Contacts of the strand formed by residues 89 - 93 (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 SER 89 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86D ARG* 3.6 0.2 - - - +
87D SER 3.4 7.4 + - - -
88D THR* 1.3 72.8 - - - +
90D ILE* 1.3 60.9 + - - +
113D ASN* 3.2 21.2 + - - -
114D ILE* 5.1 2.9 - - - -
400D ASP 3.3 7.4 + - - -
401D CYS* 3.1 14.9 - - - +
402D ILE* 3.0 24.6 + - - +
507D HIS* 2.5 41.4 + - - +
509D CYS 5.0 2.4 + - - -
512D VAL 5.2 3.5 + - - -
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Residues in contact with ILE 90 (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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86D ARG* 3.2 36.1 - - - +
88D THR 4.0 3.1 - - - +
89D SER* 1.3 72.5 - - - +
91D ILE* 1.3 71.2 + - - +
92D ALA* 4.0 1.2 + - + +
111D GLY 4.1 11.0 - - - +
112D MET* 3.9 4.2 - - - -
113D ASN* 2.9 28.0 + - - +
114D ILE* 3.2 6.1 + - - +
402D ILE* 3.5 7.9 - - + -
404D LEU* 4.5 7.2 - - + -
418D VAL* 3.9 24.5 - - + +
421D GLN* 3.5 28.0 - - + +
422D HIS* 3.6 27.1 - - + +
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Residues in contact with ILE 91 (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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89D SER 5.1 0.2 - - - -
90D ILE* 1.3 76.6 - - - +
92D ALA* 1.3 61.2 + - - +
114D ILE* 3.4 32.5 - - + +
116D ARG* 3.8 25.1 - - + -
284D PHE* 3.7 29.8 - - + -
368D VAL* 3.8 20.0 - - + -
401D CYS* 3.7 28.9 - - + -
402D ILE 3.0 8.3 + - - +
403D MET* 3.4 16.9 - - + +
404D LEU* 3.0 28.2 + - - +
508D LEU* 5.2 0.2 - - + -
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Residues in contact with ALA 92 (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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90D ILE* 4.0 2.4 + - + -
91D ILE* 1.3 74.2 - - - +
93D THR* 1.3 63.4 + - - +
94D ILE* 3.6 2.5 + - + +
107D MET* 3.5 32.1 - - + -
112D MET* 3.9 16.8 - - + -
114D ILE 2.8 9.3 + - - -
115D ALA* 3.5 4.7 - - - -
116D ARG* 2.7 26.6 + - - -
404D LEU* 4.2 2.9 - - + -
408D THR* 3.8 11.4 - - + +
418D VAL* 4.6 6.5 - - + -
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Residues in contact with THR 93 (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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92D ALA* 1.3 72.3 - - - +
94D ILE* 1.3 70.7 + - - +
98D SER* 3.4 2.9 + - - -
116D ARG* 3.0 51.7 + - - +
118D ASN* 4.2 15.9 - - + +
404D LEU 2.6 24.2 + - - -
405D SER* 3.5 13.5 - - - -
408D THR* 2.7 27.0 + - - -
409D ALA* 3.4 18.9 + - + -
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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