Contacts of the helix formed by residues 58 - 83 (chain B) in PDB entry 1GN2
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 ALA 58 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASP 4.8 1.0 + - - -
56B HIS* 3.1 1.2 - - - +
57B SER* 1.3 81.8 + - - +
59B ILE* 1.3 62.9 + - - +
60B LEU 3.3 2.7 - - - -
61B LEU* 3.2 13.6 + - + -
62B ASN* 3.0 35.5 + - - +
58C ALA* 6.1 1.1 - - + -
61C LEU* 3.8 24.0 - - + -
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Residues in contact with ILE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 4.3 8.5 - - + -
56B HIS* 3.3 32.0 + - + +
57B SER 3.3 2.8 + - - +
58B ALA* 1.3 76.5 - - - +
60B LEU* 1.3 55.6 + - - +
62B ASN* 3.2 3.9 + - - +
63B GLU* 2.8 69.2 + - + +
112D GLN* 3.9 27.6 - - + +
115D ALA* 3.8 9.2 - - + +
116D ALA* 3.8 16.8 - - - +
119D THR* 3.3 35.9 - - + +
141D GLN* 5.1 0.2 - - - +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B SER 5.3 0.4 + - - -
58B ALA 3.3 1.0 - - - -
59B ILE* 1.3 80.4 - - + +
61B LEU* 1.3 59.1 + - - +
63B GLU* 4.1 1.2 - - - +
64B LYS* 3.1 30.8 + - + +
60C LEU* 5.8 3.1 - - + -
61C LEU* 4.2 19.5 - - + -
64C LYS* 4.1 36.3 - - + +
65C ASN* 5.9 0.2 - - - +
119D THR* 3.6 29.2 - - - +
121D GLN* 3.8 28.5 - - + +
141D GLN* 3.7 23.6 - - - +
143D TYR* 4.4 10.1 - - + +
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ALA* 3.2 13.4 + - + +
60B LEU* 1.3 77.5 - - - +
62B ASN* 1.3 68.8 + - - +
63B GLU 3.2 0.2 - - - -
64B LYS* 4.0 2.4 - - - +
65B ASN* 2.8 61.2 + - - +
57C SER 4.8 4.3 - - - +
58C ALA* 4.2 23.1 - - + -
60C LEU* 3.7 38.8 - - + -
61C LEU* 3.7 31.9 - - + +
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Residues in contact with ASN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ALA* 4.5 4.3 + - - +
46B LYS* 3.6 41.7 - - - +
47B LEU* 3.8 26.2 - - + +
50B ALA* 4.3 11.6 - - - +
58B ALA* 3.0 29.5 + - - +
59B ILE* 3.8 5.0 + - - +
61B LEU* 1.3 91.2 - - - +
63B GLU* 1.3 60.6 + - - +
65B ASN* 3.8 8.8 - - - +
66B LEU* 3.2 24.3 + - - +
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Residues in contact with GLU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 5.0 2.7 - - - -
59B ILE* 2.8 40.4 + - + +
60B LEU 4.1 0.4 - - - +
62B ASN* 1.3 78.5 - - + +
64B LYS* 1.3 59.3 + - - +
66B LEU* 3.7 10.7 + - - +
67B ALA* 3.2 26.3 + - - +
112D GLN* 3.5 15.1 + - - -
116D ALA* 4.1 1.8 - - + +
139D ILE* 2.7 46.2 - - - +
140D PHE* 3.5 7.9 - - - -
141D GLN* 3.8 35.8 + - + +
148D ASN* 3.8 3.9 + - - +
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Residues in contact with LYS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLN* 2.9 37.9 + - - +
143A TYR* 4.6 25.5 + - + +
60B LEU* 3.1 24.3 + - + +
61B LEU* 3.2 3.1 + - - +
63B GLU* 1.3 76.4 - - - +
65B ASN* 1.3 61.5 - - - +
67B ALA* 4.1 0.9 - - - +
68B PHE* 3.1 26.3 + - - +
146B GLN* 4.1 21.3 - - - +
60C LEU* 4.5 19.8 - - + +
64C LYS* 5.8 4.7 - - + -
143D TYR* 3.6 27.1 - - + +
148D ASN* 3.9 15.5 - - - +
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Residues in contact with ASN 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLN* 2.8 25.2 + - - +
43B ALA* 4.0 13.7 - - + +
61B LEU* 2.8 46.9 + - - +
62B ASN* 3.8 10.5 - - - +
64B LYS* 1.3 75.9 - - - +
66B LEU* 1.3 61.6 + - - +
69B ASN* 2.8 44.4 + - - +
60C LEU* 5.3 0.5 - - - +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TYR* 5.7 0.7 - - + -
40B ALA* 4.7 2.5 - - - +
43B ALA* 3.6 16.3 - - + +
44B VAL* 4.0 27.4 - - + +
47B LEU* 4.1 14.6 - - + -
62B ASN 3.2 15.3 + - - +
63B GLU* 3.7 10.8 - - - +
64B LYS 3.3 0.2 - - - -
65B ASN* 1.3 81.1 - - - +
67B ALA* 1.3 56.4 + - - +
69B ASN* 5.4 0.2 - - - -
70B LEU* 2.9 48.3 + - + +
138D LEU* 4.6 17.9 - - + -
139D ILE 3.6 24.2 - - - +
140D PHE* 4.0 19.3 - - + -
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLU 3.2 15.8 + - - +
64B LYS 3.7 0.9 + - - +
66B LEU* 1.3 76.5 - - - +
68B PHE* 1.3 63.8 + - - +
71B ALA* 2.9 31.9 + - - +
146B GLN* 3.8 3.6 - - + +
140D PHE* 4.5 9.0 - - + -
148D ASN* 3.1 48.2 - - - +
149D PHE* 3.9 5.8 - - - +
150D PRO* 4.7 2.0 - - - -
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Residues in contact with PHE 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A VAL 4.9 1.1 - - - -
121A GLN* 3.4 68.6 - - + +
122A GLY 3.8 3.6 - - - -
36B TYR* 4.0 22.2 - + - -
64B LYS 3.1 19.0 + - - +
65B ASN 4.1 0.2 - - - +
67B ALA* 1.3 79.2 - - - +
69B ASN* 1.3 69.5 + - - +
71B ALA* 3.6 2.1 - - - +
72B GLY 2.9 23.0 + - - -
144B ASP* 4.9 1.3 - - + -
145B HIS* 3.6 20.9 - + - -
146B GLN* 3.5 32.0 - - - +
162B TRP* 4.1 13.5 - + - -
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Residues in contact with ASN 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLN* 4.5 1.2 - - - +
35B THR* 4.3 4.5 - - - +
36B TYR* 3.5 31.1 - - - +
39B GLY* 3.6 23.8 + - - -
40B ALA* 3.4 22.4 - - - +
65B ASN* 2.8 41.0 + - - +
68B PHE* 1.3 85.4 - - - +
70B LEU* 1.3 66.8 + - - +
73B HIS* 3.1 22.7 + - - +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TYR* 3.3 48.9 - - + +
40B ALA* 4.1 9.5 - - + +
66B LEU* 2.9 31.7 + - + +
69B ASN* 1.3 74.8 - - - +
71B ALA* 1.3 58.0 + - - +
73B HIS* 3.4 8.0 + - + -
74B VAL* 2.9 36.1 + - + +
131D ASP* 4.3 10.5 - - + +
133D LEU* 5.1 0.7 - - + -
138D LEU* 3.7 20.0 - - + -
140D PHE* 4.3 7.4 - - + -
150D PRO* 3.7 24.2 - - + -
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA 2.9 21.3 + - - +
68B PHE 3.6 2.9 - - - +
70B LEU* 1.3 77.0 - - - +
72B GLY* 1.3 64.9 + - - +
74B VAL* 4.0 0.8 - - - +
75B ASN* 3.0 33.0 + - - +
145B HIS* 3.6 26.2 - - + +
146B GLN* 3.7 9.2 - - + -
150D PRO* 3.9 21.7 - - + +
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Residues in contact with GLY 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TYR* 4.0 13.2 - - - -
68B PHE 2.9 12.2 + - - -
69B ASN 3.3 0.6 + - - -
71B ALA* 1.3 76.6 - - - +
73B HIS* 1.3 64.1 + - - +
75B ASN* 3.3 1.1 + - - -
76B HIS* 2.8 33.6 + - - -
145B HIS* 3.2 32.5 - - - -
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Residues in contact with HIS 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TYR* 3.7 40.7 - + + +
5B THR 3.4 26.5 + - - -
7B PRO* 4.5 2.0 - - + -
33B HIS* 3.1 22.0 + - - -
36B TYR* 3.8 11.5 - - + +
37B VAL* 3.5 17.5 - - + +
40B ALA* 5.0 1.3 - - + -
69B ASN 3.1 17.3 + - - +
70B LEU* 3.5 7.9 - - + +
72B GLY* 1.3 76.7 - - - +
74B VAL* 1.3 63.1 + - - +
76B HIS 3.4 0.2 + - - -
77B THR* 2.8 45.5 + - - -
133D LEU* 3.6 20.4 - - + +
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Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 2.9 34.0 + - + +
71B ALA* 4.0 5.4 - - - +
73B HIS* 1.3 74.8 - - - +
75B ASN* 1.3 72.6 + - - +
77B THR* 3.6 1.7 - - - -
78B ILE* 3.3 36.7 + - + +
155B PRO* 5.4 0.9 - - + -
131D ASP* 4.8 4.0 - - - +
133D LEU* 4.2 24.5 - - + -
150D PRO* 3.9 17.9 - - + -
151D LEU* 4.0 23.8 - - + +
153D ILE* 6.4 0.2 - - + -
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Residues in contact with ASN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ALA 3.0 22.4 + - - +
72B GLY* 3.8 2.7 - - - +
74B VAL* 1.3 83.3 - - - +
76B HIS* 1.3 58.2 + - - +
78B ILE* 3.2 5.4 + - - +
79B TRP* 2.9 25.3 + - - +
125B TRP* 3.4 44.2 - - + +
142B VAL* 5.1 0.8 - - - +
145B HIS* 3.2 27.9 + - - +
158B LEU* 3.9 14.8 - - + +
151D LEU* 3.6 27.2 + - - +
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Residues in contact with HIS 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B HIS* 3.0 29.2 + + - -
32B HIS* 5.2 0.4 - - - +
33B HIS* 3.0 39.5 - + + +
36B TYR* 3.6 26.4 - + - -
72B GLY 2.8 28.9 + - - +
75B ASN* 1.3 72.1 - - - +
77B THR* 1.3 66.0 + - - +
79B TRP* 3.6 11.1 - + - +
80B TRP* 2.9 34.1 + + - +
125B TRP* 3.8 15.2 - + - -
145B HIS* 3.8 9.4 - + - -
160B ASP* 3.6 1.7 + - - -
164B HIS* 4.0 0.8 + - - -
999B FE 2.3 28.4 - - - -
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Residues in contact with THR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO* 4.5 13.5 - - + +
33B HIS* 3.4 8.1 + - - -
73B HIS* 2.8 47.1 + - - -
74B VAL* 3.6 7.6 - - - +
75B ASN 3.2 0.2 - - - -
76B HIS* 1.3 80.0 - - - +
78B ILE* 1.3 66.0 + - + +
80B TRP* 3.8 5.7 + - - +
81B LYS* 3.7 22.1 + - + +
193B ARG* 6.1 1.1 - - - +
133D LEU* 4.0 19.5 - - + +
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 3.4 22.0 - - + +
75B ASN 3.2 7.1 + - - +
76B HIS 3.1 0.2 - - - -
77B THR* 1.3 81.2 - - + +
79B TRP* 1.3 66.0 + - - +
81B LYS* 3.2 2.2 + - - +
82B ASN* 2.9 44.5 + - - +
155B PRO* 3.7 33.7 - - + +
156B LEU 4.6 5.6 - - - +
158B LEU* 4.3 15.3 - - + -
193B ARG* 3.9 35.0 - - - +
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Residues in contact with TRP 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 4.5 9.0 - - + -
25B ASN* 5.3 2.4 + - - -
28B HIS* 3.5 28.0 + + - -
75B ASN 2.9 15.9 + - - +
76B HIS* 3.0 9.4 + + - +
78B ILE* 1.3 79.1 - - - +
80B TRP* 1.3 99.2 + + - +
82B ASN* 3.1 16.3 + - + +
83B LEU* 3.3 42.8 + - + +
125B TRP* 4.0 11.0 - + + -
158B LEU* 3.5 23.6 - - - -
159B LEU* 3.8 6.1 - - + -
160B ASP* 3.6 30.3 - - + -
165B ALA* 5.3 2.0 - - + -
177B PHE* 4.0 28.0 - + - -
181B PHE* 3.9 15.7 - + - -
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Residues in contact with TRP 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO* 4.4 10.1 - - + -
8B ASP 5.8 0.7 - - - +
9B LEU* 3.5 26.7 - - + -
10B ASP* 5.7 2.2 + - - +
11B TRP* 3.5 44.3 + + + -
25B ASN* 3.9 25.8 - - + -
28B HIS* 3.6 36.3 - + + -
29B HIS* 3.5 36.7 - + + -
33B HIS* 2.9 30.9 + + - -
76B HIS* 2.9 22.5 + + + +
77B THR* 4.2 4.7 - - - +
79B TRP* 1.3 98.8 - + - +
81B LYS* 1.3 64.3 + - + +
83B LEU* 3.5 7.8 - - + +
----------------------------------------------------------
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO* 6.5 1.6 - - - -
8B ASP 5.1 6.3 - - - -
10B ASP* 2.7 39.1 + - - +
77B THR* 3.7 15.9 - - + +
78B ILE 3.2 3.2 + - - +
79B TRP 3.1 0.6 - - - -
80B TRP* 1.3 78.2 - - + +
82B ASN* 1.3 56.1 + - - +
83B LEU 3.0 11.2 + - - +
186B ASN* 3.1 25.5 + - - -
189B ASP* 3.7 24.3 - - - +
193B ARG* 3.8 16.6 - - - +
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Residues in contact with ASN 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ILE* 2.9 31.8 + - - +
79B TRP* 3.1 7.7 + - + +
81B LYS* 1.3 74.9 - - - +
83B LEU* 1.3 63.2 + - + +
156B LEU 3.4 15.3 + - - -
157B LEU* 3.3 21.4 - - + +
158B LEU* 2.9 34.3 + - - +
181B PHE* 5.2 0.8 - - + -
185B VAL* 3.5 9.4 - - - +
186B ASN* 2.8 26.8 + - - +
189B ASP* 2.8 30.1 + - - -
190B VAL* 4.3 3.8 - - - +
----------------------------------------------------------
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TRP* 3.2 37.1 + - + -
16B LEU* 4.1 20.4 - - + -
20B ILE* 4.5 4.9 - - + -
25B ASN* 5.2 0.9 - - - +
79B TRP* 3.3 51.1 + - + +
80B TRP* 3.5 8.2 + - + +
81B LYS* 3.0 6.9 - - - +
82B ASN* 1.3 85.6 - - - +
84B SER* 1.3 66.1 + - - +
181B PHE* 4.0 23.6 - - + -
184B VAL* 3.3 26.7 - - + +
186B ASN* 3.7 1.4 + - - -
----------------------------------------------------------
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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