Contacts of the strand formed by residues 457 - 464 (chain A) in PDB entry 2O2C
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 CYS 457 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389A HIS* 4.8 0.2 - - - -
390A ALA* 3.5 15.0 - - - -
392A LEU* 3.8 20.6 - - + -
448A ILE* 3.9 24.2 - - - -
455A ILE* 3.4 16.3 + - - -
456A PRO* 1.3 73.5 - - - +
458A ASP* 1.3 65.9 + - - +
459A PHE* 3.6 24.0 - - + -
487A LEU* 4.5 5.4 - - - -
525A PRO 3.5 11.2 + - - +
526A SER* 3.2 2.5 - - - +
527A ASN* 2.8 27.5 + - - +
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Residues in contact with ASP 458 (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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373A LEU* 4.3 6.7 - - - +
389A HIS* 3.1 26.9 + - - -
390A ALA 2.8 14.3 + - - +
391A ILE* 3.8 5.5 - - + +
392A LEU* 2.8 32.7 + - - +
457A CYS* 1.3 71.2 - - - +
459A PHE* 1.3 61.6 - - - +
460A ILE* 3.8 3.5 + - + +
527A ASN* 3.0 36.6 + - - +
529A LEU* 4.4 7.4 - - + -
546A TYR* 2.7 37.2 + - - +
549A LYS* 4.5 1.0 + - - -
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Residues in contact with PHE 459 (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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392A LEU* 3.5 18.8 - - + -
394A TYR* 3.4 42.8 - + - -
445A TYR* 3.8 7.9 - + - -
457A CYS* 3.6 30.5 - - + -
458A ASP* 1.3 71.4 - - - +
460A ILE* 1.3 56.0 + - - +
480A PHE* 3.6 20.4 - + + -
483A GLN* 3.6 24.2 - - + -
484A THR* 3.6 25.4 - - + -
487A LEU* 3.8 21.5 - - + -
526A SER* 4.1 5.6 - - - -
527A ASN 2.8 13.5 + - - +
528A THR* 3.4 2.6 - - - +
529A LEU* 2.7 33.3 + - - +
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Residues in contact with ILE 460 (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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391A ILE* 4.3 12.8 - - + -
392A LEU 3.2 5.9 + - - -
393A PRO* 3.5 9.7 - - + +
394A TYR* 2.6 34.8 + - - +
395A ASP* 5.3 0.3 - - - +
398A LEU* 4.3 13.5 - - + -
401A LEU* 3.8 25.1 - - + -
458A ASP 4.4 5.6 - - - +
459A PHE* 1.3 76.3 - - - +
461A GLY* 1.3 62.5 + - - +
480A PHE* 3.5 2.4 - - - -
529A LEU* 3.3 28.5 - - + +
531A ILE* 5.6 3.8 - - + -
542A ILE* 4.2 25.8 - - + -
546A TYR* 3.6 27.8 - - + +
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Residues in contact with GLY 461 (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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394A TYR 4.1 9.9 - - - -
395A ASP* 5.8 1.6 - - - -
460A ILE* 1.3 77.7 - - - +
462A ALA* 1.3 60.8 + - - -
477A MET* 4.5 2.2 - - - -
480A PHE* 3.5 17.9 - - - -
529A LEU 2.9 9.1 + - - +
530A LEU* 3.4 9.7 - - - -
531A ILE* 3.0 30.6 + - - +
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Residues in contact with ALA 462 (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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394A TYR 4.5 5.6 + - - +
395A ASP* 4.4 15.4 - - - +
461A GLY* 1.3 74.1 - - - -
463A ILE* 1.3 60.2 + - - +
464A GLN 3.8 16.8 - - - +
465A SER* 5.8 0.2 - - - -
473A HIS* 3.0 26.0 + - - +
477A MET* 3.2 13.6 - - - +
530A LEU* 4.3 0.2 - - - -
531A ILE* 3.4 20.2 - - + -
533A SER* 4.1 8.3 - - - -
534A LEU 4.2 5.4 - - - +
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Residues in contact with ILE 463 (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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98A PHE* 3.7 30.1 - - + -
462A ALA* 1.3 72.1 - - - +
464A GLN* 1.3 69.1 + - + +
473A HIS* 3.1 17.3 + - - -
477A MET* 4.8 3.5 - - + +
481A PHE* 6.2 1.8 - - + -
530A LEU* 3.7 28.0 - - + -
531A ILE 2.9 17.4 + - - +
532A LYS* 3.3 14.3 + - + +
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Residues in contact with GLN 464 (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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462A ALA* 3.8 15.6 - - - +
463A ILE* 1.3 89.6 - - + +
465A SER* 1.3 66.8 + - - +
466A GLN* 4.2 2.4 + - - +
473A HIS* 4.0 3.8 - - - -
532A LYS* 2.8 46.6 + - + +
533A SER* 3.9 22.6 + - - -
534A LEU 4.6 1.0 + - - -
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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