Contacts of the strand formed by residues 609 - 613 (chain B) in PDB entry 6VSB
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 609 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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597B VAL* 3.7 0.3 - - - -
598B ILE* 2.7 41.5 + - + +
608B VAL* 1.3 81.2 - - - +
610B VAL* 1.3 56.5 + - - +
650B LEU* 4.3 6.7 - - + -
651B ILE 3.7 4.5 - - - +
652B GLY* 4.0 3.1 - - - -
653B ALA* 3.9 35.0 - - + +
692B ILE* 3.3 20.6 - - + +
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Residues in contact with VAL 610 (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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295B PRO* 4.8 19.1 - - + -
595B VAL* 3.6 24.0 - - + -
596B SER 3.2 13.7 - - - +
597B VAL* 4.0 13.7 - - + +
598B ILE* 4.2 0.4 - - - -
608B VAL 4.4 0.2 + - - -
609B ALA* 1.3 75.2 - - - +
611B LEU* 1.3 69.7 + - - +
612B TYR* 4.5 17.5 - - + +
638B THR 5.4 5.4 - - - +
650B LEU* 3.1 8.9 - - - +
651B ILE* 2.9 51.4 + - + +
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Residues in contact with LEU 611 (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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312B ILE* 4.6 4.3 - - + -
595B VAL* 3.3 6.8 - - - +
596B SER* 2.7 52.2 + - - +
598B ILE* 3.8 11.9 - - + +
610B VAL* 1.3 73.2 - - - +
612B TYR* 1.3 67.3 + - - +
613B GLN* 3.6 17.0 + - - +
645B THR* 4.8 3.1 - - + -
647B ALA* 4.9 9.6 - - + +
648B GLY 3.9 13.0 - - - +
649B CYS 3.3 32.1 - - - +
650B LEU* 3.5 13.9 - - + +
651B ILE* 4.9 0.4 - - - +
666B ILE* 3.7 31.9 - - + +
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Residues in contact with TYR 612 (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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318B PHE* 4.4 19.1 - + + -
594B GLY 4.2 1.6 - - - -
595B VAL* 3.5 30.1 - - + -
610B VAL* 4.5 14.2 - - + +
611B LEU* 1.3 71.4 - - - +
613B GLN* 1.3 66.9 + - - +
614B ASP 3.4 2.4 + - - -
615B VAL* 3.7 22.5 - - + +
617B CYS* 6.0 1.8 - - + -
620B VAL* 3.5 37.8 - - + +
648B GLY* 3.7 0.3 - - - -
649B CYS* 3.1 33.7 + - - +
651B ILE* 3.5 34.2 - - + +
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Residues in contact with GLN 613 (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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314B GLN* 5.0 10.7 + - - -
318B PHE* 4.1 6.1 - - - -
592B PHE 4.8 0.3 - - - +
593B GLY* 4.4 6.9 - - - -
594B GLY* 2.9 41.3 + - - +
595B VAL* 5.1 0.4 - - - -
596B SER* 4.5 14.6 + - - +
611B LEU* 3.6 18.7 + - + +
612B TYR* 1.3 72.3 - - - +
614B ASP* 1.3 77.5 + - + +
615B VAL* 3.1 6.6 + - - +
647B ALA* 4.0 10.7 - - + +
735C SER* 5.7 1.2 + - - -
859C THR* 4.8 12.7 + - - +
861C LEU* 3.2 35.0 - - + +
862C PRO* 5.4 5.5 - - + +
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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