Contacts of the strand formed by residues 529 - 534 (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 PHE 529 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A THR* 4.3 18.6 - - + -
308A CYS* 4.5 2.2 - - - -
452A LYS* 3.3 17.3 - - - +
453A LEU* 3.4 17.0 - - + +
455A ILE* 4.3 7.9 - - + -
520A VAL 4.4 0.4 - - - -
521A LEU* 3.3 48.2 - - + -
524A LEU* 3.4 37.9 - - + -
525A PRO 3.6 24.0 - - - -
526A PRO* 3.7 11.2 + - + +
527A ASP* 2.7 11.2 + - - +
528A SER* 1.3 84.0 - - - +
530A GLY* 1.3 62.0 + - - +
559A LEU* 3.7 19.1 - - + -
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Residues in contact with GLY 530 (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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452A LYS* 4.3 10.8 - - - -
453A LEU 2.7 18.3 + - - +
454A ASP* 4.0 5.2 - - - -
529A PHE* 1.3 77.9 - - - +
531A PRO* 1.3 73.3 - - - +
559A LEU* 3.4 21.8 - - - +
560A PRO* 4.5 3.7 - - - +
669A ARG* 5.6 1.1 - - - -
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Residues in contact with PRO 531 (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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454A ASP* 3.3 30.9 - - - +
455A ILE* 3.0 24.9 + - - +
530A GLY* 1.3 86.0 - - - +
532A TYR* 1.3 61.0 + - - +
533A ILE* 3.7 2.4 + - + -
559A LEU* 4.6 1.8 - - - -
560A PRO* 3.5 23.3 - - + +
562A VAL* 3.5 26.7 - - + -
596A GLN* 4.2 20.0 - - - +
669A ARG* 4.2 11.0 - - - +
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Residues in contact with TYR 532 (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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293A ARG* 6.0 0.9 - - - -
455A ILE* 3.5 33.7 - - + -
457A GLN* 3.7 11.6 - - + +
462A HIS* 2.5 45.5 + + - -
514A VAL* 5.2 0.9 - - - +
517A ALA* 5.9 4.4 - - + +
518A PHE* 3.5 34.0 - + - -
521A LEU* 4.5 6.7 - - + -
531A PRO* 1.3 72.5 - - - +
533A ILE* 1.3 71.6 + - - +
534A ILE* 4.4 2.7 - - + -
546A VAL* 3.8 16.4 - - + -
559A LEU* 3.1 30.0 - - + +
560A PRO 2.9 11.2 + - - +
561A VAL* 3.5 11.0 - - + +
562A VAL* 3.3 17.9 + - - -
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Residues in contact with ILE 533 (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* 3.4 32.5 - - + -
454A ASP* 3.5 20.4 - - + +
455A ILE 2.6 13.0 + - - +
456A ARG* 3.3 29.1 - - + -
457A GLN 3.3 21.7 + - - -
531A PRO* 4.3 3.1 - - + -
532A TYR* 1.3 78.3 - - - +
534A ILE* 1.3 64.1 + - - +
535A SER 3.9 0.2 - - - -
562A VAL* 3.2 30.5 - - + +
563A PRO 4.7 1.1 - - - +
564A LEU* 4.0 21.8 - - + +
598A MET* 4.1 4.0 - - + -
638A PHE* 3.6 13.5 - - + -
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Residues in contact with ILE 534 (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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457A GLN 3.7 5.8 - - - +
459A SER* 3.2 41.7 - - - +
462A HIS* 4.1 5.2 - - + -
532A TYR* 4.2 4.7 - - + +
533A ILE* 1.3 77.8 - - - +
535A SER* 1.3 65.7 + - - +
537A ALA* 3.3 17.3 + - + +
542A ASP 3.3 23.3 - - - +
543A VAL* 3.8 11.0 - - + -
546A VAL* 3.7 11.9 - - + -
561A VAL* 3.1 36.1 - - + -
562A VAL 3.0 10.7 + - - +
563A PRO* 4.9 1.8 - - + -
564A LEU 3.4 17.8 + - - -
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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