Contacts of the helix formed by residues 123 - 131 (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 TYR 123 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118G VAL 2.9 10.1 + - - +
119G ASN* 3.6 14.4 - - - +
122G LEU* 1.3 75.2 - - - +
124G LEU* 1.3 80.2 + - + +
125G GLY 3.3 0.7 - - - -
126G PRO* 3.3 8.0 - - - +
127G ILE* 3.3 36.8 - - + +
139G TRP* 3.1 39.5 + + - +
143G PHE* 3.6 20.9 - + - -
150G GLY* 3.5 17.5 - - - -
151G CYS 3.5 30.1 - - - +
194G ALA* 3.1 40.5 - - + +
195G ALA 4.2 1.8 - - - -
196G VAL* 3.7 14.0 - - + +
214G LEU* 5.2 0.4 - - + -
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Residues in contact with LEU 124 (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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80G LEU 3.4 25.8 - - - +
81G ALA* 3.8 8.3 - - + -
84G VAL* 3.7 30.5 - - + -
119G ASN* 2.9 28.8 + - - +
120G ASN* 3.8 5.4 - - - +
123G TYR* 1.3 96.0 - - + +
125G GLY* 1.3 65.2 + - - +
127G ILE* 3.2 5.5 + - - +
128G LEU* 3.0 28.0 + - + +
140G VAL* 3.9 36.1 - - + +
143G PHE* 4.0 8.3 - - + +
144G THR* 4.5 2.9 - - + -
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Residues in contact with GLY 125 (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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95G TYR* 5.6 0.9 - - - -
120G ASN 3.1 15.5 + - - -
121G SER 3.5 9.8 + - - -
123G TYR 3.3 0.2 - - - -
124G LEU* 1.3 76.7 - - - +
126G PRO* 1.4 62.9 - - - +
128G LEU* 3.3 8.4 + - - +
129G LYS* 2.9 28.6 + - - +
270G MET* 4.1 17.7 - - - +
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Residues in contact with PRO 126 (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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121G SER 3.5 7.9 - - - +
122G LEU 3.3 24.7 - - - +
123G TYR 3.3 10.5 - - - +
125G GLY* 1.4 86.9 - - - +
127G ILE* 1.3 57.0 + - - +
129G LYS* 4.3 1.8 - - + -
130G PHE* 2.7 47.4 + - + +
152G PHE* 5.1 0.9 - - + -
196G VAL* 4.4 14.4 - - + -
254G LEU* 4.1 14.4 - - + +
263G ILE* 4.2 10.8 - - + -
267G THR* 3.4 26.0 - - + +
270G MET* 4.3 1.5 - - + -
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Residues in contact with ILE 127 (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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123G TYR* 3.3 47.8 - - + +
124G LEU* 3.2 6.8 + - - +
126G PRO* 1.3 74.1 - - - +
128G LEU* 1.3 59.9 + - - +
131G GLY* 2.9 28.8 + - - -
135G GLN* 4.2 23.8 - - + +
136G LYS* 3.5 6.9 + - - +
139G TRP* 4.0 13.5 - - + +
140G VAL* 3.9 17.3 - - + -
196G VAL* 4.1 5.4 - - + -
214G LEU* 3.6 30.3 - - + -
254G LEU* 4.2 15.7 - - + -
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Residues in contact with LEU 128 (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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83G ASP 4.1 8.5 - - - +
84G VAL* 3.5 37.5 - - + -
85G PRO* 4.1 10.3 - - + -
88G LEU* 3.7 29.8 - - + -
124G LEU* 3.0 19.8 + - + +
125G GLY* 3.6 10.3 - - - +
127G ILE* 1.3 75.0 - - - +
129G LYS* 1.3 58.8 + - - +
136G LYS* 2.8 33.5 + - + +
140G VAL* 4.0 19.5 - - + -
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Residues in contact with LYS 129 (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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125G GLY 2.9 17.7 + - - +
126G PRO* 3.9 3.4 - - + +
128G LEU* 1.3 78.1 - - - +
130G PHE* 1.3 84.2 + - + +
136G LYS* 4.8 0.7 - - - -
266G GLN* 3.0 34.8 + - + -
270G MET* 4.4 20.6 - - + -
335G LYS* 6.2 0.9 - - - +
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Residues in contact with PHE 130 (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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126G PRO* 2.7 32.4 + - + +
129G LYS* 1.3 100.8 - - + +
131G GLY* 1.3 63.3 + - - +
135G GLN* 4.9 0.2 - - - +
254G LEU* 4.2 13.7 - - + -
255G GLY* 4.2 15.0 + - - +
259G MET* 3.8 24.2 - - + -
263G ILE* 3.8 50.0 - - + -
266G GLN* 3.5 35.9 - - + -
267G THR* 4.8 1.3 - - - -
270G MET* 5.9 0.4 - - + -
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Residues in contact with GLY 131 (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* 2.9 19.3 + - - -
130G PHE* 1.3 81.3 - - - +
132G SER* 1.3 64.4 + - - -
135G GLN* 3.5 16.2 - - - -
136G LYS* 2.6 24.4 + - - +
254G LEU* 3.7 9.1 - - - +
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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