B MET* 3.6 44.6 - - + +
226B ASN* 4.5 7.0 - - - -
229B ARG* 5.3 6.5 - - + -
403B GOL 5.6 0.2 - - - +
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Residues in contact with MET 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B THR 3.2 13.1 + - - +
45B TYR 2.8 8.3 + - - +
47B MET* 1.3 72.4 - - + +
49B VAL* 1.3 57.0 + - - +
52B LEU* 2.3 67.8 + - + +
74B PHE* 5.5 3.1 - - + -
123B SER* 4.2 13.0 - - - +
126B ALA* 3.4 27.1 - - + -
158B PHE 2.7 30.5 - - - +
229B ARG* 3.2 50.3 - - - +
233B PRO* 3.4 13.9 - - + -
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Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TYR* 2.8 51.8 + - + +
46B VAL* 3.4 16.4 - - + +
48B MET* 1.3 73.1 - - - +
50B PHE* 1.3 70.1 + - + +
52B LEU* 4.6 2.5 - - - -
53B GLY* 2.8 27.9 + - - +
126B ALA* 4.2 8.0 - - + +
129B THR* 5.9 3.4 - - + -
130B ILE* 4.5 18.1 - - + +
133B LEU* 6.0 5.6 - - + -
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 3.0 45.4 + - + +
47B MET 4.2 1.6 - - - +
49B VAL* 1.3 87.8 - - + +
51B GLY* 1.3 59.1 + - - +
53B GLY* 5.2 0.2 - - - -
54B SER* 3.4 24.6 + - - -
73B GLY 4.6 9.7 - - - +
77B GLY* 4.0 23.3 - - - -
80B MET* 4.3 15.3 - - + -
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Residues in contact with GLY 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B MET 2.7 23.1 + - - -
48B MET* 4.7 1.3 - - - -
50B PHE* 1.3 74.7 - - - +
52B LEU* 1.3 60.5 + - - +
54B SER* 3.7 7.5 + - - -
55B VAL* 3.2 24.6 - - - +
74B PHE* 3.7 30.9 - - - +
229B ARG* 5.7 2.9 - - - -
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B MET* 2.3 53.2 + - + +
49B VAL 4.6 0.2 - - - +
51B GLY* 1.3 66.8 - - - -
53B GLY* 1.3 64.4 + - - +
55B VAL* 3.5 0.9 + - - +
56B ALA* 3.0 25.0 + - + +
127B ALA* 3.7 15.3 - - + -
130B ILE* 3.4 35.9 - - + -
157B ILE* 3.5 28.7 - - + +
158B PHE* 3.4 39.7 - - + -
229B ARG* 5.8 0.4 - - - +
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Residues in contact with GLY 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL 2.8 21.9 + - - -
50B PHE 4.6 0.2 - - - -
52B LEU* 1.3 78.8 - - - +
54B SER* 1.3 56.1 + - - +
56B ALA* 3.4 1.6 + - - +
57B HIS* 2.9 30.7 + - - +
130B ILE* 3.4 22.7 - - - +
134B PHE* 3.9 6.5 - - - -
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Residues in contact with SER 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE 3.4 18.5 + - - -
51B GLY* 3.7 6.1 + - - -
52B LEU 3.3 0.6 - - - -
53B GLY* 1.3 76.2 - - - +
55B VAL* 1.3 62.8 + - - +
57B HIS* 3.5 10.3 - - - +
58B MET* 3.4 16.8 + - - +
63B LYS* 4.5 18.7 + - - +
69B GLY 5.0 3.0 + - - -
70B VAL* 4.9 21.3 - - - +
73B GLY* 5.2 9.1 - - - -
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLY 3.2 19.7 - - - +
52B LEU 3.5 1.3 + - - +
53B GLY 3.2 0.2 - - - -
54B SER* 1.3 75.6 - - - +
56B ALA* 1.3 62.2 + - - +
57B HIS 3.2 0.9 - - - -
58B MET* 2.9 30.5 + - + +
59B VAL* 3.2 14.6 + - + +
70B VAL* 5.0 16.8 - - + -
156B GLY 4.2 7.9 - - - +
157B ILE* 3.9 33.9 - - + +
223B TYR* 5.9 2.5 - - - +
229B ARG* 6.0 2.5 - - - +
402B GOL 6.2 3.8 - - - -
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.0 30.7 + - + +
53B GLY 3.7 0.4 - - - +
55B VAL* 1.3 75.6 - - - +
57B HIS* 1.3 62.9 + - - +
60B LEU* 3.1 42.8 + - + +
61B ASN* 4.0 1.6 - - - +
130B ILE* 4.5 2.7 - - + -
134B PHE* 3.5 31.9 - - + -
138B ILE* 6.4 0.2 - - + -
157B ILE* 4.0 11.5 - - + +
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Residues in contact with HIS 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLY 2.9 19.7 + - - +
54B SER* 3.5 11.9 - - - +
56B ALA* 1.3 77.2 - - - +
58B MET* 1.3 58.9 + - - +
61B ASN* 3.1 41.2 + - + +
63B LYS* 3.0 50.4 + - + +
134B PHE* 3.6 10.4 - + + -
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Residues in contact with MET 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B SER 3.4 9.6 + - - +
55B VAL* 2.9 22.4 + - + +
57B HIS* 1.3 81.3 - - - +
59B VAL* 1.3 63.2 + - + +
60B LEU 3.6 0.2 - - - -
62B LYS* 4.2 10.0 + - - -
63B LYS* 3.0 33.7 + - - +
64B TYR* 4.9 1.8 - - + -
65B GLY* 3.0 38.6 - - - +
70B VAL* 5.3 9.2 - - + -
64D TYR* 5.9 7.2 - - + -
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B VAL* 3.2 9.9 + - + +
58B MET* 1.3 84.4 - - + +
60B LEU* 1.3 78.5 + - + +
61B ASN 3.7 0.2 - - - -
62B LYS 4.9 1.3 + - - -
141B PHE* 3.3 44.9 - - + -
153B ALA* 4.3 14.6 - - + +
154B THR* 4.1 18.2 - - + +
156B GLY 6.0 0.2 - - - -
157B ILE* 3.6 20.9 - - + -
402B GOL 5.3 10.1 - - - +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ALA* 3.1 29.4 + - + +
59B VAL* 1.3 99.9 - - + +
61B ASN* 1.3 65.4 + - - +
62B LYS 3.8 1.1 - - - -
134B PHE* 5.3 1.1 - - + -
137B ALA* 2.8 52.0 - - + +
138B ILE* 3.4 26.9 - - + +
141B PHE* 4.0 19.5 - - + +
154B THR* 5.4 6.7 - - + -
157B ILE* 4.2 15.5 - - + -
----------------------------------------------------------
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Residues in contact with ASN 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ALA 4.0 7.4 - - - +
57B HIS* 3.1 43.4 + - + +
60B LEU* 1.3 85.8 - - - +
62B LYS* 1.3 74.7 + - - +
63B LYS* 3.2 1.5 + - - -
134B PHE* 4.1 16.0 - - - -
137B ALA* 4.2 5.5 - - - +
----------------------------------------------------------
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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