Contacts of the strand formed by residues 457 - 464 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B HIS* 4.8 0.6 - - - -
390B ALA* 3.5 14.8 - - - -
392B LEU* 3.8 20.6 - - + -
448B ILE* 3.8 24.5 - - - -
455B ILE* 3.4 16.1 + - - -
456B PRO* 1.3 73.8 - - - +
458B ASP* 1.3 65.6 + - - +
459B PHE* 3.5 23.1 - - + -
487B LEU* 4.4 5.2 - - + -
525B PRO 3.6 11.4 + - - +
526B SER* 3.2 2.7 - - - +
527B ASN* 2.8 27.7 + - - +
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Residues in contact with ASP 458 (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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373B LEU* 4.2 9.7 - - - +
389B HIS* 3.2 26.9 + - - -
390B ALA 2.9 14.3 + - - +
391B ILE* 3.9 5.3 - - + +
392B LEU* 2.8 31.9 + - - +
457B CYS* 1.3 72.0 - - - +
459B PHE* 1.3 62.2 + - - +
460B ILE* 3.9 3.5 + - + +
527B ASN* 3.0 36.2 + - - +
529B LEU* 4.7 5.2 - - + -
546B TYR* 2.7 38.7 + - - +
549B LYS* 4.6 0.3 + - - -
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Residues in contact with PHE 459 (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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392B LEU* 3.5 19.5 - - + -
394B TYR* 3.5 36.3 - + - -
445B TYR* 3.8 8.7 - + - -
457B CYS* 3.5 27.1 - - + -
458B ASP* 1.3 75.4 - - - +
460B ILE* 1.3 57.1 + - - +
480B PHE* 3.6 20.1 - + + -
483B GLN* 3.6 30.7 - - + -
484B THR* 3.6 28.7 - - + -
487B LEU* 3.9 16.6 - - + -
526B SER* 4.1 5.8 - - - -
527B ASN 2.8 12.6 + - - +
528B THR* 3.4 4.0 - - - +
529B LEU* 2.7 34.0 + - - +
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Residues in contact with ILE 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ILE* 4.3 11.9 - - + -
392B LEU 3.2 6.3 + - - -
393B PRO* 3.5 10.4 - - + +
394B TYR* 2.6 34.3 + - - +
395B ASP* 5.3 0.5 - - - +
398B LEU* 4.5 12.5 - - + +
401B LEU* 3.8 25.6 - - + -
458B ASP 4.5 5.4 - - - +
459B PHE* 1.3 76.6 - - - +
461B GLY* 1.3 62.3 + - - +
480B PHE* 3.5 3.3 - - - -
529B LEU* 3.3 28.3 - - + +
531B ILE* 5.6 3.8 - - + -
542B ILE* 4.2 27.4 - - + -
546B TYR* 3.7 29.4 - - + +
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Residues in contact with GLY 461 (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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394B TYR 4.0 9.4 - - - -
395B ASP* 5.8 1.3 - - - -
460B ILE* 1.3 77.7 - - - +
462B ALA* 1.3 59.8 + - - -
477B MET* 4.5 3.4 - - - -
480B PHE* 3.5 16.8 - - - -
529B LEU 2.9 9.3 + - - +
530B LEU* 3.5 9.2 - - - +
531B ILE* 3.0 31.7 + - - +
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Residues in contact with ALA 462 (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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394B TYR 4.5 5.2 + - - +
395B ASP* 4.5 15.2 + - - +
461B GLY* 1.3 74.8 - - - -
463B ILE* 1.3 59.9 + - - +
464B GLN 3.4 18.4 - - - +
465B SER* 5.8 0.2 - - - -
473B HIS* 3.0 25.6 + - - +
477B MET* 3.2 14.3 - - - +
530B LEU* 4.3 0.2 - - - -
531B ILE* 3.4 20.0 - - + -
533B SER* 4.1 7.9 - - - -
534B LEU* 4.2 5.6 - - + +
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Residues in contact with ILE 463 (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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98B PHE* 3.8 30.5 - - + -
462B ALA* 1.3 72.3 - - - +
464B GLN* 1.3 60.0 + - + +
473B HIS* 3.1 17.3 + - - -
530B LEU* 3.9 19.3 - - + -
531B ILE 3.0 14.6 + - - +
532B LYS* 3.3 8.7 + - + +
600C MET* 3.8 27.1 - - + +
601C PHE* 3.4 43.8 - - + +
604C LEU* 3.7 28.9 - - + +
605C SER* 3.8 7.0 - - - +
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Residues in contact with GLN 464 (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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462B ALA* 3.7 15.9 - - - +
463B ILE* 1.3 77.2 - - + +
465B SER* 1.3 66.8 + - - +
466B GLN* 4.2 1.4 + - - +
468B LYS* 5.9 0.7 - - - -
473B HIS* 4.1 3.1 - - - -
532B LYS* 2.8 47.9 + - - +
533B SER* 3.8 23.1 + - - -
534B LEU 4.6 1.4 + - - -
604C LEU 2.9 27.6 + - - +
605C SER 4.0 12.2 + - - +
606C HIS 5.5 4.2 + - - -
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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