Contacts of the helix formed by residues 56 - 85 (chain D) in PDB entry 1W72
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 GLY 56 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLU 5.2 1.0 + - - -
55D GLU* 1.3 79.5 - - - +
57D PRO* 1.3 76.1 - - - +
58D GLU* 3.2 4.9 + - - -
59D TYR* 3.2 11.5 + - - +
60D TRP* 3.2 21.3 - - - +
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Residues in contact with PRO 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLY* 1.3 80.8 - - - +
58D GLU* 1.3 61.0 + - + +
60D TRP* 3.4 10.0 + - + +
61D ASP* 2.8 32.4 + - - +
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Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D GLU 5.9 0.4 - - - +
56D GLY* 3.2 1.7 - - - -
57D PRO* 1.3 78.6 - - + +
59D TYR* 1.3 66.8 + - - +
61D ASP* 3.3 8.7 + - - +
62D GLN* 3.0 24.9 + - + +
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Residues in contact with TYR 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D TYR* 4.5 0.9 + - - -
33D PHE* 4.0 8.1 - - - -
34D VAL* 4.4 3.7 - - + +
52D ILE* 3.7 10.9 - - + +
55D GLU* 3.3 43.4 + - + +
56D GLY 3.2 11.2 + - - +
58D GLU* 1.3 82.0 - - - +
60D TRP* 1.3 90.4 + + - +
62D GLN* 3.2 9.9 + - - +
63D GLU* 2.9 62.2 + - + +
170D ARG* 3.6 15.5 - - - -
171D TYR* 2.6 31.1 + - - -
1F GLU* 4.4 6.5 + - + -
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Residues in contact with TRP 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D VAL* 3.9 7.6 - - + -
44D LYS* 6.4 1.6 - - + -
45D MET* 3.4 47.8 - - + +
47D PRO* 3.6 40.8 - - + -
52D ILE* 3.3 40.8 + - + -
53D GLU* 4.3 7.1 + - - +
55D GLU* 4.2 5.5 - - - +
56D GLY 3.2 27.8 + - - +
57D PRO* 3.4 9.0 + - + +
58D GLU 3.3 0.2 - - - -
59D TYR* 1.3 90.2 - + - +
61D ASP* 1.3 59.0 + - - +
63D GLU* 4.5 0.9 - - + +
64D THR* 2.6 41.7 + - - +
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Residues in contact with ASP 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D PRO 2.8 18.1 + - - +
58D GLU* 3.7 10.2 - - - +
60D TRP* 1.3 75.6 - - - +
62D GLN* 1.3 61.1 + - - +
64D THR* 3.7 7.3 - - - +
65D ARG* 3.1 39.4 + - - +
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Residues in contact with GLN 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D GLU* 3.0 16.1 + - + +
59D TYR* 3.6 9.9 + - - +
61D ASP* 1.3 75.4 - - - +
63D GLU* 1.3 85.8 + - - +
65D ARG* 3.2 18.5 + - - +
66D ASN* 2.8 40.9 + - - +
1F GLU* 4.1 21.5 + - - +
2F ALA 5.9 0.2 - - - -
4F PRO* 5.7 5.2 - - - +
52I TRP* 6.1 0.9 - - + -
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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
----------------------------------------------------------
7D TYR* 4.3 1.7 + - - -
45D MET* 3.9 30.2 - - + +
59D TYR* 2.9 45.2 + - + +
60D TRP* 4.2 2.0 - - - +
62D GLN* 1.3 102.6 + - - +
64D THR* 1.3 63.2 + - - +
66D ASN* 3.2 12.9 + - - +
67D MET* 3.0 29.1 + - - +
1F GLU* 3.4 17.8 - - - +
2F ALA* 3.0 33.9 + - - +
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Residues in contact with THR 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D PHE* 4.6 1.0 - - + -
43D GLN 3.6 24.2 - - - +
44D LYS* 3.5 21.0 - - + +
45D MET* 3.1 25.4 + - - +
60D TRP* 2.6 26.0 + - - +
61D ASP* 3.7 8.7 - - - +
63D GLU* 1.3 77.5 - - - +
65D ARG* 1.3 62.5 + - + +
67D MET* 3.3 5.1 + - - +
68D LYS* 3.2 38.0 + - + +
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Residues in contact with ARG 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ASP* 3.1 36.0 + - - +
62D GLN* 3.6 17.1 - - + +
64D THR* 1.3 75.2 - - + +
66D ASN* 1.3 65.6 + - - +
67D MET 3.1 0.2 + - - -
68D LYS* 3.2 7.0 + - + +
69D ALA* 3.0 26.5 + - - +
30I ASP* 3.0 44.6 + - - +
31I ASP* 2.9 26.7 + - - +
52I TRP* 3.7 29.4 + - + -
98I PHE* 4.1 14.5 - - + -
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Residues in contact with ASN 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D GLN* 2.8 32.0 + - - +
63D GLU* 3.2 38.1 + - - +
65D ARG* 1.3 72.1 - - - +
67D MET* 1.3 69.0 + - + +
69D ALA* 3.6 6.3 + - - +
70D HIS* 3.0 28.1 + - - +
2F ALA* 3.7 19.1 + - + +
3F ASP 4.9 3.9 - - - +
4F PRO* 3.3 33.6 - - + +
52I TRP* 3.5 9.9 - - - -
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Residues in contact with MET 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D TYR* 5.1 2.2 - - + -
9D PHE* 3.7 21.1 - - + -
22D PHE* 3.4 14.0 - - + -
24D ALA* 3.6 31.0 - - - -
36D PHE* 3.6 35.7 - - + -
45D MET* 3.4 26.5 - - + +
63D GLU 3.0 19.6 + - - +
64D THR 3.7 2.2 - - - +
65D ARG 3.1 0.4 - - - -
66D ASN* 1.3 81.3 - - + +
68D LYS* 1.3 59.9 + - - +
70D HIS* 3.3 4.4 + - + +
71D SER* 3.0 23.0 + - - -
99D TYR* 5.1 0.4 - - - +
2F ALA* 3.8 27.8 - - + -
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Residues in contact with LYS 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D PHE* 4.3 14.6 - - + -
43D GLN* 3.3 32.0 + - - +
44D LYS* 5.7 0.6 - - - +
64D THR* 3.2 26.3 + - + +
65D ARG* 3.2 7.4 + - + +
67D MET* 1.3 71.9 - - - +
69D ALA* 1.3 61.6 + - - +
71D SER* 2.7 23.7 + - - +
72D GLN* 2.9 21.4 + - - +
98I PHE* 3.8 24.9 - - + -
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Residues in contact with ALA 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ARG 3.0 15.4 + - - +
66D ASN 3.7 4.5 - - - +
68D LYS* 1.3 75.2 - - - +
70D HIS* 1.3 65.2 + - - +
72D GLN 3.1 1.6 + - - -
73D THR* 2.9 9.9 + - - -
4F PRO* 5.0 2.9 - - + +
52I TRP* 4.0 16.6 - - + -
98I PHE* 3.8 28.2 - - + -
99I HIS* 2.7 37.2 + - + +
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Residues in contact with HIS 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PHE* 3.3 50.4 - + + +
22D PHE* 3.2 25.8 - + + -
66D ASN 3.0 16.1 + - - +
67D MET* 3.5 11.4 - - + +
69D ALA* 1.3 77.0 - - - +
71D SER* 1.3 61.1 - - - +
73D THR* 3.3 8.9 + - + -
74D ASP* 3.0 39.2 + - - +
97D ILE* 4.1 20.7 - - + +
99D TYR* 5.0 5.8 + + - -
114D ARG* 5.5 3.3 + - - -
3F ASP 5.8 2.9 + - - +
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Residues in contact with SER 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D SER* 5.0 0.3 + - - -
22D PHE* 3.5 42.6 - - - -
36D PHE* 5.4 2.5 - - - -
38D SER* 6.0 1.1 - - - -
67D MET 3.0 8.3 + - - -
68D LYS* 2.7 26.5 + - - -
70D HIS* 1.3 76.7 - - - +
72D GLN* 1.3 59.0 + - - +
74D ASP* 3.4 4.0 + - - +
75D ARG* 2.8 31.5 + - - +
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Residues in contact with GLN 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D LYS* 2.9 17.9 + - - +
69D ALA 3.1 5.1 + - - +
71D SER* 1.3 80.5 + - - +
73D THR* 1.3 60.6 + - - +
75D ARG* 3.3 8.4 + - - +
76D ALA* 3.0 14.4 + - - +
96I ARG 5.1 1.4 + - - -
97I GLY* 3.2 14.0 - - - -
98I PHE* 3.0 50.5 + - - -
99I HIS* 3.8 10.0 - - + +
100I TYR* 2.6 40.7 - - - +
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Residues in contact with THR 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D ALA 2.9 8.1 + - - -
70D HIS* 3.3 11.8 + - + -
72D GLN* 1.3 74.6 - - - +
74D ASP* 1.3 55.9 + - - +
76D ALA* 3.1 5.5 + - - +
77D ASN* 2.8 45.8 + - - +
6F GLY* 3.8 6.6 - - - -
7F HIS 3.4 24.5 - - - +
99I HIS* 2.9 22.4 + - - -
100I TYR* 2.6 33.5 - - - +
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Residues in contact with ASP 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PHE* 4.6 2.4 - - - +
11D SER* 2.7 39.1 + - - +
22D PHE* 4.1 1.7 - - - -
70D HIS* 3.0 41.6 + - - +
71D SER 3.6 7.0 - - - +
73D THR* 1.3 80.4 - - - +
75D ARG* 1.3 57.2 + - - +
77D ASN* 3.1 9.0 + - - +
78D LEU* 2.8 36.7 + - - +
95D ILE* 3.8 23.4 - - + +
97D ILE* 4.1 8.3 - - - +
9F TYR* 5.3 0.2 + - - -
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Residues in contact with ARG 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D SER* 5.5 0.4 - - - -
19D GLU* 3.2 45.9 + - - +
20D PRO* 3.5 28.8 - - + +
71D SER 2.8 18.4 + - - +
72D GLN* 3.4 11.7 - - - +
74D ASP* 1.3 77.5 - - - +
76D ALA* 1.3 62.0 + - - +
78D LEU* 3.5 16.3 + - - +
79D GLY 3.5 8.3 + - - -
100I TYR* 3.5 44.6 + - - +
50M ASP* 4.7 13.5 + - - -
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Residues in contact with ALA 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D GLN 3.0 13.0 + - - +
73D THR 3.4 7.2 - - - +
75D ARG* 1.3 77.5 - - - +
77D ASN* 1.3 59.5 + - - +
79D GLY* 3.1 4.5 + - - -
80D THR* 2.9 29.9 + - - +
8F SER* 5.8 0.9 - - - +
100I TYR* 3.5 63.7 - - + +
91M TRP* 6.3 0.2 - - + -
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Residues in contact with ASN 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D THR* 2.8 29.4 + - - +
74D ASP* 3.1 5.0 + - - +
76D ALA* 1.3 75.3 - - - +
78D LEU* 1.3 59.4 + - - +
80D THR* 3.5 6.1 + - - -
81D LEU* 2.9 34.5 + - - +
95D ILE* 3.6 14.1 - - + -
7F HIS 3.5 15.6 + - - -
8F SER* 3.5 10.4 + - - -
9F TYR* 2.9 61.9 + - + +
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D SER* 4.4 10.8 - - - -
13D SER* 3.9 20.6 - - - +
20D PRO* 3.9 35.0 - - + -
74D ASP 2.8 20.1 + - - +
75D ARG* 3.7 6.3 - - - +
76D ALA 3.2 0.2 - - - -
77D ASN* 1.3 73.6 - - - +
79D GLY* 1.3 65.1 + - - +
81D LEU* 3.7 3.2 + - - +
82D ARG* 3.1 24.4 + - - +
93D HIS* 3.9 27.3 - - + +
95D ILE* 3.6 31.6 - - + +
118D TYR* 4.4 10.5 + - + -
----------------------------------------------------------
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Residues in contact with GLY 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ARG 3.5 6.3 + - - -
76D ALA 3.1 7.1 + - - -
78D LEU* 1.3 77.1 - - - +
80D THR* 1.3 63.7 + - - +
82D ARG* 3.2 13.6 + - - +
83D GLY* 3.1 17.8 + - - -
100I TYR* 4.9 13.5 - - - -
30M SER 4.0 15.3 - - - +
----------------------------------------------------------
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Residues in contact with THR 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ALA* 2.9 17.3 + - - +
77D ASN* 3.5 12.9 - - - -
79D GLY* 1.3 75.2 - - - +
81D LEU* 1.3 58.2 + - - +
83D GLY* 2.9 7.0 + - - -
84D TYR* 2.8 47.1 + - + -
8F SER* 4.3 4.5 + - - -
9F TYR* 3.9 17.0 - - + +
100I TYR* 5.5 2.0 - - - -
91M TRP* 4.8 2.4 + - - -
93M SER* 2.6 40.9 + - - -
----------------------------------------------------------
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Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D ASN 2.9 22.6 + - - +
78D LEU 4.3 0.4 - - - +
80D THR* 1.3 70.1 - - - +
82D ARG* 1.3 66.2 + - - +
84D TYR* 3.8 15.5 - - + +
85D TYR* 2.9 34.7 + - + +
87D GLN* 4.2 0.2 - - - +
95D ILE* 4.4 2.7 - - + -
118D TYR* 3.3 57.4 - - + -
123D TYR* 3.3 38.8 - - + +
9F TYR* 3.8 28.7 - - + -
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Residues in contact with ARG 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D LEU 3.1 19.5 + - - +
79D GLY* 3.4 9.7 + - - +
81D LEU* 1.3 75.1 - - - +
83D GLY* 1.3 56.0 + - - +
86D ASN* 3.1 8.5 + - - -
87D GLN* 3.0 63.1 + - + +
88D SER* 3.5 16.7 - - - +
89D GLU* 3.3 38.7 + - - +
93D HIS* 5.7 5.8 - - + -
118D TYR* 4.2 2.8 + - - +
29M GLY 3.0 24.5 + - - -
30M SER* 3.3 30.5 + - - +
31M ARG 5.3 0.2 + - - -
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Residues in contact with GLY 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D GLY 3.1 8.6 + - - -
80D THR* 2.9 8.9 + - - -
82D ARG* 1.3 74.9 - - - +
84D TYR* 1.3 64.9 + - - +
86D ASN* 3.3 19.8 + - - +
30M SER* 4.4 20.3 - - - -
31M ARG* 6.4 0.4 - - - -
----------------------------------------------------------
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Residues in contact with TYR 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D THR* 2.8 32.6 + - + +
81D LEU* 3.2 16.1 + - + +
83D GLY* 1.3 73.3 - - - +
85D TYR* 1.3 63.0 + - + +
86D ASN* 3.7 9.4 + - - -
123D TYR* 3.6 20.9 - - - -
139D ALA* 3.7 32.9 - - + +
142D ILE* 3.5 30.4 - - + +
143D THR* 3.8 0.4 - - - -
146D LYS* 3.6 8.0 + - - -
9F TYR* 2.8 33.2 + - - -
93M SER* 3.6 6.7 - - - -
94M ARG* 3.9 40.4 + - + +
----------------------------------------------------------
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Residues in contact with TYR 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D LEU* 2.9 43.5 + - + +
84D TYR* 1.3 75.0 - - + +
86D ASN* 1.3 73.1 + - - +
87D GLN* 3.2 26.1 + - + +
118D TYR* 3.6 31.4 - + - -
121D LYS* 4.4 13.8 + - - -
122D ASP 5.7 0.2 + - - -
123D TYR* 3.6 15.5 - + - -
137D ASP* 2.3 39.1 + - - -
139D ALA* 3.6 20.2 - - + -
----------------------------------------------------------
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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