Contacts of the helix formed by residues 89 - 116 (chain A) in PDB entry 1HNB
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 SER 89 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 1.3 77.0 - - - +
90A GLU* 1.3 66.6 + - - +
91A LYS* 2.8 11.4 + - - +
92A GLU* 2.9 31.6 + - - +
93A GLN* 2.8 26.5 + - - +
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A SER* 1.3 71.2 - - - +
91A LYS* 1.3 54.9 + - + +
93A GLN* 3.1 13.0 + - - +
94A ILE* 2.7 44.3 + - + +
67B HIS* 5.5 7.9 - - + +
78B TYR* 3.4 20.3 - - - -
81B ARG* 3.0 48.1 + - - +
82B LYS* 3.5 24.8 + - - +
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Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A SER* 2.8 10.4 + - - +
90A GLU* 1.3 77.1 - - + +
92A GLU* 1.3 65.9 + - + +
93A GLN 3.0 1.2 + - - -
94A ILE* 3.1 17.3 + - - +
95A ARG* 3.1 21.3 + - - +
66B THR* 6.2 3.0 - - - +
67B HIS* 4.7 23.0 + - + +
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Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLY* 4.2 11.0 - - - -
88A GLU* 3.0 39.5 + - - +
89A SER* 2.9 25.1 + - - +
91A LYS* 1.3 80.0 - - + +
93A GLN* 1.3 57.1 + - - +
95A ARG* 3.8 11.8 + - - +
96A GLU* 3.0 27.8 + - - +
148A LEU* 3.6 25.7 - - + +
151A LYS* 5.6 3.6 - - - +
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Residues in contact with GLN 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLY 4.0 17.1 + - - +
88A GLU 3.8 6.8 + - - +
89A SER* 2.8 37.1 + - - +
90A GLU* 3.1 13.7 + - - +
92A GLU* 1.3 76.1 - - - +
94A ILE* 1.3 65.6 + - - +
95A ARG 3.2 0.2 - - - -
96A GLU* 3.1 19.5 + - - +
97A ASP* 2.9 31.2 + - - +
81B ARG* 4.0 32.9 + - - +
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Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLU* 2.7 27.5 + - + +
91A LYS* 3.1 5.1 + - - +
93A GLN* 1.3 71.6 - - - +
95A ARG* 1.3 65.3 + - + +
97A ASP* 3.4 6.4 + - - +
98A ILE* 2.9 49.9 + - + +
67B HIS* 3.8 34.3 - - + -
68B LYS 5.1 2.2 - - - +
69B ILE* 3.6 38.4 - - + -
74B ALA* 5.8 1.1 - - + +
78B TYR* 4.1 19.1 - - + -
81B ARG* 4.9 4.5 - - - +
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Residues in contact with ARG 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LYS* 3.1 19.7 - - - +
92A GLU* 3.8 11.0 - - - +
93A GLN 3.2 0.2 - - - -
94A ILE* 1.3 79.4 - - + +
96A GLU* 1.3 56.5 + - - +
98A ILE* 3.6 5.8 - - - +
99A LEU* 2.9 37.2 + - - +
140A PHE* 3.1 67.9 + - + -
144A GLN* 2.9 21.7 + - - +
147A PHE 2.6 30.3 + - - -
148A LEU* 3.4 16.9 + - + +
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 4.3 11.2 + - - +
85A LEU 4.5 0.2 - - - +
86A CYS* 3.5 5.7 - - - +
87A GLY* 3.0 35.1 + - - +
92A GLU 3.0 18.7 + - - +
93A GLN* 3.2 18.7 + - - +
95A ARG* 1.3 77.5 - - - +
97A ASP* 1.3 63.0 + - - +
99A LEU* 3.8 2.4 - - - +
100A GLU* 2.8 29.3 + - - +
148A LEU* 4.3 9.9 - - + +
153A THR* 4.6 0.3 - - - -
154A PHE* 2.9 32.3 - - + -
155A VAL* 3.6 23.5 - - + +
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 2.7 31.4 + - - -
93A GLN* 2.9 19.8 + - - +
94A ILE* 4.1 3.9 - - - +
96A GLU* 1.3 73.6 - - - +
98A ILE* 1.3 67.9 + - - +
100A GLU* 3.9 8.3 - - - +
101A ASN* 2.9 32.0 + - - +
74B ALA* 4.0 23.7 - - + +
77B ARG* 4.1 19.0 - - - +
81B ARG* 3.3 23.7 + - - -
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Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ILE* 2.9 46.4 + - + +
95A ARG* 3.6 6.7 - - - +
97A ASP* 1.3 74.4 - - - +
99A LEU* 1.3 60.0 + - + +
102A GLN* 2.8 34.5 + - + +
140A PHE* 5.4 5.2 - - + -
55B ASP* 4.7 10.3 - - - +
56B PHE* 3.9 26.0 - - + -
68B LYS 4.7 4.9 - - - +
69B ILE* 4.1 14.8 - - + -
70B THR* 3.9 34.8 - - - +
71B GLN* 3.9 13.7 - - + +
74B ALA* 4.2 2.7 - - + -
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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
----------------------------------------------------------
95A ARG 2.9 24.6 + - - +
96A GLU 3.8 0.2 - - - +
98A ILE* 1.3 76.1 - - - +
100A GLU* 1.3 63.6 + - - +
101A ASN 3.1 0.2 + - - -
102A GLN* 4.2 2.2 - - - -
103A PHE* 2.8 50.7 + - + -
137A TYR* 4.7 0.9 - - + -
140A PHE* 3.3 41.3 - - + -
147A PHE* 4.0 17.3 - - + -
148A LEU* 3.7 26.0 - - + -
155A VAL* 3.4 20.0 - - + -
56B PHE* 4.2 18.8 - - + -
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Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 3.4 36.8 + - - +
77A ARG* 2.6 50.5 + - - +
96A GLU 2.8 23.1 + - - +
97A ASP* 3.4 7.1 - - - +
99A LEU* 1.3 74.5 - - - +
101A ASN* 1.3 74.8 + - - +
103A PHE* 4.4 2.6 - - - +
104A MET* 3.8 10.7 + - - +
154A PHE* 3.9 18.6 - - + -
155A VAL* 4.1 1.1 - - - +
158A ILE* 4.4 14.8 - - + +
77B ARG* 4.1 5.7 + - - -
100B GLU* 4.9 4.1 - - - +
101B ASN* 5.4 3.1 - - - -
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Residues in contact with ASN 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 5.6 0.4 - - - +
97A ASP* 2.9 23.4 + - - +
100A GLU* 1.3 90.2 - - - +
102A GLN* 1.3 56.8 + - - +
104A MET* 2.8 34.3 + - - +
105A ASP* 3.1 9.8 + - - +
71B GLN* 3.0 30.2 + - + +
72B SER 5.5 0.2 - - - +
73B ASN* 3.6 41.6 + - - +
74B ALA 4.3 2.4 + - - -
100B GLU* 5.4 0.2 - - - +
104B MET* 5.4 6.7 - - - +
218B GDN 4.7 5.3 + - - -
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Residues in contact with GLN 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE* 2.8 27.8 + - + +
99A LEU* 3.7 4.9 - - - +
101A ASN* 1.3 71.7 - - - +
103A PHE* 1.3 63.1 + - - +
105A ASP* 2.9 21.4 + - - +
106A SER* 2.9 33.3 + - - +
137A TYR* 3.1 27.3 - - + +
56B PHE* 3.9 32.3 - - + +
58B ASN* 5.4 4.4 + - - +
71B GLN* 3.4 18.2 + - + +
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Residues in contact with PHE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 2.8 62.9 + - + +
100A GLU 4.4 0.7 - - - +
102A GLN* 1.3 73.5 - - - +
104A MET* 1.3 50.8 + - - +
106A SER* 3.4 3.0 + - - -
107A ARG* 2.7 34.8 + - - +
137A TYR* 3.7 42.2 - + - -
147A PHE* 4.0 11.9 - + - -
155A VAL* 4.4 5.6 - - + -
158A ILE* 3.5 27.8 - - + -
159A ALA* 3.5 43.1 - - + -
162A VAL* 3.8 22.6 - - + +
163A LEU* 4.8 5.4 - - + -
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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
----------------------------------------------------------
12A LEU* 4.7 7.4 - - + -
72A SER* 4.6 3.1 - - - -
73A ASN* 3.1 31.4 - - - +
100A GLU 3.8 10.4 + - - +
101A ASN* 2.8 18.5 + - - +
103A PHE* 1.3 76.0 - - - +
105A ASP* 1.3 67.8 + - - +
107A ARG* 2.9 33.7 + - - +
108A MET* 2.9 43.2 + - + +
158A ILE* 5.4 0.6 - - - +
218A GDN 4.0 22.0 - - - +
101B ASN* 4.8 4.3 - - - +
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Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASN* 3.3 13.2 + - - +
102A GLN* 2.9 13.4 + - - +
104A MET* 1.3 77.3 - - - +
106A SER* 1.3 57.8 + - - +
108A MET* 2.9 26.4 + - - +
109A GLN* 3.0 26.8 + - + +
58B ASN* 5.4 0.5 + - - -
71B GLN* 3.2 13.5 + - - +
218B GDN 3.0 37.6 - - - +
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Residues in contact with SER 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLN* 2.9 15.5 + - - -
103A PHE* 3.4 9.6 - - - -
105A ASP* 1.3 74.4 - - - +
107A ARG* 1.3 63.8 + - - +
108A MET 3.3 0.2 + - - -
109A GLN* 3.4 19.2 + - - +
110A LEU* 3.5 10.9 + - - +
126A TYR* 4.1 7.6 + - - -
133A MET* 4.0 20.1 - - - +
137A TYR* 2.8 28.6 + - - -
162A VAL* 4.1 13.4 - - - +
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Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLY 5.3 0.8 + - - -
12A LEU* 3.4 50.5 + - + +
15A SER* 3.4 19.2 + - - -
72A SER* 4.0 15.4 + - - -
73A ASN* 6.1 0.8 - - - +
76A LEU* 6.1 0.2 - - - +
103A PHE 2.7 16.1 + - - +
104A MET* 3.2 28.3 - - - +
106A SER* 1.3 73.1 - - - +
108A MET* 1.3 64.5 + - + +
110A LEU* 3.8 3.7 + - - +
111A ALA* 3.2 23.3 + - - +
158A ILE* 4.2 21.5 - - - +
161A ASP* 3.3 27.5 + - - +
162A VAL* 4.0 24.7 - - + +
165A ARG* 6.3 3.6 - - + -
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Residues in contact with MET 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 6.3 2.0 - - - -
104A MET* 2.9 38.2 + - + +
105A ASP* 2.9 15.0 + - - +
107A ARG* 1.3 77.3 - - - +
109A GLN* 1.3 58.7 + - - +
111A ALA* 2.8 11.3 + - - +
112A LYS* 2.7 35.2 + - - +
218A GDN 6.3 2.0 - - - +
108B MET* 6.4 2.2 - - + -
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Residues in contact with GLN 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP* 3.0 28.4 + - + +
106A SER* 3.4 13.0 + - - +
108A MET* 1.3 80.1 - - - +
110A LEU* 1.3 61.7 - - - +
112A LYS* 3.3 22.3 - - - +
113A LEU* 3.8 4.3 + - - +
126A TYR* 3.6 26.7 - - + +
133A MET* 5.6 3.8 - - + -
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A SER 3.5 6.0 + - - +
107A ARG* 4.2 6.5 - - - +
108A MET 3.2 0.4 - - - -
109A GLN* 1.3 77.2 - - - +
111A ALA* 1.3 65.1 + - - +
112A LYS 3.1 1.0 + - - -
113A LEU* 3.2 26.8 + - + +
114A CYS* 3.8 4.0 + - - -
126A TYR* 3.4 42.2 - - + +
162A VAL* 6.5 0.4 - - + -
165A ARG* 3.3 41.1 - - + +
166A ASN* 3.7 15.7 - - - +
169A PHE* 3.8 21.5 - - + -
214A PHE* 4.0 15.3 - - + -
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG 3.2 13.9 + - - +
108A MET* 2.8 14.5 + - + +
110A LEU* 1.3 82.1 - - - +
112A LYS* 1.3 63.6 + - - +
114A CYS* 3.1 11.6 + - - +
115A TYR* 3.0 37.5 + - + -
165A ARG* 5.9 0.7 - - - +
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Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A MET 2.7 14.1 + - - +
109A GLN* 3.3 17.9 - - - +
110A LEU 3.1 0.2 - - - -
111A ALA* 1.3 73.3 - - - +
113A LEU* 1.3 65.1 + - + +
115A TYR* 2.9 9.7 + - + +
116A ASP* 2.9 32.4 + - + +
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLN 3.8 5.8 + - - +
110A LEU* 3.2 20.9 + - + +
112A LYS* 1.3 78.6 - - + +
114A CYS* 1.3 58.8 + - - +
116A ASP* 3.0 27.8 + - - +
119A PHE* 3.5 36.9 - - + +
122A LEU* 3.7 32.8 - - + +
123A LYS* 3.7 11.9 - - - +
125A GLU* 5.9 0.2 - - + -
126A TYR* 3.6 35.7 - - + -
169A PHE* 4.1 15.7 - - + -
214A PHE* 6.1 0.9 - - + -
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Residues in contact with CYS 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 4.1 14.8 - - - -
111A ALA* 3.1 10.4 + - - +
113A LEU* 1.3 83.6 - - - +
115A TYR* 1.3 64.8 + - + +
116A ASP 3.4 4.0 + - - +
119A PHE* 4.9 4.0 - - - +
165A ARG* 4.7 1.6 - - - -
208A PHE* 3.3 33.0 - - + -
211A MET* 4.8 5.3 - - - +
212A ALA* 3.8 20.9 + - + +
214A PHE* 3.0 42.4 - - - -
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Residues in contact with TYR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA* 3.0 28.8 + - + +
112A LYS* 2.9 12.2 + - + +
114A CYS* 1.3 82.1 - - + +
116A ASP* 1.3 60.6 + - - +
117A PRO* 3.5 8.7 - - - +
208A PHE* 5.6 4.9 - + - -
211A MET* 5.1 30.9 - - + +
218A GDN 3.0 40.3 - - - +
112B LYS* 6.2 2.2 - - - -
----------------------------------------------------------
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Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LYS* 2.9 25.8 + - + +
113A LEU* 3.0 20.3 - - - +
114A CYS 4.0 3.6 - - - +
115A TYR* 1.3 76.5 - - - +
117A PRO* 1.3 77.9 - - - +
118A ASP* 3.3 33.2 + - - +
119A PHE* 3.3 8.9 + - - +
122A LEU* 4.5 10.4 - - + +
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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