Contacts of the helix formed by residues 86 - 108 (chain A) in PDB entry 1Q11
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 PRO 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A TYR* 5.0 3.6 - - + -
83A MET* 4.7 5.6 - - + +
85A ALA* 1.3 85.3 - - + +
87A TRP* 1.3 61.2 + - - +
88A GLU* 4.3 3.4 - - + +
89A LEU* 3.4 46.6 + - + -
90A LEU* 2.9 29.6 + - - +
93A ARG* 4.7 4.3 - - - +
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Residues in contact with TRP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LEU* 3.8 27.8 - - + -
79A TYR* 3.8 37.2 - + + -
85A ALA 3.8 0.4 + - - -
86A PRO* 1.3 72.9 - - - +
88A GLU* 1.3 65.8 + - + +
90A LEU* 3.5 38.0 - - + +
91A GLU* 4.2 15.5 + - + +
121A THR* 4.0 28.9 - - + -
125A LEU* 4.7 16.6 - - + -
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Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO* 3.2 3.6 - - + +
87A TRP* 1.3 82.1 - - + +
89A LEU* 1.3 73.2 + - + +
90A LEU 3.6 0.5 + - - -
91A GLU* 4.1 9.0 + - - +
92A LEU* 4.5 10.8 + - - +
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PRO* 3.4 37.7 + - + +
88A GLU* 1.3 87.5 - - + +
90A LEU* 1.3 59.2 + - - +
91A GLU 3.3 1.3 - - - -
92A LEU* 3.0 15.2 + - + +
93A ARG* 2.8 46.9 + - - +
339A ALA 4.4 10.3 - - - +
340A ALA 4.2 7.0 - - - +
342A PRO* 4.0 29.6 - - + -
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A THR* 3.9 15.7 + - - +
75A ASP* 3.7 33.2 - - + +
78A ALA* 3.9 4.9 - - + -
79A TYR* 3.9 9.0 - - + +
85A ALA* 3.5 29.2 - - + +
86A PRO 2.9 18.8 + - - +
87A TRP* 3.5 48.9 - - + +
88A GLU 3.3 0.4 - - - -
89A LEU* 1.3 76.4 - - - +
91A GLU* 1.3 59.5 + - - +
93A ARG* 3.1 6.0 + - - +
94A VAL* 2.7 39.7 + - - +
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Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ASP* 3.4 22.0 - - - +
87A TRP* 4.2 15.4 + - + +
88A GLU 4.1 7.5 + - - +
89A LEU 3.3 0.6 - - - -
90A LEU* 1.3 81.7 - - - +
92A LEU* 1.3 63.9 + - + +
94A VAL* 3.5 6.2 + - - +
95A SER* 3.1 25.3 + - - -
119A LYS* 2.7 33.7 + - - +
121A THR* 4.2 2.5 + - - +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A GLU 4.5 7.0 - - - +
89A LEU* 3.0 21.3 + - + +
91A GLU* 1.3 78.2 - - + +
93A ARG* 1.3 59.5 + - - +
95A SER* 3.2 7.4 + - - +
96A TYR* 2.9 24.9 + - - +
336A LEU* 3.7 25.3 - - + +
339A ALA* 3.7 35.2 - - + +
340A ALA* 4.1 15.0 - - + -
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Residues in contact with ARG 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A THR* 4.0 20.0 - - - +
45A THR 3.6 19.8 + - - -
46A GLY* 5.5 0.2 - - - -
84A LYS 3.0 27.1 + - - -
85A ALA* 3.2 18.6 - - - +
86A PRO* 5.0 1.8 - - - +
89A LEU* 2.8 36.7 + - - +
90A LEU* 3.6 4.9 - - - +
92A LEU* 1.3 74.7 - - - +
94A VAL* 1.3 58.6 + - - +
96A TYR* 4.2 6.3 - - - -
97A TYR* 2.8 36.1 + - - -
340A ALA* 2.9 30.4 + - + +
341A TYR* 3.3 33.6 - - + +
342A PRO* 4.9 1.6 - - - +
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A THR* 3.8 15.9 - - + -
73A PHE* 4.5 8.5 - - + -
75A ASP* 3.7 28.7 - - + +
90A LEU 2.7 25.6 + - - +
91A GLU* 3.6 9.9 - - - +
93A ARG* 1.3 73.1 - - - +
95A SER* 1.3 58.7 + - - +
97A TYR* 3.3 1.9 + - - +
98A GLU* 2.8 60.0 + - + +
119A LYS* 3.9 31.2 - - + -
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Residues in contact with SER 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLU 3.1 12.7 + - - -
92A LEU* 3.3 10.5 - - - +
94A VAL* 1.3 80.4 - - - +
96A TYR* 1.3 59.2 + - - +
98A GLU* 3.4 10.8 + - - +
99A ASN* 2.8 37.3 + - - +
336A LEU* 4.1 17.5 - - - -
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Residues in contact with TYR 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LYS* 3.4 41.5 + - + +
48A PRO* 3.8 19.6 + - + -
92A LEU 2.9 13.8 + - - +
93A ARG* 3.7 10.3 - - - +
95A SER* 1.3 76.5 - - - +
97A TYR* 1.3 60.3 + - - +
99A ASN* 3.8 2.2 - - - +
100A VAL* 2.9 40.5 + - + +
233A ASP* 4.4 1.7 + - - -
234A LEU* 5.8 0.5 - - - +
235A LEU* 3.7 20.4 - - - +
328A PHE* 4.0 23.5 - + - -
336A LEU* 4.0 10.9 - - + +
337A ALA* 3.9 38.5 - - + +
340A ALA* 4.2 6.7 - - + -
341A TYR* 3.8 17.0 - + + -
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Residues in contact with TYR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A THR* 3.7 30.7 - - + -
43A ALA 3.5 18.4 - - - -
44A THR* 3.8 12.8 - - + -
45A THR 3.2 15.3 + - - -
46A GLY 2.4 30.8 + - - -
48A PRO* 3.6 23.1 - - + -
52A TYR* 3.4 4.6 + + - -
73A PHE* 3.8 14.6 - + + -
93A ARG* 2.8 25.8 + - + +
94A VAL 3.6 4.3 - - - +
96A TYR* 1.3 79.1 - + - +
98A GLU* 1.3 57.8 + - - +
100A VAL* 4.0 5.6 - - - -
101A ILE* 2.8 39.6 + - + +
341A TYR* 3.4 16.4 - - - -
701A K 3.0 17.7 - - - -
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Residues in contact with GLU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PHE* 3.4 37.3 - - + -
94A VAL* 2.8 48.2 + - + +
95A SER* 3.7 9.2 + - - +
97A TYR* 1.3 72.4 - - - +
99A ASN* 1.3 64.1 + - - +
101A ILE* 4.2 0.2 - - - +
102A LYS* 3.0 54.2 + - - +
117A PHE* 4.8 5.2 - - - +
119A LYS* 5.7 1.4 - - - +
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Residues in contact with ASN 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A SER* 2.8 28.5 + - - +
96A TYR 3.8 2.2 - - - +
98A GLU* 1.3 79.3 - - - +
100A VAL* 1.3 58.1 + - - +
102A LYS* 4.7 3.1 - - - +
103A ALA* 3.0 14.7 + - - +
327A LYS* 3.0 33.5 + - - +
328A PHE* 3.6 19.5 - - + -
333A LEU* 4.1 13.8 - - + +
336A LEU* 3.3 24.9 - - - +
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Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PRO* 3.9 33.4 - - + +
96A TYR* 2.9 33.8 + - + +
97A TYR* 3.5 5.4 - - - +
99A ASN* 1.3 76.0 - - - +
101A ILE* 1.3 67.5 + - + +
103A ALA* 3.3 3.0 + - - +
104A MET* 3.0 31.5 + - - +
234A LEU* 3.2 34.8 - - + -
235A LEU* 5.5 1.8 - - + -
324A ILE* 4.5 9.4 - - + -
328A PHE* 3.7 16.4 - - + -
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Residues in contact with ILE 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TRP* 4.7 5.4 - - + -
42A THR* 5.5 0.2 - - + -
48A PRO* 4.8 1.1 - - + -
52A TYR* 3.9 29.8 - - + -
56A MET* 3.8 26.7 - - + -
71A ILE* 4.2 14.1 - - + -
73A PHE* 4.1 17.0 - - + -
97A TYR* 2.8 34.2 + - + +
98A GLU 4.2 1.6 - - - +
100A VAL* 1.3 79.1 - - + +
102A LYS* 1.3 65.6 + - - +
104A MET* 3.3 19.1 + - - +
105A LEU* 3.1 32.7 + - + +
117A PHE* 4.5 6.1 - - + -
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Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLU* 3.0 48.0 + - - +
99A ASN* 3.9 7.0 - - - +
101A ILE* 1.3 76.3 - - - +
103A ALA* 1.3 55.2 + - - +
105A LEU* 3.3 6.6 + - - +
106A GLU* 3.0 37.0 + - - +
112A LEU* 3.9 17.1 - - + +
117A PHE* 3.7 49.3 - - + +
327A LYS* 4.4 7.6 - - - +
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASN 3.0 18.4 + - - +
100A VAL* 3.5 8.3 - - - +
101A ILE 3.2 0.2 - - - -
102A LYS* 1.3 78.3 - - - +
104A MET* 1.3 55.5 + - - +
106A GLU* 3.4 8.0 + - - +
107A SER* 2.9 28.8 + - - -
323A PRO* 5.6 0.7 - - - +
324A ILE* 3.9 28.8 - - + +
327A LYS* 3.9 25.3 - - + +
328A PHE* 4.2 0.9 - - + -
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Residues in contact with MET 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TYR* 3.5 20.6 - - + +
53A PHE* 3.3 61.6 - - + +
56A MET* 4.0 9.4 - - + -
100A VAL 3.0 16.9 + - - +
101A ILE* 3.6 23.1 - - - +
103A ALA* 1.3 77.5 - - - +
105A LEU* 1.3 62.1 + - - +
107A SER* 3.1 5.1 + - - -
108A ILE* 3.0 28.5 + - - +
234A LEU* 3.6 28.9 - - + -
324A ILE* 4.0 17.5 - - + +
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A MET* 3.7 29.4 - - + +
59A ILE* 4.3 12.3 - - + -
71A ILE* 3.9 18.8 - - + -
101A ILE* 3.1 22.1 + - + +
102A LYS 3.7 0.9 - - - +
104A MET* 1.3 76.3 - - - +
106A GLU* 1.3 59.4 + - - +
108A ILE* 3.4 4.5 + - + +
109A GLY 3.3 4.0 + - - -
110A VAL* 2.8 55.4 + - + +
112A LEU* 3.5 20.9 - - + -
115A LEU* 3.5 26.0 - - + -
117A PHE* 4.1 4.5 - - + -
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LYS* 3.0 22.9 + - - +
103A ALA* 3.7 8.0 - - - +
105A LEU* 1.3 75.9 - - - +
107A SER* 1.3 63.4 + - - +
109A GLY* 3.1 13.3 + - - -
110A VAL 4.5 5.4 - - - +
112A LEU* 3.3 28.3 - - + +
327A LYS* 5.3 10.5 + - - +
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Residues in contact with SER 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PHE* 5.0 1.3 - - - -
103A ALA 2.9 15.6 + - - -
104A MET* 3.1 12.3 + - - -
106A GLU* 1.3 78.6 - - - +
108A ILE* 1.3 60.4 + - - +
109A GLY 3.3 2.9 + - - -
271A LEU* 5.4 0.2 - - - +
319A LYS 4.2 0.5 + - - +
320A LEU* 2.5 45.0 + - - +
323A PRO* 3.5 20.5 - - - +
324A ILE* 4.3 2.9 - - - -
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Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PHE* 3.8 21.5 - - + -
56A MET* 3.9 35.4 - - + +
57A SER* 4.6 6.3 - - - +
60A ALA* 4.4 5.7 - - + +
104A MET 3.0 11.8 + - - +
105A LEU* 3.5 11.9 - - + +
107A SER* 1.3 74.2 - - - +
109A GLY* 1.3 59.9 + - - +
110A VAL* 3.6 21.7 + - + +
267A VAL* 5.6 3.1 - - + -
271A LEU* 3.5 33.8 - - + +
320A LEU* 3.6 25.6 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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