Contacts of the helix formed by residues 109 - 122 (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 CYS 109 (chain B).
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Specific contacts
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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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Residues in contact with ALA 110 (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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106B SER* 3.6 13.5 + - - +
109B CYS* 1.3 73.0 - - - +
111B SER* 1.3 56.8 + - - +
113B GLY* 3.3 1.7 + - - -
114B VAL* 3.1 14.2 + - - +
233B ILE* 4.1 6.7 - - + -
278B GLN* 3.0 24.0 + - - +
282B ILE* 4.0 22.4 - - + -
380B ARG* 5.3 3.6 - - - +
384B ASP* 3.5 40.0 + - + +
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Residues in contact with SER 111 (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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60B VAL* 4.2 4.5 - - - +
67B PRO* 5.3 1.1 - - - -
109B CYS* 3.3 11.4 - - - -
110B ALA* 1.3 74.1 - - - +
112B THR* 1.3 66.0 + - - +
114B VAL* 3.2 11.6 + - - +
115B ILE* 3.0 31.8 + - - +
233B ILE* 3.1 18.1 - - - -
234B ARG 3.5 0.7 + - - -
235B GLY* 3.0 27.6 + - - -
236B SER 3.6 18.2 - - - -
384B ASP* 5.9 0.2 - - - -
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Residues in contact with THR 112 (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* 3.8 17.1 - - + +
67B PRO* 3.4 22.5 - - - +
70B GLN* 5.1 0.5 - - - +
71B VAL* 4.8 6.0 - - + +
74B MET* 3.0 38.5 - - + +
105B ILE* 3.3 13.2 - - + -
109B CYS* 3.4 21.0 + - - -
111B SER* 1.3 79.0 - - - +
113B GLY* 1.3 61.5 + - - +
115B ILE* 3.8 10.1 - - - +
116B MET* 3.1 22.9 + - - +
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Residues in contact with GLY 113 (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* 3.3 20.2 - - - +
105B ILE* 3.7 9.3 - - - +
106B SER* 3.4 23.6 - - - -
109B CYS 3.2 8.4 + - - -
110B ALA 3.6 3.4 - - - -
111B SER 3.2 0.8 - - - -
112B THR* 1.3 80.1 - - - +
114B VAL* 1.3 56.2 + - - +
116B MET* 3.3 1.4 + - - +
117B SER* 2.9 23.7 + - - -
278B GLN* 4.7 1.1 - - - -
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Residues in contact with VAL 114 (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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110B ALA 3.1 11.8 + - - +
111B SER* 3.3 14.1 - - - +
113B GLY* 1.3 70.7 - - - +
115B ILE* 1.3 63.2 + - - +
117B SER* 4.2 4.7 - - - -
118B VAL* 2.8 45.8 + - + +
187B THR* 4.2 7.2 - - + +
233B ILE* 4.3 8.5 - - + -
236B SER* 3.7 26.9 - - - +
275B ILE* 4.5 9.0 - - + -
278B GLN* 3.7 8.8 - - - +
391B TYR* 3.4 39.0 - - + +
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Residues in contact with ILE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PHE* 3.5 25.1 - - + -
67B PRO* 3.6 27.6 - - + -
71B VAL* 4.3 17.9 - - + -
80B LEU* 5.4 1.6 - - + -
111B SER 3.0 23.7 + - - +
112B THR* 3.8 6.5 - - - +
114B VAL* 1.3 76.0 - - - +
116B MET* 1.3 60.9 + - - +
119B ASN* 3.2 21.7 + - - +
149B ILE* 3.8 22.4 - - + -
188B ASN* 3.4 33.8 + - - +
235B GLY 4.2 6.1 - - - +
236B SER* 4.0 10.1 - - - -
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Residues in contact with MET 116 (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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74B MET* 3.7 26.9 - - + -
79B LEU* 3.2 34.3 - - + +
80B LEU* 3.7 13.2 - - + -
82B MET* 3.9 20.6 - - - -
98B TYR* 4.3 9.9 - - + -
101B ALA* 4.1 13.9 - - + -
102B MET* 4.0 21.8 - - - +
105B ILE* 3.8 17.7 - - - -
112B THR 3.1 18.7 + - - +
113B GLY 3.6 2.0 - - - +
114B VAL 3.2 0.2 - - - -
115B ILE* 1.3 74.4 - - - +
117B SER* 1.3 61.6 + - - +
119B ASN* 3.3 1.9 + - - +
120B ASN* 2.9 37.0 + - - +
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Residues in contact with SER 117 (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* 2.8 22.5 + - - -
102B MET* 3.8 12.6 - - - -
113B GLY 2.9 16.8 + - - -
114B VAL* 3.7 7.9 - - - -
116B MET* 1.3 74.8 - - - +
118B VAL* 1.3 60.8 + - - +
121B SER* 2.9 36.9 + - - -
122B LEU* 4.5 1.5 - - - +
271B GLY 4.4 1.9 + - - -
274B GLY* 3.5 19.6 - - - -
275B ILE* 4.0 14.3 + - - +
392B GLU* 4.9 1.7 + - - -
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Residues in contact with VAL 118 (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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114B VAL* 2.8 31.9 + - + +
117B SER* 1.3 70.6 - - - +
119B ASN* 1.3 59.3 + - - +
122B LEU* 3.1 32.7 + - + +
123B TYR* 3.0 25.3 + - - +
150B GLY 3.8 11.7 - - - +
151B CYS* 3.9 14.4 - - - -
152B PHE* 4.5 2.7 - - + +
187B THR* 3.7 32.8 - - + +
188B ASN* 3.7 20.6 - - - +
392B GLU* 5.3 2.7 - - - +
501B FAD 4.9 2.2 - - - +
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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
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80B LEU* 2.8 35.9 + - + +
115B ILE 3.2 16.3 + - - +
116B MET 3.8 3.6 - - - +
117B SER 3.2 0.4 - - - -
118B VAL* 1.3 82.6 - - - +
120B ASN* 1.3 56.6 - - - +
123B TYR* 4.0 9.3 - - - -
124B LEU* 3.1 40.5 + - - +
143B PHE* 3.3 21.4 + - - +
149B ILE* 3.2 22.1 - - + +
150B GLY* 2.9 31.9 + - - +
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Residues in contact with ASN 120 (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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79B LEU 2.7 25.4 + - - -
80B LEU* 3.4 15.1 - - - +
81B ALA* 3.5 1.7 + - - -
82B MET* 3.0 34.7 + - - +
83B ASP* 4.4 2.3 + - - +
84B VAL* 5.6 0.5 - - - +
95B TYR* 4.5 5.1 + - + +
98B TYR* 3.5 26.8 - - + -
116B MET* 2.9 31.6 + - - +
119B ASN* 1.3 78.1 - - - +
121B SER* 1.3 58.9 + - - +
124B LEU* 3.8 6.2 - - - +
125B GLY* 3.2 22.5 + - - -
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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
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95B TYR* 2.9 23.2 + - - -
98B TYR* 2.9 24.0 + - - -
117B SER* 2.9 16.5 + - - -
120B ASN* 1.3 74.5 - - - +
122B LEU* 1.3 63.5 + - - +
123B TYR 3.6 0.2 - - - -
125B GLY* 3.6 5.7 - - - -
126B PRO* 3.5 9.0 - - - +
267B THR* 3.5 16.6 - - - +
270B MET* 3.6 10.6 + - - +
271B GLY* 3.6 25.5 - - - -
392B GLU* 5.8 0.2 - - - -
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Residues in contact with LEU 122 (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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117B SER 4.5 0.2 - - - +
118B VAL* 3.1 32.5 + - + +
121B SER* 1.3 80.0 - - - +
123B TYR* 1.3 60.4 + - - +
126B PRO* 3.2 19.6 - - - +
152B PHE* 3.3 50.0 - - + +
196B VAL* 4.1 1.9 - - - +
267B THR* 3.6 20.2 - - + +
268B LEU* 4.1 11.7 - - + -
271B GLY* 3.8 25.1 - - - -
392B GLU* 3.4 28.3 - - + +
501B FAD 5.0 6.1 - - + +
502B COS 5.2 3.4 - - - -
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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
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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