Contacts of the helix formed by residues 71 - 93 (chain D) in PDB entry 1R5I
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 GLU 71 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LYS* 5.2 13.2 - - + +
69D LEU* 2.9 16.7 + - + +
70D LEU* 1.3 99.0 + - + +
72D TYR* 1.3 65.1 + - - +
73D LYS 3.1 3.1 - - - -
74D GLU* 3.0 20.2 + - + +
75D ILE* 3.3 14.0 + - + +
121D PHE* 3.6 62.8 - - + +
124D GLN* 5.9 0.9 - - - +
125D ASN* 4.7 7.6 + - - +
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Residues in contact with TYR 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ILE* 4.8 10.8 - - + +
63D VAL* 3.5 39.9 - - + +
66D TYR* 3.3 25.1 - - + +
67D ASN* 3.5 32.7 - - + +
69D LEU* 2.7 33.4 + - + +
70D LEU* 3.3 3.1 - - - -
71D GLU* 1.3 72.1 - - - +
73D LYS* 1.3 98.0 + - + +
75D ILE* 3.5 10.4 + - - +
76D PHE* 2.9 31.0 + + + +
118D LEU* 5.5 0.2 - - + -
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Residues in contact with LYS 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLN* 3.7 38.8 + - + +
20D ASN* 5.3 6.7 + - - -
70D LEU* 3.9 9.1 + - + +
71D GLU 3.1 1.2 - - - -
72D TYR* 1.3 115.6 + - + +
74D GLU* 1.3 59.6 + - - +
76D PHE* 4.2 3.8 - - - -
77D ASN* 2.8 38.6 + - - +
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Residues in contact with GLU 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D GLN 4.6 1.4 - - - +
13D LYS* 3.2 31.6 - - + +
14D HIS* 2.7 10.7 + - - -
15D PHE 2.7 31.7 + - - -
16D VAL* 3.1 17.8 + - - +
17D GLN* 4.1 19.6 - - + +
71D GLU* 3.0 19.1 + - + +
73D LYS* 1.3 78.8 - - - +
75D ILE* 1.3 60.1 + - + +
77D ASN* 3.9 0.7 - - - +
78D MET* 2.8 55.1 + - - +
121D PHE* 4.9 7.5 - - + -
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Residues in contact with ILE 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ILE* 3.9 30.3 - - + -
71D GLU* 3.3 13.4 + - + +
72D TYR* 3.8 6.5 - - - +
74D GLU* 1.3 72.8 - - + +
76D PHE* 1.3 69.9 + - - +
78D MET* 3.8 5.4 - - - +
79D MET* 3.0 22.0 + - + +
114D ALA* 4.0 19.7 - - + +
117D ASP* 4.6 5.6 - - + -
118D LEU* 3.2 51.6 - - + +
121D PHE* 4.0 25.4 - - + -
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Residues in contact with PHE 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D VAL* 4.2 11.0 - - + -
23D VAL* 5.0 8.1 - - + -
59D ALA* 3.5 46.7 - - + -
60D PHE* 4.0 25.8 - + - -
62D ILE* 5.5 2.9 - - + +
63D VAL* 4.1 16.6 - - + -
72D TYR* 2.9 24.8 + + + +
73D LYS* 3.6 7.0 - - + +
75D ILE* 1.3 80.0 - - - +
77D ASN* 1.3 78.8 + - - +
79D MET* 3.0 22.4 - - - +
80D PHE* 3.4 24.9 + + - -
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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
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16D VAL* 2.7 36.8 + - + +
17D GLN* 3.6 13.1 + - - +
19D LEU* 3.4 25.6 + - - +
22D VAL* 3.6 25.2 - - + +
73D LYS* 2.8 21.4 + - - +
76D PHE* 1.3 87.3 - - - +
78D MET* 1.3 67.1 + - - +
80D PHE* 3.1 4.3 + - - +
81D LEU* 2.9 26.6 + - - +
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Residues in contact with MET 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA* 3.7 31.9 - - + +
64A ALA* 4.8 2.5 - - + -
65A VAL* 3.8 12.3 - - + -
14D HIS* 3.1 37.2 - - + +
16D VAL* 3.9 13.9 - - + -
74D GLU* 2.8 39.6 + - - +
75D ILE* 3.8 6.3 - - - +
77D ASN* 1.3 71.7 - - - +
79D MET* 1.3 65.7 + - - +
81D LEU* 3.1 6.9 + - - +
82D LYS* 2.9 46.1 + - + +
214D PO4 4.8 4.3 - - - +
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Residues in contact with MET 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D PHE* 3.4 36.0 - - + +
58D HIS* 4.1 6.5 - - + -
59D ALA* 3.3 38.8 - - + +
62D ILE* 3.2 35.9 - - + -
75D ILE* 3.0 19.0 + - + +
76D PHE* 3.0 14.1 - - - +
78D MET* 1.3 78.0 - - - +
80D PHE* 1.3 62.7 + - + +
82D LYS* 3.2 3.5 + - - +
83D LEU 3.0 21.5 + - - -
110D ILE* 4.2 11.4 - - + +
111D MET* 4.9 5.4 - - - -
114D ALA* 3.8 21.5 - - + -
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Residues in contact with PHE 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D VAL* 3.6 37.4 - - + +
23D VAL* 3.5 26.9 - - + -
24D PHE* 4.0 5.3 - + - -
55D PHE* 4.5 8.1 - + - -
56D TYR* 3.6 44.9 - + - -
59D ALA* 3.6 30.7 - - + -
60D PHE* 4.6 3.1 - + - -
76D PHE* 3.4 28.2 + + - -
77D ASN 3.1 2.8 + - - +
79D MET* 1.3 79.7 - - + +
81D LEU* 1.3 65.9 + - - +
83D LEU* 3.2 20.6 + - + +
84D SER* 2.9 24.3 + - - -
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Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ALA* 3.4 29.5 - - + +
65A VAL* 4.4 11.2 - - + -
67A LYS* 5.7 0.2 - - - +
68A ALA* 4.2 14.8 - - + -
16D VAL* 3.3 33.2 - - + -
19D LEU* 3.9 17.9 - - + -
22D VAL* 4.2 11.4 - - + -
77D ASN 2.9 20.3 + - - +
78D MET* 3.7 18.4 - - - +
80D PHE* 1.3 77.4 - - - +
82D LYS* 1.3 61.1 + - - +
84D SER* 3.3 20.1 - - - -
85D VAL* 3.4 6.8 + - - +
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Residues in contact with LYS 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLN* 3.2 28.6 + - - +
60A LEU* 4.1 17.7 - - + +
61A ALA* 3.9 24.1 - - - +
64A ALA* 3.9 14.6 - - + -
78D MET* 2.9 32.9 + - + +
79D MET* 3.5 6.3 - - - +
81D LEU* 1.3 74.6 - - - +
83D LEU* 1.3 66.2 + - - +
84D SER 3.1 0.2 - - - -
85D VAL* 3.0 5.4 + - - +
86D VAL* 3.0 23.4 + - - +
110D ILE* 3.7 31.5 + - + +
113D LYS* 3.5 25.9 - - - +
114D ALA 5.5 0.2 - - - +
117D ASP* 5.5 0.2 + - - -
214D PO4 4.2 7.0 + - - -
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Residues in contact with LEU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D PHE* 3.5 29.2 - - + -
52D VAL* 5.1 3.6 - - + -
55D PHE* 3.7 26.7 - - + -
56D TYR* 4.3 8.1 - - + -
79D MET 3.0 12.7 + - - +
80D PHE* 3.2 22.6 + - + +
82D LYS* 1.3 74.6 - - - +
84D SER* 1.3 63.1 + - - +
86D VAL* 2.9 9.4 + - + +
87D PHE* 2.9 57.8 + - + -
107D LEU* 4.0 22.4 - - + -
110D ILE* 4.2 5.7 - - - +
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Residues in contact with SER 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LYS* 3.1 28.0 + - - +
24D PHE* 3.5 25.4 - - - -
80D PHE 2.9 12.9 + - - -
81D LEU* 3.3 17.0 - - - -
83D LEU* 1.3 77.7 - - - +
85D VAL* 1.3 62.0 + - - +
87D PHE* 3.3 13.7 + - - +
88D ASP* 3.3 16.1 + - - +
91D ARG* 4.0 1.2 + - - -
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 6.0 0.4 - - + -
36A MSE 4.0 19.3 - - + +
60A LEU* 3.6 22.2 - - + -
63A ILE* 3.7 16.4 - - + +
64A ALA* 3.4 34.5 - - + +
67A LYS* 4.4 13.0 - - + +
81D LEU 3.4 4.9 + - - +
82D LYS 3.0 8.3 + - - +
84D SER* 1.3 74.4 - - - +
86D VAL* 1.3 67.9 + - - +
88D ASP* 2.9 29.9 - - + +
89D THR* 3.6 4.5 + - - -
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Residues in contact with VAL 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.8 6.5 - - + -
48D PHE* 5.3 2.2 - - + -
82D LYS 3.0 14.4 + - - +
83D LEU 2.9 9.0 + - - +
85D VAL* 1.3 75.5 - - - +
87D PHE* 1.3 71.3 + - + +
89D THR* 3.0 11.2 + - - -
90D GLN* 3.0 17.5 + - + +
103D ASN* 3.9 32.1 - - + +
106D ILE* 3.9 32.3 - - + -
107D LEU* 4.0 16.8 - - + -
110D ILE* 4.1 11.7 - - + -
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Residues in contact with PHE 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D PHE* 3.9 26.2 - + - -
29D LEU* 3.4 35.0 - - + -
32D ILE* 3.4 23.7 - - + +
33D TYR* 5.6 0.2 - + - -
48D PHE* 3.7 33.4 - + - -
52D VAL* 4.4 8.7 - - + -
83D LEU* 2.9 48.6 + - + -
84D SER 3.5 8.3 - - - +
85D VAL 3.2 0.2 - - - -
86D VAL* 1.3 80.7 - - + +
88D ASP* 1.3 53.7 + - - +
90D GLN* 3.4 8.1 - - + +
91D ARG* 2.7 50.6 + - - +
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Residues in contact with ASP 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TYR* 2.6 32.0 + - - -
18A GLN* 3.1 39.2 + - - +
67A LYS* 2.5 28.7 + - - +
84D SER 3.3 2.3 + - - -
85D VAL* 2.9 22.0 + - + +
87D PHE* 1.3 78.1 - - - +
89D THR* 1.3 60.7 + - - +
91D ARG* 3.4 9.2 + - - +
92D LYS* 3.3 25.4 + - - +
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Residues in contact with THR 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A MSE 4.6 4.0 + - - +
37A ALA* 3.6 35.4 + - + +
85D VAL* 3.6 4.2 + - - +
86D VAL* 3.0 11.0 + - - -
88D ASP* 1.3 77.0 - - - +
90D GLN* 1.3 65.7 + - - +
91D ARG 3.1 0.2 - - - -
92D LYS* 3.0 12.3 + - + +
93D GLU* 2.9 28.3 + - + +
99D GLN* 3.7 31.6 - - + +
103D ASN* 4.2 7.6 - - - +
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Residues in contact with GLN 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D ILE* 3.7 25.1 - - + +
33D TYR* 6.2 0.2 - - - -
35D LEU* 5.3 0.2 - - - +
36D SER* 4.0 14.0 + - - -
45D LEU* 5.3 0.3 - - - +
48D PHE* 3.4 37.6 - - + -
86D VAL* 3.0 12.6 + - + +
87D PHE* 3.4 16.6 - - + +
89D THR* 1.3 76.7 - - - +
91D ARG* 1.3 58.1 + - - +
93D GLU* 4.6 2.5 - - - +
94D ALA* 3.0 35.6 + - + +
100D ILE* 3.6 31.0 - - - +
103D ASN* 2.8 25.4 + - - +
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Residues in contact with ARG 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLN* 2.6 35.8 + - - +
67A LYS* 4.2 2.8 - - - +
24D PHE* 5.7 4.0 - - - -
32D ILE* 4.8 21.4 - - + +
35D LEU* 4.3 33.0 - - + +
84D SER* 4.0 4.2 + - - +
87D PHE* 2.7 41.8 + - - +
88D ASP* 3.4 23.1 + - - +
89D THR 3.1 0.2 - - - -
90D GLN* 1.3 75.1 - - - +
92D LYS* 1.3 58.8 + - + +
94D ALA* 4.5 3.5 - - - +
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Residues in contact with LYS 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASP 3.0 27.0 + - - -
18A GLN* 3.2 22.0 + - - +
19A SER* 4.5 6.5 - - - +
88D ASP* 3.3 21.1 - - - +
89D THR* 3.0 12.1 + - + +
91D ARG* 1.3 79.1 - - - +
93D GLU* 1.3 80.2 + - + +
94D ALA 3.6 2.2 - - - -
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Residues in contact with GLU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ALA* 6.0 1.1 - - + -
89D THR* 2.9 20.5 + - + +
90D GLN* 3.5 5.1 - - - -
92D LYS* 1.3 97.7 - - + +
94D ALA* 1.3 59.5 + - - +
95D ASN 3.1 8.8 + - - -
96D ASN* 2.9 37.0 + - + +
99D GLN* 3.8 25.7 - - + +
100D ILE* 3.2 18.5 - - - +
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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