Contacts of the helix formed by residues 132 - 140 (chain G) 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 SER 132 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130G PHE 4.1 0.2 + - - -
131G GLY* 1.3 74.6 - - - -
133G LYS* 1.3 66.0 + - - +
134G GLU* 4.1 8.7 + - - +
135G GLN* 3.1 34.7 + - - +
136G LYS* 3.0 24.6 + - - +
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Residues in contact with LYS 133 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88G LEU* 5.5 0.2 - - - +
132G SER* 1.3 71.8 - - - +
134G GLU* 1.3 57.5 + - - +
136G LYS* 3.3 13.2 + - - +
137G GLN* 2.9 36.2 + - + +
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Residues in contact with GLU 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G SER* 3.2 8.5 + - - +
133G LYS* 1.3 78.1 - - - +
135G GLN* 1.3 59.5 + - + +
137G GLN* 3.3 8.6 + - - +
138G ALA* 2.9 30.7 + - - +
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Residues in contact with GLN 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G ILE* 4.2 4.9 - - + +
130G PHE 4.9 0.3 - - - +
131G GLY* 3.5 12.0 - - - -
132G SER* 3.1 35.4 + - - +
134G GLU* 1.3 76.9 - - + +
136G LYS* 1.3 57.7 + - - +
138G ALA* 4.7 0.2 - - - -
139G TRP* 2.7 49.3 + - + +
214G LEU* 3.8 28.6 - - + +
251G ASP 3.0 20.3 + - - +
252G SER 4.1 0.2 - - - -
253G ILE 2.9 30.7 + - - +
254G LEU* 3.9 6.7 - - - +
255G GLY 5.0 1.0 + - - -
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Residues in contact with LYS 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G LEU* 4.2 26.7 - - + -
127G ILE* 3.5 13.7 + - - +
128G LEU* 2.8 41.4 + - + +
129G LYS 4.8 0.6 - - - -
130G PHE 4.7 0.4 - - - +
131G GLY 2.6 29.7 + - - +
132G SER 3.0 18.6 + - - +
133G LYS* 3.5 11.0 - - - +
135G GLN* 1.3 75.9 - - - +
137G GLN* 1.3 64.2 + - - +
140G VAL* 2.8 38.6 + - + +
141G THR* 3.2 3.5 + - - -
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Residues in contact with GLN 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G GLU 5.4 2.1 - - - +
88G LEU* 4.1 15.4 - - + +
133G LYS* 2.9 25.3 + - + +
134G GLU* 3.5 9.2 - - - +
136G LYS* 1.3 78.2 - - - +
138G ALA* 1.3 61.8 + - - +
141G THR* 3.7 13.2 + - - +
142G PRO* 3.4 16.1 - - - +
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Residues in contact with ALA 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134G GLU 2.9 20.1 + - - +
135G GLN* 4.7 0.2 - - - -
137G GLN* 1.3 74.5 - - - +
139G TRP* 1.3 79.2 + - + +
142G PRO* 3.2 20.7 - - - +
143G PHE* 4.5 3.1 - - - -
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Residues in contact with TRP 139 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123G TYR* 3.1 44.1 + + - +
124G LEU* 4.2 0.2 - - - +
127G ILE* 4.0 14.9 - - + +
135G GLN* 2.7 30.6 + - - +
138G ALA* 1.3 89.0 - - + +
140G VAL* 1.3 60.3 + - - +
143G PHE* 3.1 17.1 - + - -
194G ALA* 3.5 21.5 - - + -
214G LEU* 3.3 48.0 - - + +
215G VAL 3.8 13.7 - - - -
216G PRO* 3.5 33.9 - - + -
252G SER* 5.2 7.4 - - - +
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Residues in contact with VAL 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G VAL* 4.0 19.7 - - + -
88G LEU* 4.0 12.3 - - + -
124G LEU* 3.9 18.1 - - + +
127G ILE* 3.9 28.9 - - + -
128G LEU* 4.0 22.9 - - + +
135G GLN 3.7 0.2 + - - -
136G LYS* 2.8 21.2 + - + +
139G TRP* 1.3 78.3 - - - +
141G THR* 1.3 59.3 + - - +
142G PRO 3.3 0.2 - - - -
143G PHE* 2.7 32.1 + - - +
144G THR* 3.3 21.3 - - + +
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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