Contacts of the helix formed by residues 102 - 131 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS* 5.4 2.0 - - - +
44B LYS 3.5 7.0 - - - -
101B TYR* 1.3 78.9 - - - +
103B ILE* 1.3 66.8 + - - +
104B HIS* 4.3 2.0 - - + +
105B ASP* 3.0 37.2 + - - +
106B HIS* 3.2 10.7 + - - -
160C GLU* 2.4 49.4 + - + +
161C LYS* 5.4 1.6 - - + +
162C SER* 3.5 28.7 - - - +
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Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 4.0 15.0 - - + -
44B LYS 3.4 22.0 - - - +
45B GLY 3.8 14.4 - - - +
46B PRO* 5.3 0.2 - - + -
47B GLN* 3.6 15.3 - - + +
48B PHE* 3.5 35.7 - - - +
51B VAL* 4.3 19.5 - - + -
101B TYR 4.1 0.9 - - - -
102B LYS* 1.3 71.1 - - - +
104B HIS* 1.3 58.2 + - - +
106B HIS* 3.2 7.8 + - - +
107B LEU* 2.8 47.1 + - + +
162C SER* 3.0 13.3 + - - +
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Residues in contact with HIS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LYS* 3.2 1.7 - - + -
103B ILE* 1.3 74.2 - - - +
105B ASP* 1.4 61.4 + - - +
107B LEU* 3.3 9.1 + - + +
108B ASP* 2.9 51.2 + - - -
158B VAL* 3.9 28.4 - - + +
161B LYS* 5.9 9.4 - - + -
162C SER* 2.8 28.9 + - - +
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Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ILE* 3.8 31.2 - - + +
101B TYR 5.0 0.3 + - - -
102B LYS* 3.0 36.8 + - + +
104B HIS* 1.4 78.3 - - - +
106B HIS* 1.4 63.6 + - - +
108B ASP* 3.4 11.1 + - - +
109B ALA* 3.1 22.7 + - - +
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Residues in contact with HIS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLN* 4.5 1.6 - - + -
39B ALA* 3.6 24.1 - - + -
42B ASN* 3.6 19.7 + - + -
43B LEU* 3.8 28.9 - - + -
96B TYR* 2.8 31.0 + + - +
97B PRO 5.1 0.7 - - - -
100B ILE* 3.0 40.0 + - + +
101B TYR* 3.4 22.9 - - - -
102B LYS 3.2 10.9 + - - -
103B ILE 3.6 5.4 - - - +
105B ASP* 1.4 71.8 - - - +
107B LEU* 1.3 62.7 + - + +
109B ALA 3.2 0.9 + - - -
110B LEU* 2.8 37.2 + - + +
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLN* 5.2 2.7 - - - +
51B VAL* 4.5 17.0 - - + -
103B ILE* 2.8 39.0 + - + +
104B HIS* 3.6 10.1 - - + +
106B HIS* 1.3 77.2 - - + +
108B ASP* 1.3 57.9 + - - +
110B LEU* 3.8 5.7 - - + +
111B ILE* 2.8 38.9 + - + +
154B LEU* 3.9 35.2 - - + +
157B HIS* 3.8 32.5 - - + +
158B VAL* 4.0 19.3 - - + -
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Residues in contact with ASP 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B HIS* 2.9 42.3 + - - +
105B ASP* 3.8 10.2 - - - +
106B HIS 3.2 0.2 - - - -
107B LEU* 1.3 76.6 - - - +
109B ALA* 1.3 61.4 + - - +
111B ILE* 3.4 10.0 + - - +
112B GLU* 3.1 23.2 + - - +
158B VAL* 4.5 9.4 - - - +
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TYR* 3.5 29.4 - - + +
97B PRO* 4.5 7.2 - - + -
100B ILE* 4.2 7.6 - - + -
105B ASP 3.1 17.4 + - - +
108B ASP* 1.3 73.0 - - - +
110B LEU* 1.3 65.1 + - - +
112B GLU* 3.5 3.1 + - - -
113B ARG* 2.9 44.5 + - - +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 3.6 29.6 - - + +
36B THR* 4.3 6.1 - - - -
39B ALA* 3.8 25.4 - - + -
43B LEU* 5.6 0.4 - - + -
51B VAL* 5.8 0.7 - - + -
55B LEU* 3.9 24.5 - - + -
96B TYR* 3.8 6.1 - - - +
106B HIS* 2.8 27.5 + - + +
107B LEU* 3.8 7.9 - - + +
109B ALA* 1.3 73.7 - - - +
111B ILE* 1.3 57.7 + - - +
113B ARG* 3.2 2.1 + - - -
114B TYR* 2.7 56.5 + - + -
154B LEU* 4.1 21.1 - - + -
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Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 2.8 28.3 + - + +
108B ASP* 3.8 8.3 - - - +
110B LEU* 1.3 77.0 - - - +
112B GLU* 1.3 59.1 + - - +
115B GLY* 2.8 28.8 + - - -
151B LEU* 3.9 5.0 - - + +
154B LEU* 3.6 37.5 - - + +
155B GLU* 3.8 31.4 - - + +
158B VAL* 3.8 31.2 - - + -
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LYS* 4.2 15.2 - - - +
108B ASP 3.1 14.3 + - - +
109B ALA* 3.7 7.8 - - - +
110B LEU 3.2 0.2 - - - -
111B ILE* 1.3 80.2 - - - +
113B ARG* 1.3 84.5 + - - +
115B GLY* 3.9 0.5 - - - -
116B GLU* 3.1 54.1 + - + +
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Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.7 17.0 - - + -
35B VAL* 4.2 13.0 - - - -
93B LEU* 4.3 16.2 - - + -
94B LYS* 3.0 30.7 + - - +
95B ALA 3.1 24.9 + - - -
96B TYR* 3.8 26.7 - - - +
97B PRO* 4.0 5.0 - - - +
109B ALA* 2.9 42.1 + - - +
110B LEU* 3.2 3.9 + - - +
112B GLU* 1.3 93.8 + - - +
114B TYR* 1.3 67.4 + - - +
116B GLU* 3.3 16.2 + - - +
117B VAL* 3.0 28.1 + - - +
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Residues in contact with TYR 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.5 32.8 - - + -
36B THR* 2.7 30.4 + - + +
55B LEU* 5.5 0.2 - - + -
58B PHE* 3.3 32.5 - + + +
62B LEU* 3.5 8.9 - - + +
110B LEU* 2.7 42.7 + - + +
111B ILE 4.2 1.3 - - - +
113B ARG* 1.3 73.6 - - - +
115B GLY* 1.4 58.7 + - - +
117B VAL* 4.1 0.3 - - - +
118B ALA* 2.8 32.2 + - - +
147B LEU* 4.3 14.5 - - + +
150B SER* 3.9 29.8 - - - -
151B LEU* 4.2 13.6 - - + +
154B LEU* 3.6 21.3 - - + -
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Residues in contact with GLY 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ILE 2.8 19.0 + - - -
112B GLU 3.9 0.9 - - - -
114B TYR* 1.4 77.8 - - - +
116B GLU* 1.3 62.2 + - - +
118B ALA* 3.4 0.6 + - - +
119B ASN* 2.9 36.4 + - - -
151B LEU* 3.7 22.3 - - - +
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Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LYS* 4.5 6.3 - - + +
93B LEU* 3.5 29.7 - - + +
94B LYS* 4.8 5.5 + - - +
112B GLU* 3.1 37.7 + - - +
113B ARG* 3.6 10.3 - - - +
114B TYR 3.3 0.2 - - - -
115B GLY* 1.3 77.5 - - - +
117B VAL* 1.3 57.4 + - - +
119B ASN* 3.3 5.1 + - - +
120B MET* 2.9 34.4 + - + +
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B SER* 3.9 26.9 - - - +
29B VAL* 4.1 22.4 - - + +
32B LEU* 3.9 21.1 - - + -
62B LEU* 5.4 0.4 - - + -
93B LEU* 4.0 15.5 - - + -
113B ARG 3.0 17.9 + - - +
114B TYR 4.1 1.1 - - - +
116B GLU* 1.3 71.6 - - - +
118B ALA* 1.3 66.6 + - - +
120B MET* 3.2 9.2 + - + +
121B ILE* 2.9 26.2 + - + +
147B LEU* 3.8 24.9 - - + -
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TYR 2.8 22.7 + - - +
115B GLY* 3.8 5.8 - - - +
117B VAL* 1.3 71.7 - - - +
119B ASN* 1.4 60.0 + - - +
121B ILE* 3.4 2.8 + - - +
122B ARG* 2.9 35.7 + - - +
144B SER* 5.1 1.9 + - - -
147B LEU* 4.0 29.5 - - + +
148B ASP* 3.6 22.1 - - - +
151B LEU* 4.5 7.6 - - + -
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Residues in contact with ASN 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLY* 2.9 26.7 + - - +
116B GLU* 3.9 4.4 - - - +
118B ALA* 1.4 74.6 - - - +
120B MET* 1.3 65.0 + - - +
122B ARG* 2.9 34.9 + - - +
123B LYS* 3.1 23.0 + - - +
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Residues in contact with MET 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 4.5 14.4 - - - +
25B SER* 4.0 30.5 - - - +
28B SER* 3.6 36.3 - - - +
92B LYS* 4.0 25.8 - - + +
93B LEU* 5.5 0.9 - - + -
116B GLU* 2.9 22.8 + - + +
117B VAL* 3.6 11.9 - - + +
119B ASN* 1.3 77.9 - - - +
121B ILE* 1.4 60.3 + - + +
123B LYS* 3.3 10.1 + - + +
124B ALA* 2.9 25.7 + - + +
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER* 3.6 30.5 - - - +
29B VAL* 4.5 12.8 - - + -
69B ILE* 4.5 4.5 - - + -
117B VAL* 2.9 25.3 + - + +
118B ALA 3.8 3.1 - - - +
120B MET* 1.4 75.8 - - + +
122B ARG* 1.3 65.6 + - - +
124B ALA* 3.1 12.2 + - - +
125B ILE* 3.1 13.5 + - - +
140B PHE* 3.2 42.6 - - + +
143B ALA* 4.1 6.5 - - + -
144B SER* 3.6 19.3 - - - +
147B LEU* 3.5 17.5 - - + -
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Residues in contact with ARG 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ALA* 2.9 18.9 + - - +
119B ASN* 2.9 37.5 + - - +
121B ILE* 1.3 76.2 - - - +
123B LYS* 1.3 63.2 + - - +
125B ILE* 3.3 28.7 + - + +
126B ASP* 3.6 11.7 + - - +
144B SER* 4.2 9.1 + - - +
148B ASP* 2.9 42.4 + - - -
151B LEU* 5.4 3.8 - - - +
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Residues in contact with LYS 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 5.8 4.0 - - - -
119B ASN 3.1 13.3 + - - +
120B MET* 3.6 10.5 - - - +
122B ARG* 1.3 77.6 - - - +
124B ALA* 1.3 56.0 + - - +
126B ASP* 3.1 9.9 + - + +
127B ASP* 2.7 58.2 + - - +
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 3.7 24.2 - - + +
25B SER* 4.1 4.7 - - - +
120B MET 2.9 13.9 + - - +
121B ILE* 3.1 10.7 + - - +
123B LYS* 1.3 73.2 - - - +
125B ILE* 1.3 65.2 + - - +
127B ASP* 4.2 4.0 - - - +
128B SER* 2.8 31.8 + - - -
140B PHE* 3.7 27.1 - - + -
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Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE 3.1 11.2 + - - +
122B ARG* 3.5 16.8 - - + +
123B LYS 3.2 0.2 - - - -
124B ALA* 1.3 77.3 - - - +
126B ASP* 1.3 68.6 - - - +
128B SER* 3.4 3.4 + - - -
129B ASP* 3.0 29.0 + - + +
137B ALA* 3.7 11.3 - - + +
140B PHE* 3.7 21.8 - - + -
141B THR* 3.5 30.1 - - + +
144B SER* 3.8 29.2 - - - +
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Residues in contact with ASP 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG* 3.6 12.2 + - - +
123B LYS* 3.1 10.3 + - + +
125B ILE* 1.3 87.6 - - - +
127B ASP* 1.3 63.8 + - - +
129B ASP* 3.3 6.8 + - - +
130B GLU* 2.9 31.4 + - - +
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Residues in contact with ASP 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 5.1 1.4 - - + +
21B ILE* 3.7 24.2 - - + +
123B LYS* 2.7 59.5 + - - +
124B ALA* 4.2 3.8 + - - +
126B ASP* 1.3 80.4 - - - +
128B SER* 1.3 62.3 + - - +
130B GLU* 3.5 16.8 + - - +
131B ALA* 3.1 22.2 + - - +
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Residues in contact with SER 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 4.4 10.7 - - - +
21B ILE* 4.2 7.5 - - - +
124B ALA 2.8 23.5 + - - -
125B ILE 3.6 3.6 - - - -
127B ASP* 1.3 73.3 - - - +
129B ASP* 1.3 65.4 + - - +
131B ALA* 3.3 9.0 + - - +
132B GLY 3.3 0.2 + - - -
133B ASP* 3.1 26.7 + - - +
136B THR* 3.5 9.6 - - - +
137B ALA* 3.8 23.1 - - - -
140B PHE* 3.3 21.3 - - - -
----------------------------------------------------------
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Residues in contact with ASP 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ILE* 3.0 19.6 + - + +
126B ASP* 3.8 6.7 - - - +
128B SER* 1.3 75.9 - - - +
130B GLU* 1.3 58.0 + - - +
132B GLY* 2.9 21.4 + - - +
133B ASP 4.6 2.9 - - - +
134B PRO* 4.4 20.3 - - - +
137B ALA* 4.0 10.6 - - + +
----------------------------------------------------------
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASP 2.9 17.7 + - - +
127B ASP* 3.8 19.1 - - - +
128B SER 3.2 0.2 - - - -
129B ASP* 1.3 77.9 + - - +
131B ALA* 1.3 58.4 + - - +
132B GLY* 3.4 1.0 + - - -
----------------------------------------------------------
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ALA* 3.3 27.6 - - + +
17B THR* 4.2 19.3 - - + -
18B VAL* 3.8 22.7 - - + -
127B ASP 3.1 14.3 + - - +
128B SER 3.6 9.2 - - - +
129B ASP 3.2 0.4 - - - -
130B GLU* 1.3 75.4 - - - +
132B GLY* 1.3 57.8 + - - +
----------------------------------------------------------
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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