Contacts of the strand formed by residues 700 - 705 (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 TYR 700 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504B ILE* 5.4 1.4 - - - -
505B LYS 5.5 0.7 + - - -
645B ILE* 3.7 2.7 - - - -
646B ALA* 3.2 29.2 - - + -
647B TYR* 3.5 6.5 - - - -
648B GLY* 2.9 35.9 + - - -
681B VAL* 3.1 16.8 + - + -
683B VAL* 5.6 0.3 - - - +
692B ARG* 3.3 57.7 + - + +
693B VAL* 4.1 24.5 - - + +
696B SER* 3.5 22.7 - - - +
698B GLY* 3.2 6.6 - - - -
699B LYS* 1.3 80.5 - - - +
701B ALA* 1.3 77.0 + - - +
702B TYR* 4.2 19.1 - + - -
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Residues in contact with ALA 701 (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* 5.1 5.6 - - + -
503B MET 3.8 11.4 - - - +
504B ILE* 4.0 17.0 - - + +
633B ILE* 6.1 0.9 - - + -
639B LEU* 5.0 10.3 - - + -
645B ILE* 3.4 12.4 - - + +
646B ALA 2.6 14.7 + - - +
647B TYR* 3.3 22.2 - - + -
648B GLY 3.8 0.2 + - - -
700B TYR* 1.3 96.8 - - - +
702B TYR* 1.3 62.9 + - - +
703B LEU* 5.9 0.2 - - + -
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Residues in contact with TYR 702 (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* 3.7 1.4 - - - +
503B MET* 2.9 46.3 + - + +
648B GLY 4.4 3.4 - - - -
649B THR 5.1 4.3 - - - -
650B LEU* 4.1 16.7 - - - +
683B VAL* 4.3 11.7 - - + +
686B THR* 3.6 33.8 + - + +
689B GLY* 3.4 33.6 - - - -
690B VAL* 5.5 1.8 - - + -
693B VAL* 3.6 19.2 - - + +
700B TYR* 4.2 19.3 - + - -
701B ALA* 1.3 75.8 - - - +
703B LEU* 1.3 86.9 + - - +
704B LEU* 3.3 38.7 - - + +
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Residues in contact with LEU 703 (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* 5.4 7.9 - - + -
501B SER 3.7 2.5 - - - +
502B ILE* 3.6 34.5 - - + -
639B LEU* 5.1 7.6 - - + -
647B TYR* 3.7 33.7 - - + -
648B GLY 3.4 21.1 + - - +
649B THR* 3.7 28.2 - - + +
650B LEU* 4.8 1.2 + - - +
655B THR* 5.3 5.6 - - + +
659B PHE* 5.0 11.0 - - + -
670B MET* 4.7 9.2 - - + -
674B MET* 4.4 6.1 - - - -
701B ALA* 5.9 0.4 - - + -
702B TYR* 1.3 99.4 - - - +
704B LEU* 1.3 60.8 + - - +
727B LEU* 6.5 0.7 - - + -
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Residues in contact with LEU 704 (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* 3.9 6.6 - - - +
501B SER* 2.7 51.8 + - - +
503B MET* 3.6 43.3 - - + +
655B THR* 5.5 6.3 - - - -
686B THR* 4.8 9.2 - - + -
690B VAL* 6.4 0.7 - - + -
702B TYR* 3.3 23.8 - - + +
703B LEU* 1.3 74.5 - - - +
705B GLU* 1.3 64.0 + - - +
708B MET* 3.7 13.7 - - + -
709B ASN* 3.4 31.9 - - + +
712B ILE* 5.4 1.3 - - + -
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Residues in contact with GLU 705 (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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450B TYR* 3.1 42.9 + - - -
480B THR* 3.4 15.1 + - - +
498B LEU* 4.6 8.3 - - + -
499B GLY 4.5 3.1 - - - -
500B ILE* 5.2 1.1 - - - +
501B SER* 3.0 10.6 + - - -
654B SER* 4.7 3.6 + - - +
655B THR* 5.1 10.1 + - - +
704B LEU* 1.3 77.4 - - - +
706B SER* 1.3 66.6 + - - +
707B THR 3.4 1.2 + - - +
708B MET* 3.2 20.4 + - - +
709B ASN 3.1 14.4 + - - -
732B TYR* 2.3 37.6 + - - +
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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