Contacts of the strand formed by residues 401 - 404 (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 CYS 401 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88D THR* 3.9 1.3 - - - -
89D SER* 3.1 15.3 - - - +
91D ILE* 3.7 27.6 - - + -
114D ILE* 4.7 0.9 - - - -
366D PRO* 5.7 0.4 - - - -
367D VAL 3.1 3.7 + - - +
368D VAL* 3.5 12.0 - - + -
369D CYS 3.0 23.4 + - - -
399D ALA* 3.9 4.0 - - - +
400D ASP* 1.3 83.2 - - - +
402D ILE* 1.3 68.0 + - - +
507D HIS 3.8 20.9 - - - -
508D LEU* 3.9 25.1 - - - -
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Residues in contact with ILE 402 (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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88D THR* 4.0 13.9 - - + -
89D SER 3.0 9.4 + - - +
90D ILE* 3.5 7.1 - - + -
91D ILE* 3.0 25.5 + - - +
369D CYS* 3.5 4.9 - - + +
373D MET* 4.0 26.0 - - + -
391D VAL* 3.7 19.7 - - + -
394D ALA* 4.1 14.6 - - + -
395D VAL* 4.8 5.6 - - + -
399D ALA* 4.9 1.6 - - + -
401D CYS* 1.3 79.5 - - - +
403D MET* 1.3 61.2 + - - +
421D GLN* 3.3 43.3 + - + +
425D ALA* 4.4 11.9 - - + -
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Residues in contact with MET 403 (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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91D ILE* 3.4 28.0 - - + +
116D ARG* 3.7 40.2 - - - +
284D PHE* 4.3 1.3 - - - -
334D MET* 3.7 27.4 - - + -
368D VAL* 4.5 6.7 - - + -
369D CYS 3.0 16.1 + - - +
370D ALA* 3.7 25.4 - - + -
371D THR* 4.7 8.7 + - - +
373D MET* 4.0 13.4 + - - +
402D ILE* 1.3 74.3 - - - +
404D LEU* 1.3 75.6 + - - +
405D SER* 3.8 15.0 - - - +
407D GLU* 5.0 0.3 - - - +
421D GLN* 3.1 16.9 - - - +
581D PGA 4.8 3.6 - - - +
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Residues in contact with LEU 404 (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* 4.5 4.5 - - + -
91D ILE 3.0 10.3 + - - +
92D ALA* 5.1 0.2 - - + -
93D THR* 2.6 33.4 + - - -
371D THR* 6.0 0.4 - - - +
374D LEU* 4.1 10.3 - - + +
403D MET* 1.3 77.3 - - - +
405D SER* 1.3 57.5 + - - +
407D GLU* 3.7 30.5 - - + +
408D THR* 3.6 33.4 - - + +
417D ALA* 3.8 15.9 - - + +
418D VAL* 3.7 20.6 - - + -
421D GLN* 3.2 35.2 - - + +
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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