Contacts of the helix formed by residues 587 - 595 (chain B) in PDB entry 1R9J
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 PRO 587 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585B ALA 3.9 2.2 - - - +
586B GLN* 1.3 99.9 - - + +
588B ASP* 1.3 68.5 + - - +
589B THR* 3.2 13.9 - - + +
590B TYR* 3.1 23.7 + - + +
591B ARG* 3.2 10.1 + - - +
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Residues in contact with ASP 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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587B PRO* 1.3 73.3 - - - +
589B THR* 1.3 59.9 + - + +
591B ARG* 3.2 31.9 + - - +
592B GLN* 2.8 33.2 + - + +
666B SER 5.0 3.3 - - - +
667B SER 5.6 1.2 - - - +
669B SER 6.1 1.0 - - - -
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Residues in contact with THR 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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587B PRO* 4.2 13.1 - - + +
588B ASP* 1.3 78.7 - - + +
590B TYR* 1.3 64.7 + - - +
592B GLN* 3.5 6.2 + - - +
593B ALA* 3.1 23.6 + - - +
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Residues in contact with TYR 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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534B HIS* 3.3 38.9 - + + +
536B ALA 2.6 28.7 + - - -
537B TYR* 3.5 14.6 - - - +
583B PHE* 3.9 11.0 - + - -
586B GLN* 3.6 23.3 - - + +
587B PRO* 3.1 23.5 + - + +
589B THR* 1.3 79.5 + - - +
591B ARG* 1.3 66.6 + - - +
593B ALA* 3.2 9.5 + - + +
594B VAL* 3.1 39.6 + - + +
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Residues in contact with ARG 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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583B PHE* 3.5 51.7 - - + +
584B ASP* 4.2 17.8 + - - +
586B GLN* 2.9 27.5 + - + +
587B PRO 3.2 6.8 + - - +
588B ASP* 3.5 41.3 + - - +
590B TYR* 1.3 77.1 - - - +
592B GLN* 1.3 58.5 + - - +
594B VAL* 3.2 1.7 + - - +
595B LEU* 2.9 33.7 + - - +
666B SER* 3.8 34.1 + - - -
667B SER* 5.7 0.2 - - - +
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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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588B ASP 2.8 18.7 + - - +
589B THR* 3.8 7.2 - - - +
591B ARG* 1.3 77.8 - - - +
593B ALA* 1.3 60.1 + - - +
595B LEU 4.0 3.7 + - - -
596B PRO* 3.2 26.9 - - - +
597B ALA* 2.5 46.9 + - - +
667B SER* 6.1 0.8 - - - -
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Residues in contact with ALA 593 (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 SER* 5.4 0.3 + - - -
573B ARG* 2.7 30.9 + - - -
589B THR 3.1 19.1 + - - +
590B TYR* 3.2 12.5 + - + +
592B GLN* 1.3 78.5 - - - +
594B VAL* 1.3 52.8 + - + +
596B PRO* 4.4 0.4 - - - +
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Residues in contact with VAL 594 (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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536B ALA 4.3 0.9 - - - +
537B TYR* 4.5 11.0 - - - +
538B SER* 4.9 4.0 - - - +
548B VAL* 4.5 1.0 - - - +
573B ARG* 2.8 27.2 + - - +
575B VAL* 3.7 34.3 - - + +
583B PHE* 3.9 13.9 - - + -
590B TYR* 3.1 49.6 + - + +
591B ARG 3.2 3.5 + - - +
593B ALA* 1.3 81.2 - - + +
595B LEU* 1.3 69.6 + - + +
596B PRO* 3.2 2.0 - - - +
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Residues in contact with LEU 595 (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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548B VAL* 3.8 24.0 - - + -
550B VAL* 4.9 4.7 - - + -
575B VAL* 4.4 10.5 - - + -
577B MET* 4.2 8.3 - - + -
583B PHE* 3.6 28.0 - - + -
591B ARG 2.9 14.3 + - - +
592B GLN* 3.6 7.4 + - - +
594B VAL* 1.3 89.8 - - + +
596B PRO* 1.3 66.0 - - - +
597B ALA* 3.4 2.8 + - - -
601B VAL* 4.4 22.0 - - + -
615B TYR* 3.9 29.6 - - + +
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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