Contacts of the helix formed by residues 584 - 592 (chain B) in PDB entry 1JQO
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 VAL 584 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487B GLN* 5.2 4.3 - - - +
491B LEU* 3.3 48.5 - - + -
495B ARG* 4.4 2.9 - - - +
540B PRO* 6.3 0.4 - - + -
544B LEU* 5.1 10.1 - - + -
580B ARG* 3.8 24.0 - - + +
581B LEU* 3.5 13.8 + - + +
583B SER* 1.3 73.7 - - - +
585B ASP* 1.3 71.0 + - - +
586B TRP* 3.9 11.9 - - + +
587B TYR* 3.0 18.2 + - + +
588B MET* 3.0 13.1 + - - +
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Residues in contact with ASP 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B ARG* 5.2 6.2 + - - +
583B SER 3.1 11.2 + - - +
584B VAL* 1.3 73.8 - - - +
586B TRP* 1.3 63.9 + - - +
588B MET* 3.3 7.5 + - - +
589B ASP* 3.1 32.6 + - - +
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Residues in contact with TRP 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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491B LEU* 4.2 10.1 - - + -
494B LEU* 3.8 46.3 + - + +
495B ARG* 4.2 32.0 - - + +
544B LEU* 4.2 6.5 - - + -
547B GLU* 3.5 29.4 - - + -
551B ARG* 3.7 27.8 - - - -
584B VAL* 3.9 11.6 - - + +
585B ASP* 1.3 80.7 - - - +
587B TYR* 1.3 108.0 + + + +
589B ASP* 3.2 7.3 + - - +
590B ARG* 3.2 26.3 + - + +
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Residues in contact with TYR 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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543B VAL* 3.5 32.9 - - + +
544B LEU* 4.2 9.2 - - + -
547B GLU* 4.2 15.6 + - + -
561B VAL 3.8 14.0 + - - -
563B PRO* 5.8 0.3 - - - +
581B LEU* 3.4 43.7 - - + +
582B PHE* 4.9 2.7 - + - -
584B VAL* 3.0 15.9 + - + +
586B TRP* 1.3 98.9 - + + +
588B MET* 1.3 58.0 + - - +
590B ARG* 2.8 9.7 + - + +
591B ILE* 2.7 72.7 + - + +
595B GLN* 3.5 19.0 + - - -
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Residues in contact with MET 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B PHE* 3.1 57.4 - - + +
584B VAL 3.0 8.7 + - - +
585B ASP* 3.6 11.7 - - - +
587B TYR* 1.3 78.9 - - - +
589B ASP* 1.3 63.6 + - - +
591B ILE* 3.5 39.1 + - + +
592B LYS* 3.6 6.1 + - - -
593B GLY* 4.6 4.8 + - - +
631B TYR* 5.0 6.7 - - - +
633B VAL* 3.9 16.8 - - + -
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Residues in contact with ASP 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B ASP* 3.1 20.4 + - - +
586B TRP* 3.4 11.7 - - - +
587B TYR 3.0 0.8 - - - -
588B MET* 1.3 82.5 - - - +
590B ARG* 1.3 60.1 + - - +
591B ILE 3.6 0.3 + - - -
592B LYS* 3.8 13.2 + - - +
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Residues in contact with ARG 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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547B GLU* 2.7 36.5 + - - -
551B ARG* 3.4 20.2 - - - +
558B PRO* 3.3 39.8 + - - +
559B LEU 3.3 17.6 + - - -
560B PRO* 3.3 17.7 - - - +
561B VAL 3.4 3.2 - - - +
586B TRP* 3.2 25.0 + - + +
587B TYR* 2.8 21.5 + - + +
589B ASP* 1.3 75.0 - - - +
591B ILE* 1.3 72.9 + - - +
592B LYS* 3.5 5.1 + - - +
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Residues in contact with ILE 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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582B PHE* 5.1 0.7 - - + -
587B TYR* 2.7 53.0 + - + +
588B MET* 3.6 26.9 - - + +
589B ASP 3.3 0.2 - - - -
590B ARG* 1.3 83.6 - - + +
592B LYS* 1.3 66.9 + - - +
593B GLY 3.3 15.3 - - - +
594B LYS* 2.8 41.4 + - - +
595B GLN* 3.2 25.6 - - + +
633B VAL* 4.7 3.1 - - + -
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Residues in contact with LYS 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 MET 3.6 7.1 + - - -
589B ASP 3.8 10.2 + - - +
590B ARG 3.3 6.5 - - - +
591B ILE* 1.3 82.1 - - - +
593B GLY* 1.3 57.5 + - - +
594B LYS* 3.2 10.9 + - + +
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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
------------------------------------------------------------
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