Contacts of the helix formed by residues 95 - 121 (chain A) in PDB entry 4I1Q
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 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A TYR* 3.6 8.7 - - - -
94A ASP* 1.3 72.4 - - - +
96A HIS* 1.3 58.9 + - - +
97A GLU 3.2 3.4 - - - -
98A GLU* 3.3 6.5 + - - -
99A LEU* 2.8 30.1 + - - +
234A VAL* 3.4 18.5 - - - +
237A LYS* 4.2 14.6 - - - +
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Residues in contact with HIS 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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86A GLN* 4.9 5.0 + - - +
89A TYR* 3.5 42.4 + + + -
90A SER 3.5 12.1 - - - +
91A SER* 3.5 30.2 + - - +
93A TRP 3.3 17.5 + - - +
94A ASP 3.2 3.4 + - - -
95A GLY* 1.3 79.8 - - - +
97A GLU* 1.3 67.8 + - - +
99A LEU* 3.6 6.2 + - + +
100A LYS* 3.1 48.3 + - - +
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLY 3.2 0.8 - - - +
96A HIS* 1.3 84.1 + - - +
98A GLU* 1.3 66.9 + - - +
100A LYS* 3.0 49.2 + - + +
101A ALA* 3.1 12.5 + - - +
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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
----------------------------------------------------------
95A GLY* 3.3 11.7 + - - +
97A GLU* 1.3 77.8 - - - +
99A LEU* 1.3 52.8 + - - +
101A ALA* 2.7 30.9 + - + +
102A ILE* 2.8 19.4 + - + +
230A ASN* 3.7 33.8 - - + +
233A GLU* 5.0 4.3 - - - +
234A VAL* 3.7 13.6 + - + +
237A LYS* 3.3 21.4 + - - -
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 3.6 24.5 - - + -
86A GLN* 4.1 23.3 - - + +
89A TYR* 3.5 41.3 - - + -
95A GLY 2.8 20.7 + - - +
96A HIS* 3.7 8.5 - - + +
98A GLU* 1.3 71.6 - - - +
100A LYS* 1.3 64.3 + - - +
101A ALA 3.0 0.2 + - - -
102A ILE* 3.1 12.3 + - + +
103A VAL* 3.0 38.1 + - + +
231A LEU* 4.5 7.0 - - + -
234A VAL* 3.9 19.8 - - + +
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Residues in contact with LYS 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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86A GLN* 3.9 21.5 - - + +
96A HIS* 3.1 32.6 + - + +
97A GLU* 3.0 47.1 + - - +
99A LEU* 1.3 77.3 - - - +
101A ALA* 1.3 55.5 + - - +
103A VAL* 4.2 1.6 - - - +
104A TRP* 3.2 28.8 + - + +
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Residues in contact with ALA 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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97A GLU 3.1 8.8 + - - +
98A GLU* 2.7 21.3 + - + +
100A LYS* 1.3 71.0 - - - +
102A ILE* 1.3 65.9 + - + +
103A VAL 3.3 0.2 - - - -
104A TRP* 4.1 4.9 - - - -
105A ASN* 2.8 40.8 + - - +
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU* 2.8 20.9 + - + +
99A LEU* 3.1 11.0 + - + +
101A ALA* 1.3 77.4 - - - +
103A VAL* 1.3 70.5 + - + +
105A ASN* 3.8 0.5 - - - +
106A ASN* 2.8 31.9 + - + +
227A LEU* 4.2 27.5 - - + +
230A ASN* 3.7 27.1 - - + +
231A LEU* 3.7 42.8 - - + +
234A VAL* 3.8 19.7 - - + -
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Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LYS* 6.6 0.2 - - + -
82A SER* 3.1 40.2 - - - +
83A GLU* 5.1 6.1 - - - +
85A LEU* 6.0 0.2 - - + -
86A GLN* 3.6 39.0 - - + +
99A LEU* 3.0 27.5 + - + +
100A LYS 4.2 0.2 - - - +
102A ILE* 1.3 80.9 - - + +
104A TRP* 1.3 66.4 + - - +
106A ASN* 3.2 8.9 + - - +
107A ASP* 3.2 18.8 + - + +
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Residues in contact with TRP 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS* 3.2 22.3 + - + +
101A ALA* 3.1 9.3 + - - +
103A VAL* 1.3 79.6 - - - +
105A ASN* 1.3 67.3 + - - +
107A ASP* 2.8 28.0 + - + +
108A LEU* 3.2 42.3 + - + +
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Residues in contact with ASN 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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101A ALA* 2.8 34.7 + - - +
102A ILE* 4.0 1.3 - - - +
104A TRP* 1.3 80.0 - - - +
106A ASN* 1.3 64.6 + - - +
107A ASP 3.0 2.0 - - - -
108A LEU* 3.1 14.6 + - + +
109A LEU* 2.8 31.6 + - + +
227A LEU* 4.0 22.6 - - + +
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Residues in contact with ASN 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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78A SER* 3.2 29.1 + - - -
79A LYS* 5.2 2.2 - - - +
82A SER* 5.4 6.3 + - - -
102A ILE* 2.8 27.7 + - - +
103A VAL* 3.2 10.4 + - - +
105A ASN* 1.3 72.7 - - - +
107A ASP* 1.3 64.3 + - - +
109A LEU* 3.5 3.5 + - - +
110A TRP* 3.1 39.8 + - - +
224A MET* 3.7 20.3 - - - +
227A LEU* 3.5 17.2 - - + +
217B ARG* 5.0 6.8 + - - -
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Residues in contact with ASP 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A HIS* 3.0 28.6 + - - -
79A LYS* 3.7 29.5 + - + +
103A VAL* 3.6 10.1 - - + +
104A TRP* 2.8 15.4 + - + +
106A ASN* 1.3 81.4 - - - +
108A LEU* 1.3 65.2 + - - +
110A TRP* 3.8 2.1 + - - -
111A GLU* 3.1 37.0 + - - +
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Residues in contact with LEU 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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104A TRP* 3.2 47.5 + - + +
105A ASN* 3.1 15.4 + - - +
107A ASP* 1.3 82.2 - - - +
109A LEU* 1.3 59.1 + - + +
111A GLU* 3.3 8.5 + - + +
112A ASP* 2.8 32.0 + - - +
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Residues in contact with LEU 109 (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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105A ASN* 2.8 20.6 + - + +
106A ASN 3.7 3.8 - - - +
108A LEU* 1.3 69.3 - - + +
110A TRP* 1.3 70.0 + - - +
111A GLU 2.8 0.7 + - - -
112A ASP* 2.9 9.1 + - + +
113A TYR* 2.8 25.5 + - - +
219A VAL* 6.0 0.7 - - + -
220A PHE* 4.5 15.9 - - + -
223A GLU* 3.4 48.2 - - + +
224A MET* 4.1 10.3 - - + +
227A LEU* 3.5 33.2 - - + -
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Residues in contact with TRP 110 (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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71A VAL* 4.0 40.4 - - + -
74A MET* 3.7 37.7 - - + -
75A HIS* 3.4 40.8 - + + +
78A SER* 3.6 19.4 + - - -
79A LYS 5.9 0.2 - - - -
106A ASN* 3.1 32.5 + - - +
107A ASP* 4.8 0.4 - - - -
109A LEU* 1.3 77.0 - - - +
111A GLU* 1.3 51.6 + - - +
113A TYR* 3.2 8.2 + + - +
114A GLU* 2.8 40.5 + - - +
220A PHE* 3.6 25.9 - + - -
224A MET* 3.0 28.2 - - + +
74B MET* 6.0 1.1 - - + -
217B ARG* 5.6 3.4 - - - -
221B TYR* 5.2 3.8 - - - -
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Residues in contact with GLU 111 (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 HIS* 3.7 20.9 + - + +
79A LYS* 5.3 4.0 + - - -
107A ASP* 3.1 27.5 + - - +
108A LEU* 3.4 14.1 - - + +
109A LEU 3.0 0.6 - - - -
110A TRP* 1.3 75.1 - - - +
112A ASP* 1.3 66.7 + - - +
114A GLU* 3.1 12.2 + - - +
115A GLU* 2.9 48.2 + - - +
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Residues in contact with ASP 112 (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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108A LEU 2.8 20.9 + - - +
109A LEU* 3.5 8.0 - - + +
111A GLU* 1.3 74.0 - - - +
113A TYR* 1.3 58.6 + - - +
115A GLU* 3.3 15.4 + - - +
116A LYS* 3.0 64.4 + - - +
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Residues in contact with TYR 113 (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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67A PHE* 4.4 8.1 - - - -
71A VAL* 4.1 26.0 - - + -
109A LEU 2.8 11.2 + - - +
110A TRP* 3.3 9.9 - + - +
112A ASP* 1.3 78.1 - - - +
114A GLU* 1.3 52.4 + - - +
116A LYS* 3.2 3.7 + - - -
117A LEU* 2.8 63.7 + - + +
216A LEU* 4.2 26.2 - - + -
217A ARG* 3.2 34.6 - - + +
220A PHE* 3.8 55.9 - + + -
221A TYR* 5.0 0.7 + - - -
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Residues in contact with GLU 114 (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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68A LEU* 3.8 16.5 - - + +
71A VAL* 3.5 20.7 - - + +
72A LYS* 3.5 37.0 - - + +
75A HIS* 2.2 51.8 + - - +
110A TRP* 2.8 16.4 + - - +
111A GLU* 3.1 12.9 + - - +
113A TYR* 1.3 73.6 - - - +
115A GLU* 1.3 65.7 + - - +
117A LEU* 4.6 1.3 - - - -
118A ALA* 2.9 24.6 + - - +
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Residues in contact with GLU 115 (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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111A GLU* 2.9 40.8 + - - +
112A ASP* 3.7 17.5 - - - +
114A GLU* 1.3 74.9 - - - +
116A LYS* 1.3 59.9 + - + +
118A ALA* 3.3 8.7 - - - +
119A ASP* 3.1 31.8 + - - +
123A ARG* 5.0 0.5 + - - -
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Residues in contact with LYS 116 (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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112A ASP* 3.0 47.4 + - - +
113A TYR* 3.8 3.4 - - - +
115A GLU* 1.3 76.7 - - + +
117A LEU* 1.3 62.0 + - - +
119A ASP* 3.1 3.4 + - + +
120A GLN* 2.8 52.6 + - - +
216A LEU* 3.6 33.5 - - + +
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Residues in contact with LEU 117 (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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64A LEU* 6.3 0.2 - - + -
67A PHE* 4.0 24.7 - - + -
68A LEU* 4.2 16.8 - - + -
71A VAL* 3.8 25.1 - - + -
113A TYR* 2.8 57.5 + - + +
114A GLU 3.9 2.2 - - - +
116A LYS* 1.3 70.5 - - - +
118A ALA* 1.3 63.2 + - - +
121A ALA* 3.1 27.4 + - + +
122A VAL* 3.2 11.1 + - + +
213A ILE* 4.3 26.0 - - + -
216A LEU* 3.7 10.5 - - + +
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Residues in contact with ALA 118 (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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68A LEU* 4.0 21.9 - - + +
72A LYS* 6.2 0.2 - - - +
114A GLU 2.9 16.1 + - - +
115A GLU* 3.3 12.6 - - - +
116A LYS 3.2 0.2 - - - -
117A LEU* 1.3 78.2 - - - +
119A ASP* 1.3 57.7 + - - +
122A VAL* 3.5 4.2 + - + +
123A ARG* 2.8 58.2 + - + +
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Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLU* 3.1 16.3 + - - +
116A LYS* 3.1 6.2 + - + +
118A ALA* 1.3 76.9 - - - +
120A GLN* 1.3 68.4 + - + +
123A ARG* 2.9 36.8 + - - +
124A THR* 3.3 22.3 + - - -
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Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LYS* 2.8 37.1 + - - +
119A ASP* 1.3 85.6 - - + +
121A ALA* 1.3 55.6 + - + +
124A THR* 3.1 20.5 + - - +
209A ILE* 4.3 3.3 - - - +
212A ASN* 3.2 48.3 + - + +
215A ASN* 5.8 1.0 - - - +
216A LEU* 3.5 31.3 - - + +
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 3.7 16.0 - - + +
117A LEU* 3.1 21.6 + - + +
119A ASP 3.5 0.2 - - - -
120A GLN* 1.3 79.8 - - + +
122A VAL* 1.3 68.0 + - + +
124A THR* 4.0 1.3 - - - -
125A MET* 3.2 29.8 + - - +
209A ILE* 3.7 7.2 - - + +
213A ILE* 4.0 31.9 - - + -
216A LEU* 6.1 0.2 - - + -
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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