Contacts of the strand formed by residues 634 - 640 (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 LYS 634 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593B GLY 2.8 14.7 + - - +
594B LYS* 3.4 48.2 - - + +
595B GLN 3.4 11.4 + - - +
632B GLY 4.2 0.8 + - - -
633B VAL* 1.3 67.6 - - - +
635B LEU* 1.3 64.2 + - - +
636B THR* 3.3 25.7 - - + +
665B ASN* 6.2 2.2 - - - +
666B GLY* 6.1 6.3 - - - -
667B SER* 4.1 11.8 + - - +
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Residues in contact with LEU 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B VAL* 4.7 7.9 - - + -
595B GLN* 3.2 16.6 - - + +
597B VAL* 3.6 28.3 - - + -
624B MET* 3.7 31.4 - - + +
625B ALA* 5.0 11.2 - - + +
628B ALA* 3.6 21.3 - - + -
633B VAL* 2.7 10.2 + - + -
634B LYS* 1.3 73.2 - - - +
636B THR* 1.3 62.5 + - - +
637B LEU* 3.3 34.5 - - + -
663B THR 4.5 11.3 - - - +
664B ILE 5.5 1.2 - - - +
665B ASN* 5.9 0.7 + - - -
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Residues in contact with THR 636 (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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594B LYS* 5.9 0.4 - - + -
595B GLN 3.0 10.0 + - - +
596B GLN* 3.3 36.2 + - + +
597B VAL 3.4 4.2 + - - -
634B LYS* 3.3 34.1 - - + +
635B LEU* 1.3 76.5 - - - +
637B LEU* 1.3 66.3 + - - +
663B THR 5.4 1.3 - - - -
664B ILE 5.9 0.2 - - - -
667B SER* 2.9 37.7 + - - +
669B ARG* 4.9 6.6 - - - +
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Residues in contact with LEU 637 (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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596B GLN* 5.1 0.2 - - - -
597B VAL* 3.5 25.4 - - + +
599B VAL* 4.7 5.4 - - + -
621B GLN* 3.5 39.9 - - + +
624B MET* 4.0 17.7 - - + -
625B ALA* 6.1 0.2 - - + -
635B LEU* 3.3 28.9 - - + -
636B THR* 1.3 75.3 + - - +
638B PHE* 1.3 62.2 + - - +
639B HIS* 3.5 22.5 - - + +
659B GLN* 5.7 0.2 - - - +
663B THR* 4.4 22.5 + - - +
667B SER 4.7 4.4 + - - -
668B ILE* 3.8 2.5 - - - +
669B ARG* 3.2 21.7 + - - -
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Residues in contact with PHE 638 (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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173B VAL* 3.5 24.2 - - + -
288B TRP* 3.8 12.3 - + - -
454B ASP* 3.2 22.9 - - - -
533B ILE* 3.8 13.2 - - + -
596B GLN* 2.8 28.9 - - - +
597B VAL 3.1 7.3 + - - -
598B MET* 3.2 33.7 - - + +
599B VAL* 2.9 29.8 + - - +
636B THR 4.1 0.4 + - - -
637B LEU* 1.3 72.1 - - - +
639B HIS* 1.3 65.3 + - - +
669B ARG* 3.3 31.0 - - + -
671B THR* 3.3 30.1 - - + -
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Residues in contact with HIS 639 (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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599B VAL* 4.3 6.5 - - + +
601B TYR* 3.0 22.0 + - + -
621B GLN* 3.5 17.9 - - - -
637B LEU* 3.5 24.0 - - + +
638B PHE* 1.3 72.5 - - - +
640B GLY* 1.3 58.3 + - - +
641B ARG* 2.9 31.8 + - + +
659B GLN* 3.2 35.5 + - - -
664B ILE* 5.4 1.2 - - - +
668B ILE* 3.5 32.7 - - + +
669B ARG 2.8 13.8 + - - +
670B VAL* 3.6 5.1 - - + +
671B THR* 3.2 23.4 + - - +
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Residues in contact with GLY 640 (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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598B MET* 3.8 24.7 - - - +
599B VAL 3.3 17.1 + - - -
600B GLY* 4.6 2.2 - - - -
601B TYR* 3.5 25.9 + - - +
602B SER* 4.3 7.1 + - - -
638B PHE 3.7 2.2 + - - -
639B HIS* 1.3 69.6 - - - +
641B ARG* 1.3 60.2 + - - -
642B GLY 3.6 0.9 + - - -
647B ARG 4.1 0.5 - - - +
671B THR* 3.5 9.0 - - - -
673B GLN* 5.0 2.6 + - - -
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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