Contacts of the helix formed by residues 102 - 131 (chain A) in PDB entry 1O9R
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 LYS 102 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS 3.6 6.7 - - - -
101A TYR* 1.3 78.5 - - - +
103A ILE* 1.3 66.7 - - - +
104A HIS* 4.3 2.0 - - + +
105A ASP* 2.9 43.8 + - - +
106A HIS* 3.1 9.4 + - - -
160D GLU* 3.6 28.7 - - + +
161D LYS* 5.0 3.5 - - + +
162D SER* 3.6 32.2 + - - +
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Residues in contact with ILE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.9 17.3 - - + -
44A LYS 3.5 22.7 - - - +
45A GLY 3.8 13.0 - - - +
47A GLN* 3.5 34.1 - - + +
48A PHE* 3.5 35.7 - - - +
51A VAL* 4.3 14.6 - - + -
101A TYR 4.1 0.2 - - - -
102A LYS* 1.3 72.7 - - - +
104A HIS* 1.3 59.0 + - - +
106A HIS* 3.1 7.0 + - - +
107A LEU* 2.8 44.6 + - + +
162D SER* 3.0 9.1 + - - +
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Residues in contact with HIS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN* 4.4 2.4 + - - +
102A LYS* 3.2 2.9 - - + -
103A ILE* 1.3 80.2 - - - +
105A ASP* 1.3 59.3 - - - +
107A LEU* 3.4 8.8 + - + +
108A ASP* 2.9 49.5 + - - -
158A VAL* 3.9 25.9 - - + +
161A LYS* 4.4 20.6 + - + -
162D SER* 2.9 27.3 + - - +
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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
----------------------------------------------------------
100A ILE* 3.7 31.5 - - + +
101A TYR 5.1 0.5 + - - -
102A LYS* 2.9 40.5 + - + +
104A HIS* 1.3 75.8 - - - +
106A HIS* 1.4 64.7 + - - +
108A ASP* 3.4 10.9 + - - +
109A ALA* 3.1 23.0 + - - +
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Residues in contact with HIS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLN* 4.5 1.1 - - + -
39A ALA* 3.5 24.3 - - + +
42A ASN* 3.5 19.7 + - + -
43A LEU* 3.7 28.3 - - + -
96A TYR* 2.7 30.3 + + - +
97A PRO 5.1 0.7 - - - -
100A ILE* 3.0 38.9 + - + +
101A TYR* 3.4 23.3 - - - -
102A LYS 3.1 11.4 + - - -
103A ILE 3.6 6.3 - - - +
105A ASP* 1.4 75.7 - - - +
107A LEU* 1.3 60.8 + - + +
109A ALA 3.2 0.5 + - - -
110A LEU* 2.8 37.4 + - + +
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN* 4.1 10.5 - - - +
51A VAL* 4.5 17.3 - - + -
103A ILE* 2.8 43.8 + - + +
104A HIS* 3.6 7.6 - - - +
106A HIS* 1.3 71.4 - - - +
108A ASP* 1.4 58.4 + - - +
110A LEU* 3.3 6.7 + - + +
111A ILE* 2.8 37.3 + - + +
154A LEU* 3.8 34.3 - - + +
157A HIS* 3.8 30.1 - - + +
158A VAL* 4.0 20.2 - - + -
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Residues in contact with ASP 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A HIS* 2.9 44.0 + - - +
105A ASP* 3.8 9.8 - - - +
106A HIS 3.2 0.2 - - - -
107A LEU* 1.4 76.3 - - - +
109A ALA* 1.3 61.4 + - - +
111A ILE* 3.4 10.1 + - - +
112A GLU* 3.1 31.7 + - - +
158A VAL* 4.5 9.9 - - - +
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 3.5 27.6 - - + +
97A PRO* 4.5 7.2 - - + -
100A ILE* 4.2 8.3 - - + -
105A ASP 3.1 17.3 + - - +
106A HIS 3.7 1.8 - - - +
108A ASP* 1.3 73.3 - - - +
110A LEU* 1.3 65.1 + - - +
112A GLU* 3.4 5.2 + - - -
113A ARG* 2.9 43.8 + - - +
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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
----------------------------------------------------------
35A VAL* 3.7 29.4 - - + +
36A THR* 4.4 5.8 - - - -
39A ALA* 3.9 25.8 - - + -
43A LEU* 5.6 0.7 - - + -
51A VAL* 5.8 0.4 - - + -
55A LEU* 3.9 25.8 - - + -
96A TYR* 3.9 6.1 - - - +
106A HIS* 2.8 28.0 + - + +
107A LEU* 3.7 8.5 - - + +
109A ALA* 1.3 75.6 - - - +
111A ILE* 1.3 56.4 + - - +
113A ARG* 3.1 2.9 + - - -
114A TYR* 2.7 54.8 + - + -
154A LEU* 4.1 20.9 - - + -
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Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 2.8 27.9 + - + +
108A ASP* 3.7 9.6 - - - +
109A ALA 3.4 0.2 - - - -
110A LEU* 1.3 75.8 - - - +
112A GLU* 1.4 64.6 + - + +
115A GLY* 2.9 21.7 + - - -
151A LEU* 3.9 8.2 - - + +
154A LEU* 3.6 35.0 - - + +
155A GLU* 3.7 20.6 - - + +
158A VAL* 3.8 31.6 - - + -
7E LYS* 3.7 30.2 - - + +
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LYS* 4.6 10.6 - - + +
108A ASP* 3.1 21.7 + - + +
109A ALA* 3.8 8.3 - - - +
110A LEU 3.2 0.4 - - - -
111A ILE* 1.4 78.2 - - - +
113A ARG* 1.3 73.0 + - + +
115A GLY* 3.9 0.7 - - - -
116A GLU* 3.1 40.4 + - - +
7E LYS* 4.6 23.0 + - - +
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Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.6 17.7 - - + -
35A VAL* 4.2 14.4 - - + -
93A LEU* 4.1 6.2 - - + +
94A LYS* 2.8 67.4 + - - +
95A ALA 3.0 24.4 + - - -
96A TYR* 3.8 26.8 - - - +
97A PRO* 3.9 5.9 - - - +
109A ALA* 2.9 41.3 + - - +
110A LEU* 3.1 4.7 + - - +
112A GLU* 1.3 83.8 + - - +
114A TYR* 1.3 66.7 + - - +
116A GLU* 3.3 2.0 + - - +
117A VAL* 3.0 29.8 + - - +
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Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.8 33.0 - - + -
36A THR* 2.8 30.2 + - + +
55A LEU* 5.5 0.4 - - + -
58A PHE* 3.3 41.6 - + + +
62A LEU* 3.5 10.0 - - + +
110A LEU* 2.7 46.0 + - + +
113A ARG* 1.3 73.4 - - - +
115A GLY* 1.4 56.6 + - - +
117A VAL* 3.7 0.7 - - - +
118A ALA* 2.8 33.0 + - - +
147A LEU* 4.3 14.6 - - + +
150A SER* 3.9 19.5 - - - -
151A LEU* 4.2 15.0 - - + -
154A LEU* 3.6 22.9 - - + -
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Residues in contact with GLY 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE 2.9 18.8 + - - -
112A GLU 3.9 0.9 - - - -
114A TYR* 1.4 75.2 - - - +
116A GLU* 1.4 58.9 + - - +
118A ALA* 3.7 0.3 - - - +
119A ASN* 2.9 40.8 + - - -
151A LEU* 3.8 12.2 - - - +
7E LYS* 3.9 21.8 - - - -
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Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LYS* 4.4 6.1 - - + +
93A LEU* 3.5 9.2 - - + +
94A LYS* 2.3 44.9 + - - -
112A GLU* 3.1 20.9 + - - +
113A ARG 3.3 3.5 + - - +
115A GLY* 1.4 76.4 - - - +
117A VAL* 1.3 58.1 + - - +
119A ASN* 3.3 5.7 + - - +
120A MET* 2.8 35.3 + - + +
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Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER* 4.0 21.8 - - - +
29A VAL* 4.2 22.9 - - + +
32A LEU* 3.9 23.1 - - + -
62A LEU* 5.5 0.4 - - + -
93A LEU* 3.9 19.1 - - + -
113A ARG 3.0 17.6 + - - +
114A TYR 4.0 0.9 - - - +
116A GLU* 1.3 72.8 - - - +
118A ALA* 1.3 67.9 + - - +
120A MET* 3.2 7.9 + - + +
121A ILE* 2.9 26.6 + - + +
147A LEU* 4.0 22.4 - - + -
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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
----------------------------------------------------------
114A TYR 2.8 23.4 + - - +
115A GLY* 3.7 6.1 - - - +
117A VAL* 1.3 73.2 - - - +
119A ASN* 1.3 61.0 + - - +
121A ILE* 3.4 1.9 + - - +
122A ARG* 3.0 34.7 + - - +
144A SER* 5.1 2.5 + - - +
147A LEU* 3.9 28.4 - - + +
148A ASP* 3.6 22.0 - - - +
151A LEU* 4.5 8.3 - - + -
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Residues in contact with ASN 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLY 2.9 24.3 + - - +
116A GLU* 3.8 4.8 - - - +
118A ALA* 1.3 75.9 - - - +
120A MET* 1.3 65.7 + - - +
122A ARG* 2.9 28.9 + - - +
123A LYS* 3.1 22.2 + - - +
7E LYS* 2.9 24.0 + - - +
8E ASN* 3.7 2.7 - - - -
9E ASP* 2.9 43.0 + - - +
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Residues in contact with MET 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU* 4.5 15.5 - - - +
25A SER* 4.0 29.4 - - - +
28A SER* 3.7 36.3 - - - +
92A LYS* 4.2 21.1 - - + -
93A LEU* 5.5 0.9 - - + -
116A GLU* 2.8 24.0 + - + +
117A VAL* 3.5 12.6 - - + +
119A ASN* 1.3 77.5 - - - +
121A ILE* 1.3 61.9 + - + +
123A LYS* 3.3 7.8 + - - +
124A ALA* 2.9 24.8 + - - +
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Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A SER* 3.7 29.6 - - - +
29A VAL* 4.4 13.2 - - + -
69A ILE* 4.5 4.7 - - + -
117A VAL* 2.9 25.1 + - + +
118A ALA 3.8 3.6 - - - +
120A MET* 1.3 75.9 - - + +
122A ARG* 1.3 65.0 + - - +
124A ALA* 3.1 5.1 + - - +
125A ILE* 3.1 21.8 + - - +
140A PHE* 3.3 42.4 - - + +
143A ALA* 4.1 7.4 - - + -
144A SER* 3.7 17.7 - - - +
147A LEU* 3.5 18.4 - - + -
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Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ALA* 3.0 19.8 + - - +
119A ASN* 2.9 24.2 + - - +
121A ILE* 1.3 76.1 - - - +
123A LYS* 1.4 61.7 + - - +
125A ILE* 3.3 28.6 + - + +
126A ASP* 3.6 12.8 + - - +
144A SER* 4.2 10.6 + - - +
148A ASP* 2.8 40.8 + - - -
8E ASN* 3.4 25.9 + - - +
9E ASP* 2.9 25.3 + - - +
10E LEU* 4.2 24.9 - - + +
11E PRO* 6.0 0.2 - - - -
72E ARG* 4.3 7.5 - - - +
134E PRO* 6.2 3.8 - - + -
135E THR* 4.9 3.2 + - - +
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Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASN 3.1 13.4 + - - +
120A MET* 3.6 9.9 - - - +
122A ARG* 1.4 74.2 - - - +
124A ALA* 1.4 61.6 + - - +
126A ASP* 3.0 10.7 + - + +
127A ASP* 2.7 56.3 + - - +
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 3.7 24.4 - - + +
25A SER* 4.2 4.7 - - - +
120A MET 2.9 14.3 + - - +
121A ILE* 3.1 11.2 + - - +
123A LYS* 1.4 72.7 - - - +
125A ILE* 1.4 65.5 + - - +
127A ASP* 4.1 4.0 - - - +
128A SER* 2.9 31.5 + - - -
140A PHE* 3.7 26.2 - - + -
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Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE 3.1 12.9 + - - +
122A ARG* 3.5 14.6 - - + +
123A LYS 3.2 0.4 - - - -
124A ALA* 1.4 75.6 - - - +
126A ASP* 1.3 69.5 + - - +
128A SER 3.4 0.2 + - - -
129A ASP* 3.0 28.8 + - + +
137A ALA* 3.6 15.0 - - + +
140A PHE* 3.7 21.3 - - + +
141A THR* 3.5 27.1 - - + +
144A SER* 3.8 16.2 - - - +
134E PRO* 4.2 17.9 - - + -
135E THR* 3.4 28.0 - - - +
----------------------------------------------------------
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Residues in contact with ASP 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG* 3.6 12.1 + - - +
123A LYS* 3.0 11.6 + - + +
125A ILE* 1.3 82.9 - - - +
127A ASP* 1.3 60.0 + - - +
129A ASP* 3.3 7.1 + - - +
130A GLU* 2.8 43.8 + - + +
132E GLY 5.4 2.8 - - - +
134E PRO* 3.6 28.7 - - - +
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Residues in contact with ASP 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 5.1 1.8 - - + +
21A ILE* 3.6 26.0 - - + +
123A LYS* 2.7 60.1 + - - +
124A ALA* 4.1 3.5 + - - +
126A ASP* 1.3 73.6 - - - +
128A SER* 1.4 61.9 + - - +
130A GLU* 3.5 19.7 + - - +
131A ALA* 3.1 22.0 + - - +
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Residues in contact with SER 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 4.4 10.7 - - - +
21A ILE* 4.1 7.6 - - - +
124A ALA 2.9 24.4 + - - -
125A ILE 3.7 2.9 - - - -
127A ASP* 1.4 74.7 - - - +
129A ASP* 1.3 65.2 - - - +
131A ALA* 3.2 9.4 + - - +
132A GLY 3.4 0.2 + - - -
133A ASP* 3.1 24.9 + - - +
136A THR* 3.4 9.8 - - - +
137A ALA* 3.8 22.9 - - - -
140A PHE* 3.4 20.8 - - - -
----------------------------------------------------------
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Residues in contact with ASP 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 3.0 19.4 + - + +
126A ASP* 3.6 7.7 - - - +
128A SER* 1.3 74.7 - - - +
130A GLU* 1.3 72.5 + - - +
132A GLY* 2.9 15.1 + - - -
133A ASP 4.6 5.2 - - - +
134A PRO* 5.1 8.4 - - - +
137A ALA* 4.0 11.4 - - + +
----------------------------------------------------------
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASP* 2.8 29.8 + - + +
127A ASP* 3.5 22.7 - - - +
128A SER 3.2 0.2 - - - -
129A ASP* 1.3 83.6 - - - +
131A ALA* 1.3 60.0 + - - +
132A GLY* 3.3 0.9 + - - -
----------------------------------------------------------
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Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA* 3.3 28.5 - - + +
17A THR* 4.2 16.8 - - + -
18A VAL* 3.8 23.6 - - + -
127A ASP 3.1 13.7 + - - +
128A SER 3.6 8.7 - - - +
129A ASP 3.1 0.6 - - - -
130A GLU* 1.3 75.4 - - - +
132A GLY* 1.3 58.2 + - - +
----------------------------------------------------------
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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