Contacts of the strand formed by residues 152 - 156 (chain D) in PDB entry 2VGB
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 ALA 152 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D ASN 2.9 9.0 + - - +
114D ILE* 3.9 22.2 - - + -
115D ALA 3.0 21.5 + - - -
151D VAL* 1.3 80.6 - - - +
153D ILE* 1.3 62.4 + - - +
154D ALA 4.2 0.4 - - - -
281D ASP* 4.6 1.6 - - + -
282D ILE* 3.9 17.7 - - + -
504D ARG* 3.4 37.5 - - + +
507D HIS* 4.1 1.8 - - - -
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Residues in contact with ILE 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ALA* 3.4 7.9 - - + +
117D LEU* 4.1 31.6 - - + -
131D ILE* 4.2 27.1 - - + -
134D VAL* 4.0 30.3 - - + -
135D ARG* 4.2 19.3 - - + +
151D VAL 4.4 4.5 - - - +
152D ALA* 1.3 81.9 - - - +
154D ALA* 1.3 61.8 + - - +
280D VAL* 3.9 16.1 - - + +
281D ASP* 3.0 37.9 + - - +
282D ILE* 3.5 4.5 + - - -
504D ARG* 5.6 2.0 - - - -
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Residues in contact with ALA 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ILE* 3.9 10.1 - - + -
115D ALA 2.7 14.8 + - - +
116D ARG* 3.5 1.8 - - - +
117D LEU* 2.8 31.5 + - - +
152D ALA 4.2 0.2 - - - -
153D ILE* 1.3 72.9 - - - +
155D LEU* 1.3 62.3 + - - +
156D ASP 3.6 0.3 + - - -
282D ILE* 3.3 17.7 - - + +
284D PHE* 3.7 37.7 - - + -
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Residues in contact with LEU 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU* 3.9 6.7 - - - -
119D PHE* 3.7 33.4 - - + -
153D ILE 4.0 1.8 + - - -
154D ALA* 1.3 70.3 - - - +
156D ASP* 1.3 71.3 + - - +
157D THR* 3.9 14.1 - - - +
271D ASP* 3.4 29.8 - - + +
272D LEU* 4.4 16.8 - - + -
274D PHE* 4.7 0.4 - - + -
275D GLY* 3.8 20.6 - - - +
280D VAL* 4.2 17.7 - - + +
282D ILE 2.9 12.4 + - - +
283D VAL* 3.4 7.7 - - + -
284D PHE* 2.9 24.7 + - - +
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Residues in contact with ASP 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D ARG* 2.6 47.8 + - + +
117D LEU 2.6 19.3 + - - +
118D ASN* 4.1 2.0 - - - -
119D PHE* 2.8 31.4 + - - +
154D ALA 3.6 1.4 + - - -
155D LEU* 1.3 72.0 - - - +
157D THR* 1.3 64.3 + - - +
284D PHE* 3.6 13.1 - - + +
313D LYS* 2.6 31.2 + - - +
334D MET* 4.1 1.0 - - - +
594D K 2.6 23.9 - - - -
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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