Contacts of the helix formed by residues 58 - 83 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ALA* 5.9 2.0 - - + -
61A LEU* 4.0 22.0 - - + -
55D ASP 4.8 1.2 + - - -
56D HIS* 3.1 1.0 - - - +
57D SER* 1.3 82.8 + - - +
59D ILE* 1.3 63.1 + - - +
60D LEU 3.3 2.9 - - - -
61D LEU* 3.2 13.9 + - + -
62D ASN* 3.0 34.8 + - - +
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Residues in contact with ILE 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLN* 3.9 26.9 - - + +
115B ALA* 4.0 8.3 - - + +
116B ALA* 4.1 16.4 - - + +
119B THR* 3.5 34.1 - - + +
141B GLN* 5.3 0.4 - - - +
47D LEU* 4.3 9.9 - - + -
56D HIS* 3.3 34.4 + - + +
57D SER 3.3 3.0 + - - +
58D ALA* 1.3 75.9 - - - +
60D LEU* 1.3 56.3 + - + +
62D ASN* 3.2 4.4 + - - +
63D GLU* 2.8 69.0 + - + +
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Residues in contact with LEU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 5.7 2.7 - - + -
61A LEU* 3.9 26.4 - - + +
64A LYS* 4.2 29.4 - - + +
119B THR* 3.7 25.4 - - - +
121B GLN* 3.9 26.0 - - + +
141B GLN* 3.7 27.6 - - - +
143B TYR* 4.3 12.6 - - + +
57D SER 5.3 0.2 + - - -
58D ALA 3.3 0.8 - - - -
59D ILE* 1.3 81.6 - - + +
61D LEU* 1.3 59.7 + - - +
63D GLU* 4.1 1.4 - - - +
64D LYS* 3.1 30.4 + - + +
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Residues in contact with LEU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A SER 4.5 4.5 - - - +
58A ALA* 4.0 33.2 - - + -
60A LEU* 3.8 38.4 - - + +
61A LEU* 3.7 23.4 - - + +
58D ALA* 3.2 14.6 + - + +
60D LEU* 1.3 78.5 - - - +
62D ASN* 1.3 68.7 + - - +
63D GLU 3.2 0.2 - - - -
64D LYS* 3.2 3.2 + - - +
65D ASN* 2.8 58.8 + - - +
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Residues in contact with ASN 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D ALA* 4.5 4.3 + - - +
46D LYS* 3.6 43.1 - - + +
47D LEU* 3.8 28.6 - - + +
50D ALA* 4.3 11.4 - - - +
56D HIS* 5.9 0.2 + - - -
58D ALA* 3.0 29.0 + - - +
59D ILE* 3.8 4.3 + - - +
61D LEU* 1.3 89.4 - - - +
63D GLU* 1.3 61.0 + - - +
65D ASN* 3.8 9.6 - - - +
66D LEU* 3.2 23.7 + - - +
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Residues in contact with GLU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLN* 3.4 21.5 + - - -
116B ALA* 4.4 1.7 - - + +
139B ILE* 2.6 39.3 - - - +
140B PHE* 3.5 11.2 - - - -
141B GLN* 4.0 27.7 + - + +
148B ASN* 3.9 3.9 + - - -
47D LEU* 5.0 3.4 - - - -
59D ILE* 2.8 41.1 + - + +
60D LEU 4.1 2.9 - - - +
62D ASN* 1.3 77.9 - - - +
64D LYS* 1.3 59.9 + - - +
66D LEU* 3.7 11.5 + - - +
67D ALA* 3.2 26.2 + - - +
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Residues in contact with LYS 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.2 24.9 - - + +
64A LYS* 5.7 5.4 - - + -
143B TYR* 3.8 26.0 - - + +
148B ASN* 4.0 15.9 - - - +
121C GLN* 2.7 34.5 + - - +
143C TYR* 4.6 19.6 + - - -
60D LEU* 3.1 23.7 + - + +
61D LEU* 4.0 3.6 - - - +
63D GLU* 1.3 76.3 - - - +
65D ASN* 1.3 61.5 + - - +
67D ALA* 4.1 0.7 - - - +
68D PHE* 3.1 26.9 + - - +
146D GLN* 4.1 20.4 - - - +
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Residues in contact with ASN 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 5.4 0.9 - - - +
121C GLN* 3.1 22.1 + - - +
43D ALA* 4.0 13.5 - - + +
61D LEU* 2.8 46.7 + - - +
62D ASN* 3.8 10.5 - - - +
64D LYS* 1.3 75.8 - - - +
66D LEU* 1.3 61.8 + - - +
69D ASN* 2.8 45.0 + - - +
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Residues in contact with LEU 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 4.6 22.9 - - + -
139B ILE 3.8 22.2 - - - +
140B PHE* 4.0 18.8 - - + -
4D TYR* 5.7 0.4 - - + -
40D ALA* 4.7 2.9 - - - +
43D ALA* 3.6 15.5 - - + +
44D VAL* 4.0 28.3 - - + +
47D LEU* 4.1 15.3 - - + -
62D ASN 3.2 15.1 + - - +
63D GLU* 3.7 10.5 - - - +
65D ASN* 1.3 81.3 - - - +
67D ALA* 1.3 57.1 + - - +
70D LEU* 2.9 45.2 + - + +
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Residues in contact with ALA 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B PHE* 4.5 9.2 - - + -
148B ASN* 3.1 46.9 - - - +
149B PHE* 3.9 7.6 - - - +
150B PRO* 4.7 2.6 - - - +
63D GLU 3.2 14.9 + - - +
64D LYS 4.1 0.4 - - - +
66D LEU* 1.3 77.2 - - - +
68D PHE* 1.3 63.1 - - - +
71D ALA* 2.9 32.1 + - - +
146D GLN* 3.8 3.7 - - + +
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Residues in contact with PHE 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C VAL 5.0 1.1 - - - -
121C GLN* 3.2 69.5 - - + +
122C GLY 4.0 2.7 - - - -
36D TYR* 4.0 21.8 - + - -
64D LYS 3.1 19.9 + - - +
65D ASN 4.1 0.9 - - - +
66D LEU 3.4 0.2 - - - -
67D ALA* 1.3 78.9 - - - +
69D ASN* 1.3 68.2 + - - +
71D ALA* 3.6 2.3 - - - +
72D GLY 2.9 22.7 + - - -
144D ASP* 4.9 0.9 - - + -
145D HIS* 3.6 20.7 - + - -
146D GLN* 3.5 32.9 - - - +
162D TRP* 4.1 12.6 - + - -
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Residues in contact with ASN 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C GLN* 4.7 1.0 - - - +
35D THR* 4.3 4.2 - - - +
36D TYR* 3.5 30.8 - - - +
39D GLY* 3.6 24.0 + - - -
40D ALA* 3.4 22.9 - - - +
65D ASN* 2.8 40.5 + - - +
68D PHE* 1.3 86.7 - - - +
70D LEU* 1.3 68.0 + - - +
73D HIS* 3.1 22.7 + - - +
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Residues in contact with LEU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ASP* 4.2 12.1 - - + +
133B LEU* 4.9 0.9 - - + -
138B LEU* 3.9 20.0 - - + -
140B PHE* 4.5 4.9 - - + -
150B PRO* 3.7 24.2 - - + -
4D TYR* 3.3 48.5 - - + +
40D ALA* 4.1 8.8 - - + +
66D LEU* 2.9 31.9 + - + +
69D ASN* 1.3 74.0 - - - +
71D ALA* 1.3 57.6 + - - +
73D HIS* 3.4 8.0 + - + +
74D VAL* 2.9 36.9 + - + +
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Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B PRO* 3.9 21.3 - - + +
151B LEU 5.2 0.4 - - - +
67D ALA 2.9 22.7 + - - +
68D PHE 3.6 2.7 - - - +
70D LEU* 1.3 75.9 - - - +
72D GLY* 1.3 64.8 + - - +
74D VAL* 4.0 1.3 - - - +
75D ASN* 3.0 32.2 + - - +
145D HIS* 3.6 26.5 - - + +
146D GLN* 3.7 8.7 - - + -
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Residues in contact with GLY 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D TYR* 4.0 12.1 - - - -
68D PHE 2.9 12.9 + - - -
69D ASN 3.3 0.8 + - - -
71D ALA* 1.3 77.4 - - - +
73D HIS* 1.3 63.9 + - - +
75D ASN* 3.3 0.8 + - - -
76D HIS* 2.8 31.8 + - - -
145D HIS* 3.2 32.3 - - - -
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Residues in contact with HIS 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 3.5 24.4 - - + +
4D TYR* 3.7 36.2 - + + +
5D THR 3.4 26.8 + - - -
7D PRO* 4.5 1.6 - - + -
33D HIS* 3.1 22.7 + - - -
36D TYR* 3.8 12.9 - - + +
37D VAL* 3.5 15.7 - - + +
40D ALA* 5.0 1.3 - - + -
69D ASN 3.1 16.8 + - - +
70D LEU* 3.5 7.2 - - + +
72D GLY* 1.3 78.0 - - - +
74D VAL* 1.3 61.1 + - - +
76D HIS 3.4 0.2 + - - -
77D THR* 2.8 46.2 + - - -
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Residues in contact with VAL 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ASP* 4.9 4.0 - - - +
133B LEU* 4.2 24.5 - - + -
150B PRO* 4.1 16.6 - - + -
151B LEU* 4.0 24.0 - - + +
70D LEU* 2.9 33.9 + - + +
71D ALA* 4.0 5.6 - - - +
73D HIS* 1.3 75.9 - - - +
75D ASN* 1.3 72.0 + - - +
77D THR* 3.5 2.4 + - - -
78D ILE* 3.3 36.4 + - + +
155D PRO* 5.4 0.7 - - + -
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Residues in contact with ASN 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 3.4 26.9 + - - +
71D ALA* 3.0 22.1 + - - +
72D GLY* 3.8 2.7 - - - +
74D VAL* 1.3 83.1 - - - +
76D HIS* 1.3 59.1 + - - +
78D ILE* 3.2 5.0 + - - +
79D TRP* 2.9 25.5 + - - +
125D TRP* 3.4 44.0 - - + +
142D VAL* 5.1 1.0 - - - +
145D HIS* 3.2 28.0 + - - +
158D LEU* 3.9 15.4 - - + +
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Residues in contact with HIS 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D HIS* 3.0 29.9 + + - -
32D HIS* 5.2 0.2 - - - +
33D HIS* 3.0 39.5 - + + +
36D TYR* 3.6 26.3 - + - -
72D GLY 2.8 29.4 + - - +
75D ASN* 1.3 72.1 - - - +
77D THR* 1.3 65.5 + - - +
79D TRP* 3.9 10.3 - + - -
80D TRP* 2.9 34.4 + + - +
125D TRP* 3.8 15.4 - + - -
145D HIS* 3.8 9.6 - + - -
160D ASP* 3.6 1.5 + - - -
164D HIS* 4.0 0.4 + - - -
999D FE 2.3 28.4 - - - -
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Residues in contact with THR 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 4.1 18.0 - - + +
7D PRO* 4.5 14.1 - - + +
33D HIS* 3.4 7.9 + - - -
73D HIS* 2.8 48.0 + - - -
74D VAL* 3.6 8.7 - - - +
76D HIS* 1.3 78.4 - - - +
78D ILE* 1.3 63.9 + - + +
80D TRP* 3.8 5.7 + - - +
81D LYS* 3.7 22.1 + - + +
193D ARG* 6.1 1.3 - - - +
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Residues in contact with ILE 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D VAL* 3.3 21.7 + - + +
75D ASN 3.2 7.7 + - - +
76D HIS 3.1 0.2 - - - -
77D THR* 1.3 82.9 - - + +
79D TRP* 1.3 64.4 + - - +
81D LYS* 3.2 1.4 + - - +
82D ASN* 2.9 44.9 + - - +
155D PRO* 3.7 34.1 - - + +
156D LEU 4.6 5.6 - - - +
158D LEU* 4.3 15.7 - - + -
193D ARG* 3.9 33.9 - - - +
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Residues in contact with TRP 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ILE* 4.5 10.1 - - + -
25D ASN* 5.3 2.2 + - - -
28D HIS* 3.5 27.8 + + - -
75D ASN 2.9 16.3 + - - +
76D HIS* 3.0 10.0 + + - +
78D ILE* 1.3 78.2 - - - +
80D TRP* 1.3 99.9 + + - +
82D ASN* 3.1 16.5 + - + +
83D LEU* 3.3 42.1 + - + +
125D TRP* 4.0 11.0 - + + -
158D LEU* 3.5 24.0 - - - -
159D LEU* 3.8 5.6 - - + -
160D ASP* 3.6 31.9 - - + -
165D ALA* 5.3 2.0 - - + -
177D PHE* 4.0 26.5 - + - -
181D PHE* 3.9 16.2 - + - -
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Residues in contact with TRP 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D PRO* 4.4 10.3 - - + -
8D ASP 5.8 0.4 - - - +
9D LEU* 3.5 28.0 - - + -
10D ASP* 5.7 2.0 + - - +
11D TRP* 3.5 44.2 + + + -
25D ASN* 3.9 26.2 - - + -
28D HIS* 3.6 35.9 - + + -
29D HIS* 3.5 36.3 - + + -
33D HIS* 2.9 30.2 + + - -
76D HIS* 2.9 23.7 + + + +
77D THR* 4.2 4.3 - - - +
78D ILE 3.3 0.2 - - - -
79D TRP* 1.3 101.8 - + - +
81D LYS* 1.3 64.9 + - + +
83D LEU* 3.5 8.0 - - + +
----------------------------------------------------------
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Residues in contact with LYS 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D PRO* 6.5 1.6 - - - -
8D ASP 5.1 5.8 - - - -
10D ASP* 2.7 38.5 + - - +
77D THR* 3.7 15.9 - - + +
78D ILE 3.2 3.4 + - - +
79D TRP 3.1 0.2 - - - -
80D TRP* 1.3 77.1 - - + +
82D ASN* 1.3 56.8 + - - +
83D LEU 3.0 11.1 + - - +
186D ASN* 3.1 25.5 + - - +
189D ASP* 3.7 24.3 - - - +
193D ARG* 3.8 16.6 - - - +
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Residues in contact with ASN 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D ILE* 2.9 32.0 + - - +
79D TRP* 3.1 7.9 + - + +
81D LYS* 1.3 75.1 - - - +
83D LEU* 1.3 63.1 + - + +
156D LEU 3.4 15.1 + - - -
157D LEU* 3.2 21.1 - - + +
158D LEU* 2.9 34.3 + - - +
181D PHE* 5.2 0.4 - - + -
185D VAL* 3.5 9.0 - - - +
186D ASN* 2.8 26.5 + - - +
189D ASP* 2.8 30.9 + - - -
190D VAL* 4.3 3.8 - - - +
----------------------------------------------------------
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Residues in contact with LEU 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D TRP* 3.2 36.8 + - + -
16D LEU* 4.1 20.9 - - + -
20D ILE* 4.5 5.8 - - + -
25D ASN* 5.2 1.1 - - - +
79D TRP* 3.3 50.8 + - + +
80D TRP* 3.5 8.8 - - + +
81D LYS 3.0 6.4 - - - +
82D ASN* 1.3 86.9 - - - +
84D SER* 1.3 66.6 + - - +
181D PHE* 4.0 23.6 - - + -
184D VAL* 3.3 26.5 - - + +
186D 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