Contacts of the helix formed by residues 115 - 136 (chain B) in PDB entry 3C7N
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 TYR 115 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ASP* 4.0 11.6 + - + +
100B ARG* 3.6 46.5 + - + -
101B PRO 3.8 11.4 - - - -
102B LYS* 3.3 41.1 - - + +
103B VAL* 5.8 0.2 - - - -
114B PHE* 1.3 76.8 - - - +
116B PRO* 1.3 70.1 - - - +
117B GLU* 3.2 30.1 - - - +
118B GLU* 3.0 35.8 + - + +
119B VAL* 3.1 14.0 + - - +
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Residues in contact with PRO 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA* 4.2 6.8 - - + +
73B LEU* 3.1 45.3 - - + +
74B ILE* 3.6 22.9 - - + +
75B GLY 4.9 0.7 - - - +
101B PRO* 3.6 25.4 - - + +
102B LYS* 4.4 1.3 - - - -
103B VAL* 5.0 3.6 - - + +
114B PHE 4.3 1.6 - - - +
115B TYR* 1.3 83.0 - - + +
117B GLU* 1.3 72.1 + - - +
118B GLU 2.8 5.1 + - - -
119B VAL* 2.9 10.4 + - + +
120B SER* 2.8 24.5 + - - -
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 3.9 15.8 - - + +
75B GLY* 4.7 4.2 + - - -
101B PRO* 6.2 0.2 - - - +
115B TYR* 3.2 30.9 - - - +
116B PRO* 1.3 83.9 - - - +
118B GLU* 1.3 58.1 + - + +
120B SER* 4.5 0.2 - - - -
121B SER* 2.9 30.5 + - - -
157B ALA* 3.3 45.1 - - + +
160B ASP* 4.4 6.3 - - + +
161B ALA* 3.5 4.2 - - - +
164B ILE* 4.1 16.3 - - + +
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Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LYS* 4.6 1.0 + - - -
113B SER 4.6 1.4 - - - +
114B PHE* 3.5 28.4 - - + -
115B TYR* 3.0 47.0 + - + +
116B PRO 2.8 2.0 + - - -
117B GLU* 1.3 77.9 - - + +
119B VAL* 1.3 64.9 + - - +
121B SER* 3.2 6.8 + - - -
122B MET* 3.0 35.2 + - + +
164B ILE* 5.0 17.8 - - + +
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B SER 5.5 3.8 - - - +
42B VAL* 3.9 18.2 - - + +
44B PHE* 4.9 10.3 - - + -
67B VAL* 4.0 31.9 - - + +
68B PHE* 5.8 0.4 - - - -
70B ALA* 3.7 22.4 - - + -
103B VAL* 5.2 6.5 - - + -
114B PHE* 4.5 15.0 - - + +
115B TYR 3.1 12.6 + - - +
116B PRO* 2.9 11.8 + - + +
118B GLU* 1.3 70.5 - - - +
120B SER* 1.3 63.6 + - - +
122B MET* 3.1 27.2 + - - +
123B VAL* 3.2 11.0 + - + +
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Residues in contact with SER 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.8 21.8 - - - +
70B ALA* 4.3 12.5 - - - +
71B LYS* 4.5 9.7 + - - +
74B ILE* 4.0 23.5 - - - +
116B PRO 2.8 18.2 + - - -
119B VAL* 1.3 75.3 - - - +
121B SER* 1.3 59.8 + - - +
123B VAL* 3.2 9.6 + - - +
124B LEU* 3.1 29.1 + - - +
161B ALA* 4.0 7.9 - - - -
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Residues in contact with SER 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLU 2.9 22.3 + - - -
118B GLU* 3.2 7.2 + - - -
119B VAL 3.1 0.4 - - - -
120B SER* 1.3 77.5 - - - +
122B MET* 1.3 61.2 + - - +
123B VAL 3.1 0.2 - - - -
124B LEU* 3.4 1.6 + - - +
125B THR* 3.0 22.3 + - - -
161B ALA* 3.1 32.7 - - - +
164B ILE* 3.5 24.4 + - - +
165B ALA* 3.1 16.5 + - - +
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Residues in contact with MET 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 3.6 35.9 - - + -
44B PHE* 4.3 13.5 - - + -
49B ARG* 3.7 29.2 - - - +
51B ILE* 2.9 31.5 - - + +
114B PHE* 4.6 18.2 - - + -
118B GLU* 3.0 30.8 + - + +
119B VAL* 3.1 16.5 + - - +
121B SER* 1.3 78.4 + - - +
123B VAL* 1.3 62.3 + - - +
125B THR* 3.8 12.0 - - + -
126B LYS 3.8 4.5 + - - -
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.7 23.3 - - + -
16B SER* 4.2 9.2 - - - +
39B PRO 5.0 1.3 - - - +
40B SER* 4.1 30.7 - - - +
41B TYR 4.4 0.7 - - - +
42B VAL* 4.1 17.7 - - + -
51B ILE* 3.9 11.2 - - + -
119B VAL* 3.2 13.0 + - + +
120B SER* 3.4 12.1 - - - +
121B SER 3.1 0.8 - - - -
122B MET* 1.3 75.3 - - - +
124B LEU* 1.3 67.9 + - + +
125B THR 3.1 1.6 - - - -
126B LYS* 2.9 16.5 + - - +
127B MET* 3.0 24.8 + - + +
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 4.5 14.1 - - + -
11B LEU* 3.3 35.2 - - + -
120B SER 3.1 15.0 + - - +
121B SER 3.4 7.6 + - - +
123B VAL* 1.3 73.0 - - + +
125B THR* 1.3 56.3 + - - +
127B MET* 3.5 7.7 - - + +
128B LYS* 2.6 37.4 + - - +
144B VAL* 4.1 19.7 - - + -
158B THR 5.1 1.1 - - - +
161B ALA* 4.4 6.3 - - + -
162B GLY* 3.9 23.3 - - - +
165B ALA* 4.1 4.5 - - + -
167B LEU* 3.8 30.7 - - + +
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Residues in contact with THR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ARG* 6.4 0.2 - - - +
51B ILE* 5.1 7.0 - - + -
121B SER* 3.0 18.5 + - - -
122B MET* 3.9 14.4 - - + +
123B VAL 3.1 0.6 - - - -
124B LEU* 1.3 78.0 - - - +
126B LYS* 1.3 51.4 + - - +
128B LYS* 3.1 11.0 + - - +
129B GLU* 2.8 56.4 + - + +
165B ALA* 3.4 23.0 + - - +
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Residues in contact with LYS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASN* 5.3 3.2 - - - +
32B ASP* 4.1 23.3 + - - -
38B THR* 4.9 7.6 - - + +
51B ILE* 3.6 51.2 + - + +
52B GLY* 5.1 0.6 - - - -
53B ASP* 5.3 3.0 + - - +
54B ALA* 5.9 1.6 - - - +
122B MET 3.8 1.4 + - - +
123B VAL 2.9 10.9 + - - +
125B THR* 1.3 79.1 - - - +
127B MET* 1.3 56.8 + - + +
129B GLU* 3.2 25.8 + - - +
130B ILE* 2.7 56.6 + - + +
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Residues in contact with MET 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 4.1 26.2 - - + -
16B SER* 3.8 38.4 - - - +
17B CYS 4.7 0.2 - - - -
18B VAL* 4.3 21.0 - - + +
36B ARG 6.0 0.2 - - - +
38B THR* 3.0 45.3 - - + +
39B PRO 5.2 0.9 - - - +
51B ILE* 6.3 0.4 - - + -
123B VAL* 3.0 22.6 + - + +
124B LEU* 3.5 12.6 - - + +
126B LYS* 1.3 74.4 - - + +
128B LYS* 1.3 69.9 + - - +
130B ILE* 3.4 12.1 + - + +
131B ALA* 3.0 20.3 + - - +
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 6.3 0.9 - - - -
9B ILE* 4.9 3.3 - - - +
124B LEU 2.6 16.5 + - - +
125B THR* 3.1 15.9 + - - +
127B MET* 1.3 68.5 - - - +
129B GLU* 1.3 72.9 + - - +
131B ALA* 2.8 20.0 + - - +
132B GLU* 2.8 42.2 + - - +
139B VAL* 3.3 24.0 - - + +
140B THR* 5.9 0.2 - - - -
165B ALA 3.7 23.3 + - - +
166B GLY* 4.5 9.4 - - - -
167B LEU* 3.8 21.8 - - + -
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ILE* 6.1 0.8 - - - +
125B THR* 2.8 40.5 + - + +
126B LYS* 3.2 32.0 - - + +
128B LYS* 1.3 76.9 + - + +
130B ILE* 1.3 56.4 + - + +
132B GLU* 3.0 17.7 + - - +
133B ALA* 2.9 29.3 + - - +
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Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B VAL* 4.1 13.9 - - + -
29B ILE* 3.5 20.0 - - + +
30B ALA 3.6 24.3 - - - +
31B ASN* 3.3 30.1 - - + +
32B ASP* 5.0 4.0 - - - +
38B THR* 3.4 16.8 - - + +
126B LYS* 2.7 40.5 + - + +
127B MET* 3.7 20.4 - - + +
128B LYS 3.0 0.6 + - - -
129B GLU* 1.3 71.8 - - + +
131B ALA* 1.3 63.5 + - - +
133B ALA* 3.5 12.9 + - - +
134B TYR* 3.6 5.0 + - - +
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 4.1 18.2 - - + -
18B VAL* 4.4 1.1 - - + +
29B ILE* 3.7 23.6 - - + -
127B MET 3.0 13.3 + - - +
128B LYS* 2.8 16.5 + - - +
130B ILE* 1.3 71.7 - - - +
132B GLU* 1.3 61.3 + - - +
133B ALA 3.2 0.3 + - - -
134B TYR* 3.3 3.3 + - - +
135B LEU* 3.1 28.1 + - + +
139B VAL* 3.8 20.0 - - + -
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LYS* 2.8 46.7 + - - +
129B GLU* 3.0 16.8 + - - +
131B ALA* 1.3 76.8 - - - +
133B ALA* 1.3 62.5 + - - +
135B LEU* 4.8 0.2 - - - -
136B GLY* 3.1 22.2 + - - +
137B LYS 3.5 7.8 - - - +
138B THR* 3.6 27.1 - - + +
139B VAL* 3.2 40.6 + - + +
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A THR* 3.5 29.4 + - - +
365A THR* 4.0 4.3 - - - +
32B ASP* 6.5 0.9 - - + -
129B GLU 2.9 11.6 + - - +
130B ILE* 3.7 12.6 - - - +
131B ALA 3.2 0.4 - - - -
132B GLU* 1.3 77.6 - - - +
134B TYR* 1.3 63.2 + - - +
135B LEU 3.4 0.2 + - - -
136B GLY* 3.7 5.7 + - - -
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Residues in contact with TYR 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A THR 3.4 9.2 - - - -
365A THR* 3.1 51.4 + - - +
366A LEU 3.9 17.0 - - - -
367A ASN* 3.9 12.1 - - + -
670A SO4 3.0 17.0 + - - -
20B VAL* 4.5 4.0 - - + -
22B GLN* 2.9 38.9 + - - -
27B GLU* 3.6 19.9 + - + -
29B ILE* 3.5 42.0 - - + -
30B ALA 5.6 0.9 - - - +
130B ILE 3.6 1.0 + - - +
131B ALA 3.3 4.6 + - - +
133B ALA* 1.3 80.0 - - - +
135B LEU* 1.3 70.5 + - + +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LYS* 5.6 3.8 + - - -
365A THR* 4.7 2.5 - - - +
5B PRO* 4.5 17.5 - - + -
6B ALA 6.0 0.2 - - - +
7B VAL* 5.3 3.6 - - + -
20B VAL* 4.1 31.2 - - + -
22B GLN* 3.9 21.1 - - - +
29B ILE* 4.7 3.8 - - + -
131B ALA* 3.1 22.8 + - + +
132B GLU* 4.5 1.3 - - - +
134B TYR* 1.3 90.6 - - + +
136B GLY* 1.3 59.8 + - - +
137B LYS* 3.3 27.7 + - + +
139B VAL* 4.3 17.9 - - + -
384B LYS* 4.8 6.3 - - - +
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Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A THR* 4.4 11.7 - - - -
132B GLU 3.1 13.4 + - - +
133B ALA 3.7 4.9 + - - -
134B TYR 3.4 2.6 - - - -
135B LEU* 1.3 74.6 - - - +
137B LYS* 1.3 62.0 + - - +
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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
------------------------------------------------------------
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