Contacts of the strand formed by residues 531 - 538 (chain A) in PDB entry 2OR4
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 ALA 531 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A VAL 3.8 5.6 + - - +
448A ALA* 3.1 5.4 - - - +
449A TYR 2.9 23.6 + - - -
467A THR* 3.9 14.8 - - + -
469A LEU* 4.5 2.9 - - + -
470A MET* 3.9 3.4 - - + -
530A ILE* 1.4 70.8 - - - +
532A SER* 1.3 59.1 + - - +
595A PHE* 3.7 34.5 - - + -
669A MET 5.8 0.6 + - - +
672A GLU* 3.7 30.2 - - + +
673A ARG* 4.8 0.4 - - - +
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Residues in contact with SER 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A TYR* 3.0 23.4 - - - +
466A CYS* 3.5 1.2 - - - +
467A THR* 3.0 31.2 + - - +
470A MET* 3.8 5.8 - - - -
515A LEU* 3.4 21.3 - - - +
521A PHE* 4.4 13.2 + - - -
524A PHE* 4.1 1.9 - - - +
525A PHE* 3.7 22.1 + - - +
530A ILE 2.9 19.4 + - - -
531A ALA* 1.3 74.2 + - - +
533A GLY* 1.3 58.2 + - - +
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Residues in contact with GLY 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A TYR* 3.0 7.4 + - - +
450A ILE* 3.4 10.7 - - - +
451A ASN* 3.0 26.7 + - - +
465A ASP 3.4 9.9 - - - -
466A CYS* 3.6 9.2 - - - -
470A MET* 3.9 9.2 - - - -
515A LEU* 4.8 3.4 - - - -
521A PHE* 5.4 1.6 - - - +
532A SER* 1.3 78.2 - - - +
534A ARG* 1.3 63.6 + - - +
583A MET* 5.1 2.7 - - - -
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Residues in contact with ARG 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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450A ILE* 5.1 2.5 - - - -
451A ASN* 4.1 12.1 - - + -
453A ASP* 4.8 1.0 - - - +
464A VAL* 3.3 8.2 - - - +
465A ASP* 2.9 47.6 + - + +
466A CYS* 4.6 0.2 - - - +
515A LEU* 4.0 10.5 - - - -
517A SER 4.6 5.9 + - - -
518A GLY* 5.0 2.2 + - - -
519A ASN* 3.5 25.8 - - - +
521A PHE* 3.4 38.5 - - + -
533A GLY* 1.3 75.3 - - - +
535A ALA* 1.4 62.6 + - - +
536A ARG* 3.4 34.2 - - - +
583A MET* 5.6 3.9 - - - +
1754A CL 3.3 32.9 - - + +
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Residues in contact with ALA 535 (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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450A ILE* 5.9 0.2 - - - +
451A ASN 5.1 0.2 + - - -
462A LEU* 4.5 4.3 - - + -
463A ARG 3.2 7.6 - - - -
464A VAL* 3.9 15.9 - - + -
534A ARG* 1.4 77.9 - - - +
536A ARG* 1.3 65.1 + - - +
576A VAL* 3.8 2.3 - - + +
579A VAL* 3.6 32.3 - - + -
580A ARG* 2.8 41.9 + - + +
583A MET* 5.2 4.0 - - - -
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Residues in contact with ARG 536 (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 SER 3.4 23.1 - - - +
455A SER 3.5 9.0 - - - +
457A GLU* 4.6 15.2 + - + +
462A LEU* 3.5 5.5 - - - +
463A ARG* 2.7 91.0 + - + +
465A ASP* 3.0 33.9 + - - +
534A ARG* 3.4 44.0 + - - +
535A ALA* 1.3 78.4 - - - +
537A TYR* 1.3 65.7 + - - +
576A VAL* 4.1 9.2 - - - -
580A ARG* 4.3 0.2 - - - +
1754A CL 4.3 14.6 - - - -
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Residues in contact with TYR 537 (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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455A SER 2.8 13.8 + - - +
456A ILE* 3.4 10.7 - - + -
457A GLU* 2.8 34.5 + - - +
458A GLY 3.7 10.3 - - - +
459A ASN* 3.9 11.0 - - - -
460A TYR 3.7 3.8 - - - -
461A THR* 3.4 38.5 + - - -
462A LEU* 4.0 22.6 + - + -
484A PRO* 3.3 16.8 - - + +
485A ASP* 2.6 30.5 + - - -
493A LEU* 3.6 9.9 - - + +
496A SER* 4.5 0.2 + - - -
536A ARG* 1.3 75.7 - - - +
538A THR* 1.3 54.9 + - - +
572A TYR* 3.5 28.0 - + + -
575A THR* 3.9 21.1 - - + -
576A VAL* 3.7 12.1 - - + +
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Residues in contact with THR 538 (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 GLU* 2.6 32.8 + - - +
458A GLY* 3.6 7.6 - - - +
460A TYR* 2.9 28.2 + - - +
461A THR* 2.8 32.9 + - + +
462A LEU 4.3 0.7 - - - +
463A ARG* 3.7 28.1 + - + -
537A TYR* 1.3 73.9 - - - +
539A LYS* 1.3 82.0 + - - +
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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