Contacts of the helix formed by residues 94 - 109 (chain B) in PDB entry 2VIG
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 ASP 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B HIS* 2.9 26.2 + - - -
82B MET* 5.3 1.0 - - - +
83B ASP* 3.6 10.9 - - - +
93B LEU* 1.3 80.9 - - - +
95B TYR* 1.3 59.2 + - - +
96B LEU* 3.5 2.5 + - - +
97B ALA* 2.8 34.7 + - - +
98B TYR* 3.0 22.2 + - - +
336B ASP* 3.5 25.9 - - + +
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Residues in contact with TYR 95 (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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83B ASP* 3.7 30.5 + - + -
94B ASP* 1.3 70.2 - - - +
96B LEU* 1.3 58.1 + - - +
98B TYR* 3.2 34.9 + + + +
99B ALA* 2.9 31.2 + - - +
120B ASN* 4.5 3.9 + - + -
121B SER* 2.9 28.6 + - - -
125B GLY* 5.8 0.3 - - - -
270B MET* 3.5 33.1 - - + +
273B ILE* 3.9 25.1 - - + -
332B ALA* 3.8 15.5 - - + +
335B LYS* 3.5 34.5 - - + -
336B ASP* 2.7 20.5 + - - +
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Residues in contact with LEU 96 (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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34B LEU* 5.1 3.8 - - + -
35B PRO* 5.0 12.8 - - + -
38B HIS* 3.7 23.8 - - + +
94B ASP* 3.3 6.3 - - - +
95B TYR* 1.3 77.0 - - - +
97B ALA* 1.3 61.9 + - - +
99B ALA* 3.3 1.8 + - - +
100B ILE* 3.2 32.0 + - + +
329B TRP* 3.9 46.0 - - + +
332B ALA* 3.8 8.3 - - + +
333B MET* 4.3 25.8 - - + -
336B ASP* 3.0 17.3 + - - +
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Residues in contact with ALA 97 (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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38B HIS* 3.4 16.7 + - + +
41B LEU* 3.3 27.9 - - + +
82B MET* 4.5 2.0 - - + -
93B LEU* 3.9 21.1 - - + -
94B ASP* 2.8 27.1 + - - +
96B LEU* 1.3 71.8 - - - +
98B TYR* 1.3 58.9 + - - +
100B ILE* 3.2 4.7 + - - +
101B ALA* 2.8 30.7 + - - +
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Residues in contact with TYR 98 (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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82B MET* 3.9 27.0 - - + +
83B ASP 5.7 1.1 - - - +
94B ASP 3.0 12.6 + - - +
95B TYR* 3.5 44.2 - + + +
97B ALA* 1.3 77.2 - - - +
99B ALA* 1.3 54.0 + - - +
101B ALA* 3.4 0.5 + - - +
102B MET* 2.7 57.9 + - + +
116B MET* 4.3 2.5 - - + -
117B SER* 2.8 34.6 + - - -
120B ASN* 3.5 36.3 - - + -
121B SER* 2.9 26.5 + - - -
273B ILE* 5.3 1.1 - - + -
274B GLY* 3.9 13.9 - - - -
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Residues in contact with ALA 99 (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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95B TYR 2.9 18.4 + - - +
96B LEU 3.9 4.3 - - - +
97B ALA 3.3 0.2 - - - -
98B TYR* 1.3 75.9 - - - +
100B ILE* 1.3 61.3 + - - +
102B MET* 4.2 0.7 - - - -
103B GLU* 3.1 22.7 + - - +
273B ILE* 4.4 14.6 - - + -
277B SER* 3.2 30.5 + - - +
280B LEU* 5.7 0.9 - - + +
328B THR* 4.4 8.5 - - + -
329B TRP* 4.5 12.7 + - + -
332B ALA* 4.5 7.4 - - + -
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Residues in contact with ILE 100 (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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34B LEU* 4.1 14.8 - - + -
38B HIS* 3.7 37.7 - - + +
41B LEU* 5.0 3.8 - - + -
42B LEU* 3.7 47.8 - - + +
96B LEU* 3.2 22.2 + - + +
97B ALA* 3.5 5.8 - - - +
99B ALA* 1.3 73.6 - - - +
101B ALA* 1.3 65.8 + - - +
103B GLU* 3.2 9.0 + - - +
104B GLU* 3.2 22.7 + - + +
329B TRP* 4.2 24.9 - - + +
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Residues in contact with ALA 101 (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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41B LEU* 4.7 3.3 - - + +
45B CYS* 3.6 31.1 - - - +
79B LEU* 3.8 6.1 - - + -
82B MET* 3.7 28.0 - - + -
97B ALA 2.8 19.7 + - - +
98B TYR 3.8 0.2 - - - +
100B ILE* 1.3 73.6 - - - +
102B MET* 1.3 58.9 + - - +
104B GLU* 3.3 2.1 + - - +
105B ILE* 2.9 33.1 + - - +
116B MET* 4.1 3.8 - - + -
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Residues in contact with MET 102 (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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98B TYR* 2.7 47.6 + - + +
101B ALA* 1.3 72.1 - - - +
103B GLU* 1.3 58.0 + - - +
105B ILE* 4.1 0.2 - - - +
106B SER* 2.7 64.6 + - - +
113B GLY* 3.3 27.6 - - - +
116B MET* 4.0 18.4 - - + +
117B SER* 3.8 19.1 - - - -
274B GLY 3.7 10.8 - - - +
277B SER* 3.4 18.8 - - - -
278B GLN* 3.5 23.1 - - + -
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Residues in contact with GLU 103 (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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46B ARG* 5.8 0.3 + - - -
99B ALA 3.1 18.0 + - - +
100B ILE* 3.2 7.6 + - - +
102B MET* 1.3 76.8 - - - +
104B GLU* 1.3 69.7 + - - +
106B SER 3.4 0.2 + - - -
107B ARG* 2.9 33.1 + - + +
277B SER* 3.5 13.9 - - - +
280B LEU* 3.7 17.2 - - + +
281B GLY* 3.4 21.1 - - - +
284B GLN* 4.1 10.7 - - + +
325B ARG* 2.9 45.3 + - - +
329B TRP* 4.9 5.4 + - - -
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Residues in contact with GLU 104 (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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42B LEU* 4.0 29.9 - - + +
45B CYS* 3.6 26.7 - - + -
46B ARG* 3.3 56.5 + - - +
49B ALA* 3.5 13.1 - - - +
100B ILE* 3.2 14.2 + - + +
101B ALA 3.8 1.6 - - - +
103B GLU* 1.3 88.2 - - - +
105B ILE* 1.3 67.3 + - - +
107B ARG* 3.5 15.7 + - - +
108B GLY 3.3 13.5 + - - -
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Residues in contact with ILE 105 (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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45B CYS* 4.4 13.0 - - + +
48B PHE* 3.9 21.1 - - + -
53B LEU* 3.4 18.6 - - + +
74B MET* 4.0 7.4 - - + -
79B LEU* 4.1 17.0 - - + -
101B ALA 2.9 23.6 + - - +
102B MET 4.1 2.9 - - - +
104B GLU* 1.3 71.7 - - - +
106B SER* 1.3 59.0 + - - +
108B GLY* 2.9 7.1 + - - -
109B CYS 2.9 22.9 + - - +
112B THR* 3.3 31.4 - - + -
113B GLY* 3.7 15.9 - - - +
116B MET* 3.8 20.0 - - - -
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Residues in contact with SER 106 (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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102B MET* 2.7 43.3 + - - +
103B GLU 4.0 2.0 - - - -
105B ILE* 1.3 73.0 - - - +
107B ARG* 1.3 66.0 + - - +
108B GLY 3.4 0.2 + - - -
109B CYS 3.5 21.9 + - - -
110B ALA* 3.6 8.6 + - - +
113B GLY* 3.4 8.2 - - - -
278B GLN* 3.4 32.8 - - - +
281B GLY* 4.2 6.0 - - - -
282B ILE* 4.3 3.9 + - - +
285B THR* 5.1 1.2 - - - +
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Residues in contact with ARG 107 (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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46B ARG* 3.3 40.6 - - - +
49B ALA* 5.6 0.8 - - - +
50B GLU* 3.4 26.3 + - - +
54B PHE* 3.4 33.4 - - + -
103B GLU* 2.9 19.3 + - - +
104B GLU* 3.5 18.9 + - - +
106B SER* 1.3 77.9 - - - +
108B GLY* 1.3 59.7 + - - +
281B GLY* 3.4 18.0 - - - +
284B GLN* 3.9 15.2 - - - +
285B THR* 3.5 27.6 + - - +
288B ASP* 2.9 29.7 + - - +
380B ARG* 6.0 0.2 + - - -
381B HIS* 5.4 1.6 - - - -
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Residues in contact with GLY 108 (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 ALA* 4.2 2.0 - - - -
53B LEU* 3.8 18.9 - - - +
54B PHE* 3.6 26.8 + - - -
57B ALA* 3.6 17.8 - - - +
104B GLU 3.3 5.9 + - - -
105B ILE 2.9 9.4 + - - -
107B ARG* 1.3 82.0 - - - +
109B CYS* 1.3 60.4 + - - +
380B ARG* 4.8 2.3 + - - -
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Residues in contact with CYS 109 (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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53B LEU* 4.2 14.6 - - + +
56B ILE* 5.3 2.5 - - + -
57B ALA* 4.5 15.3 - - + -
60B VAL* 4.2 24.0 - - - -
67B PRO* 5.2 0.4 - - - -
105B ILE 2.9 13.9 + - - +
106B SER* 3.5 4.9 + - - -
108B GLY* 1.3 77.1 - - - +
110B ALA* 1.3 68.6 + - - +
111B SER* 3.3 12.3 + - - -
112B THR* 3.4 30.9 + - - +
113B GLY 3.2 16.1 + - - -
380B ARG* 5.2 3.1 - - - +
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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
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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