Contacts of the strand formed by residues 561 - 565 (chain A) 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 561 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532A TYR* 3.5 6.3 - - + +
534A ILE* 3.1 39.7 - - + -
543A VAL* 3.6 27.2 - - + +
546A VAL* 3.9 19.3 - - + -
547A GLU* 4.2 12.1 - - - +
550A GLN* 3.7 22.0 - - - +
560A PRO* 1.3 78.9 - - - +
562A VAL* 1.3 65.8 + - - +
563A PRO* 4.4 1.5 - - - +
587A TYR* 3.7 17.3 + - - +
590A ARG* 4.3 3.0 - - - +
591A ILE* 6.2 0.8 - - - +
595A GLN* 3.7 12.0 + - - -
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Residues in contact with VAL 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A PRO* 3.5 26.9 - - + -
532A TYR 3.3 1.0 + - - -
533A ILE* 3.2 31.9 - - + +
534A ILE 3.0 22.8 + - - -
561A VAL* 1.3 80.0 - - - +
563A PRO* 1.3 66.2 - - - +
596A GLN* 2.9 40.4 - - + +
597A VAL* 3.4 14.6 - - - -
598A MET* 3.4 15.3 - - + +
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Residues in contact with PRO 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534A ILE* 4.1 9.2 - - + +
537A ALA* 4.7 10.8 - - + +
543A VAL* 4.6 19.7 - - + -
561A VAL* 4.4 2.5 - - + +
562A VAL* 1.3 89.9 - - + +
564A LEU* 1.3 61.3 + - - +
565A PHE* 4.0 27.8 - - + -
578A VAL* 6.4 0.4 - - + -
581A LEU* 5.2 9.0 - - + -
595A GLN* 4.7 3.8 - - - +
596A GLN 3.7 8.5 - - - +
597A VAL* 3.7 13.1 - - + +
598A MET* 2.9 31.1 + - - +
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Residues in contact with LEU 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A TRP* 5.0 1.6 - - + -
456A ARG* 3.7 37.0 - - - +
533A ILE* 4.0 7.9 - - + -
534A ILE 3.4 17.4 + - - +
535A SER* 4.1 9.2 - - - +
536A MET* 4.0 16.9 + - - +
537A ALA 4.7 2.7 + - - +
563A PRO* 1.3 73.7 - - - +
565A PHE* 1.3 64.8 + - - +
566A GLU* 3.7 20.8 + - + +
570A ASP* 5.4 2.1 - - - +
598A MET* 3.1 46.7 - - + +
600A GLY* 4.2 14.1 - - - +
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Residues in contact with PHE 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537A ALA 4.1 18.4 - - - -
538A THR* 5.1 3.4 - - - -
563A PRO* 4.0 16.4 - - + -
564A LEU* 1.3 74.6 - - - +
566A GLU* 1.3 59.2 + - - +
570A ASP* 3.8 31.2 - - + +
571A LEU* 3.7 21.6 - - + +
573A SER 5.2 0.4 - - - -
574A ALA* 4.0 26.5 - - + -
577A SER* 4.5 17.9 - - - -
578A VAL* 4.0 19.3 - - + -
597A VAL* 3.3 35.0 - - + -
598A MET 2.9 10.6 + - - +
599A VAL* 3.4 5.0 - - + -
600A GLY 2.8 23.5 + - - -
624A MET* 4.3 6.3 - - + -
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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