Contacts of the strand formed by residues 500 - 505 (chain B) in PDB entry 5VOT
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 ILE 500 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499B GLY* 1.3 73.6 - - - -
501B SER* 1.3 66.9 + - - +
502B ILE* 5.5 1.6 - - + -
655B THR* 5.2 13.9 - - + +
658B PHE* 3.6 40.4 - - + -
659B PHE* 4.3 13.7 - - + -
703B LEU* 5.4 5.6 - - + -
704B LEU 4.0 11.7 - - - +
705B GLU* 5.2 1.1 - - - +
725B GLY 4.1 1.0 - - - +
726B ASN* 3.4 9.7 - - - +
727B LEU* 3.4 55.0 + - + +
728B ASP* 3.5 19.8 + - - +
730B LYS* 4.6 10.5 - - + +
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Residues in contact with SER 501 (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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500B ILE* 1.3 76.4 - - - +
502B ILE* 1.3 64.0 + - - +
703B LEU* 3.7 3.1 - - - -
704B LEU* 2.7 53.0 + - - +
705B GLU 3.0 16.3 + - - -
706B SER* 3.5 20.4 - - - -
709B ASN* 3.3 22.6 - - - +
722B LYS* 4.2 10.5 - - - +
725B GLY 5.5 1.1 - - - -
726B ASN* 4.8 1.1 - - - -
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Residues in contact with ILE 502 (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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500B ILE* 5.5 0.2 - - + -
501B SER* 1.3 76.6 - - - +
503B MET* 1.3 65.3 + - - +
504B ILE* 4.7 4.9 - - + -
633B ILE* 6.0 3.4 - - + -
635B SER* 5.0 5.2 - - - -
636B ALA* 4.4 24.7 - - + +
639B LEU* 4.6 15.7 - - + -
670B MET* 6.1 1.1 - - + -
701B ALA* 5.1 4.0 - - + -
702B TYR 3.7 4.9 - - - +
703B LEU* 3.6 26.0 - - + -
709B ASN* 3.8 2.2 - - - +
722B LYS* 3.5 5.1 - - - +
723B VAL* 2.9 61.1 + - + +
724B GLY* 5.8 1.6 - - - -
725B GLY 5.3 4.0 + - - +
727B LEU* 4.2 23.8 - - + -
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Residues in contact with MET 503 (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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501B SER 4.2 0.4 - - - -
502B ILE* 1.3 72.9 - - - +
504B ILE* 1.3 78.1 + - - +
690B VAL* 5.0 11.2 - - + -
693B VAL* 5.2 10.0 - - + +
701B ALA* 3.8 0.9 - - - +
702B TYR* 2.9 49.4 + - + +
704B LEU* 3.6 37.0 - - + -
709B ASN* 3.1 29.2 - - - +
712B ILE* 4.1 22.0 - - + -
720B THR* 4.1 24.9 - - + -
721B MET 3.1 10.8 - - - +
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Residues in contact with ILE 504 (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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502B ILE* 4.7 3.1 - - + -
503B MET* 1.3 81.5 - - - +
505B LYS* 1.3 71.7 + - - +
507B PRO* 5.5 0.7 - - + -
631B SER* 5.7 0.4 - - - -
632B PRO* 3.9 31.4 - - + -
633B ILE* 5.1 16.6 - - + +
645B ILE* 6.1 2.0 - - + -
693B VAL* 4.3 9.9 - - - -
700B TYR 5.4 0.7 - - - +
701B ALA* 4.0 21.3 - - + +
720B THR* 3.5 4.5 - - - -
721B MET* 2.9 43.6 + - + +
723B VAL* 3.6 39.3 - - + -
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Residues in contact with LYS 505 (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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504B ILE* 1.3 88.3 - - - +
506B LYS* 1.4 78.7 + - - +
507B PRO* 3.5 6.9 - - - +
632B PRO* 5.3 2.1 - - - +
693B VAL* 4.1 23.6 - - + +
694B ARG* 5.4 9.1 + - + +
697B LYS* 5.4 2.5 - - - -
698B GLY* 4.3 28.1 - - - +
700B TYR 5.5 0.8 + - - -
719B ASP* 3.3 44.5 + - + +
720B THR* 4.9 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