Contacts of the strand formed by residues 631 - 636 (chain B) in PDB entry 1VDV
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 PHE 631 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622B VAL* 5.2 2.2 - - + -
625B ALA* 3.6 32.3 - - + +
626B GLN* 3.5 40.8 - - + +
628B VAL* 3.2 17.9 + - + +
629B PRO 3.2 4.0 + - - -
630B GLY* 1.3 78.9 - - - +
632B VAL* 1.3 64.2 + - - +
633B CYS* 3.4 40.2 - - - -
634B PHE* 3.6 10.8 - - + -
670B VAL* 3.8 24.2 - - + -
671B VAL 4.2 2.2 - - - -
672B ALA* 4.3 4.7 - - - +
677B HIS 6.0 0.2 - - - -
681B ALA* 4.0 5.2 - - + -
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Residues in contact with VAL 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603B LEU* 4.4 28.5 - - + -
630B GLY 3.6 14.6 - - - +
631B PHE* 1.3 83.0 - - - +
633B CYS* 1.3 73.5 + - + +
671B VAL* 2.8 22.8 + - + +
672B ALA* 3.9 10.8 - - - -
673B ASP* 4.4 2.2 - - + +
818B LYS* 5.9 1.3 - - - +
819B THR* 4.4 7.0 - - + -
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Residues in contact with CYS 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631B PHE* 3.4 17.3 - - - -
632B VAL* 1.3 92.1 - - + +
634B PHE* 1.3 61.2 + - - +
635B LEU* 3.9 21.3 - - + -
669B ALA 3.9 0.3 - - - +
670B VAL* 3.4 2.9 - - - -
671B VAL* 2.9 50.3 + - - +
818B LYS* 4.3 15.3 - - - +
819B THR* 4.3 11.9 - - - -
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Residues in contact with PHE 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608B VAL* 3.6 29.6 - - + -
620B ILE* 3.9 34.3 - - + -
622B VAL* 3.7 30.5 - - + -
631B PHE* 3.6 12.3 - - + -
633B CYS* 1.3 75.8 - - - +
635B LEU* 1.3 76.0 + - - +
636B SER* 3.9 22.8 + - - -
639B ASP* 3.9 6.1 - - - +
667B ILE* 4.9 1.1 - - + -
668B GLY* 4.2 8.3 - - - -
669B ALA 3.3 12.6 - - - -
670B VAL* 4.0 13.7 - - + +
685B VAL* 4.4 6.3 - - + -
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Residues in contact with LEU 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605B LEU* 4.7 7.0 - - + -
633B CYS* 3.9 16.6 - - - -
634B PHE* 1.3 80.1 - - - +
636B SER* 1.3 62.2 + - - +
639B ASP* 3.3 17.5 - - + +
655B PHE* 4.1 14.8 - - + -
668B GLY* 3.1 5.9 - - - -
669B ALA* 2.7 39.0 + - + +
671B VAL* 4.0 10.1 - - + -
811B ALA 4.8 0.9 - - - +
814B LEU* 4.3 8.7 - - + -
815B ALA* 3.5 41.5 - - + +
818B LYS* 3.6 33.2 - - + -
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Residues in contact with SER 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620B ILE* 5.3 6.3 - - - -
634B PHE* 3.9 19.6 + - - -
635B LEU* 1.3 75.4 - - - +
637B ALA* 1.3 67.0 + - - +
638B ASP* 3.3 10.8 + - - +
639B ASP* 2.8 30.5 + - - +
640B ILE 4.0 1.0 + - - -
655B PHE* 3.3 17.5 - - - -
656B ALA 6.1 0.4 - - - -
667B ILE 4.2 10.1 - - - -
814B LEU* 4.4 0.2 - - - +
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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