Contacts of the helix formed by residues 585 - 592 (chain B) in PDB entry 2R8P
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 SER 585 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490B THR 3.3 12.3 + - - -
491B TRP* 3.4 32.7 - - - -
539B GLY* 2.9 17.1 + - - +
583B MET* 3.2 1.8 - - - -
584B PRO* 1.3 79.4 - - - +
586B THR* 1.3 58.8 + - - +
587B ASP* 2.9 24.6 + - - -
588B ALA* 3.1 15.1 + - - +
589B PHE* 3.0 23.1 + - - +
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Residues in contact with THR 586 (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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483B ARG* 3.3 45.4 + - - +
490B THR 4.4 1.1 + - - -
583B MET* 3.8 22.0 - - + +
584B PRO 4.3 0.2 - - - -
585B SER* 1.3 73.3 - - - +
587B ASP* 1.3 63.0 + - - +
589B PHE* 3.3 0.5 + - - +
590B ASP* 2.8 37.2 + - - +
618B TYR* 3.4 22.1 + - + +
619B TRP* 4.4 2.9 - - + -
622B TYR* 3.4 27.6 - - + -
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Residues in contact with ASP 587 (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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483B ARG* 5.5 8.8 - - - +
488B MET 3.7 11.8 - - - +
489B SER* 2.8 35.1 + - - -
490B THR* 2.9 27.9 + - - +
505B TYR* 4.5 3.1 + - - -
585B SER* 2.9 11.9 + - - -
586B THR* 1.3 82.2 + - - +
588B ALA* 1.3 72.0 + - - +
590B ASP* 3.4 7.2 + - - +
591B LYS* 3.2 41.0 + - - +
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Residues in contact with ALA 588 (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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491B TRP* 3.9 16.4 - - + -
505B TYR* 4.2 15.7 - - + +
537B ALA 4.1 7.0 - - - +
538B ARG 3.7 2.2 - - - -
539B GLY* 3.8 17.9 - - - +
585B SER* 3.1 18.8 + - - +
587B ASP* 1.3 76.1 + - - +
589B PHE* 1.3 66.3 + - - +
591B LYS* 3.1 14.3 + - - +
592B GLN* 2.9 24.6 + - - +
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Residues in contact with PHE 589 (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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538B ARG 3.3 9.8 + - - -
540B GLY* 3.6 26.9 - - - +
583B MET* 3.6 29.6 - - + -
585B SER 3.0 18.7 + - - +
586B THR 3.6 2.7 - - - +
587B ASP 3.3 0.2 - - - -
588B ALA* 1.3 76.5 - - - +
590B ASP* 1.3 73.2 + - - +
592B GLN* 3.0 21.1 + - - +
596B TYR* 4.1 5.2 - + - -
597B ARG* 3.5 49.6 - - + -
600B VAL* 3.8 28.7 - - + -
601B LEU* 4.0 21.3 - - + -
622B TYR* 4.0 8.1 - + - -
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Residues in contact with ASP 590 (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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672A EDO 4.4 5.5 + - - -
586B THR* 2.8 25.8 + - - +
587B ASP* 3.8 7.6 - - - +
588B ALA 3.3 0.2 - - - -
589B PHE* 1.3 76.7 - - - +
591B LYS* 1.3 62.0 + - + +
592B GLN 3.3 1.8 + - - +
597B ARG* 3.6 21.7 + - - +
621B LYS* 2.5 32.7 + - - -
622B TYR* 2.7 30.5 + - - -
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Residues in contact with LYS 591 (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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487B ASN* 4.9 5.0 + - - +
488B MET 5.2 2.6 + - - -
505B TYR* 4.8 4.8 + - - +
509B ARG* 3.5 28.7 - - - +
587B ASP* 3.2 32.3 + - - +
588B ALA* 3.1 12.7 + - - +
589B PHE 3.1 1.2 - - - -
590B ASP* 1.3 76.2 - - + +
592B GLN* 1.3 67.5 + - - +
593B ASP* 3.9 0.3 + - - -
672B EDO 5.0 2.4 + - - -
675B EDO 3.7 23.3 + - - +
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Residues in contact with GLN 592 (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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537B ALA 4.7 2.4 + - - -
538B ARG* 2.7 54.2 + - - +
588B ALA* 2.9 20.4 + - - +
589B PHE* 3.0 16.9 + - - +
590B ASP 3.7 1.0 - - - +
591B LYS* 1.3 85.2 - - - +
593B ASP* 1.3 62.7 + - - +
596B TYR* 3.6 26.7 - - + -
597B ARG* 2.8 26.3 + - + -
672B EDO 2.7 33.0 + - - -
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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