Contacts of the helix formed by residues 590 - 594 (chain B) in PDB entry 2OBF
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 590 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565B PHE* 3.2 35.9 - - + -
575B LEU* 4.1 17.7 - - + -
586B GLN 4.6 3.4 - - - +
587B LEU* 3.4 20.8 + - + +
588B LEU 3.3 0.6 - - - -
589B SER* 1.3 77.3 - - - +
591B CYS* 1.3 54.7 + - - +
592B SER 3.1 2.7 - - - -
593B HIS* 2.8 32.7 + - - +
594B PHE* 3.5 7.4 + - - -
597B ILE* 4.9 1.3 - - + -
679B VAL* 5.1 0.7 - - + -
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Residues in contact with CYS 591 (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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587B LEU 3.1 14.5 + - - +
588B LEU* 3.4 18.8 - - - -
590B ALA* 1.3 75.7 - - - +
592B SER* 1.3 52.9 + - - +
593B HIS 3.0 0.8 + - - -
594B PHE 3.3 1.7 - - - +
597B ILE* 3.8 15.2 - - + +
643B LYS* 4.2 17.0 - - - -
646B GLN* 3.9 14.1 - - + -
647B LEU* 3.6 41.7 - - + +
650B ARG* 2.7 41.2 + - - -
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Residues in contact with SER 592 (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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589B SER 3.3 16.1 + - - -
591B CYS* 1.3 80.7 - - - +
593B HIS* 1.3 73.0 + - - +
634B GLU* 4.8 0.9 + - - -
636B LYS* 4.3 14.9 + - - -
638B GLU* 5.8 1.3 - - - -
643B LYS* 4.7 9.2 + - - -
646B GLN* 3.5 21.3 + - - +
650B ARG* 3.7 8.8 + - - +
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Residues in contact with HIS 593 (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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565B PHE* 3.4 46.4 + + + +
566B ALA* 5.5 0.4 - - - -
568B GLY* 5.5 5.6 - - - -
570B VAL 3.9 10.3 + - - +
571B SER* 4.3 8.2 - - - -
572B GLY 3.2 22.0 + - - +
589B SER 3.3 23.9 + - - -
590B ALA 2.8 6.9 + - - +
592B SER* 1.3 97.3 + - - +
594B PHE* 1.3 78.4 + - + +
595B GLU* 5.6 0.8 - - - +
636B LYS* 5.0 9.3 + - - -
650B ARG* 4.0 2.2 - - - -
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Residues in contact with PHE 594 (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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565B PHE* 3.9 11.7 - + - -
570B VAL* 3.7 9.6 - - + -
571B SER* 3.5 36.6 - - - -
572B GLY* 3.7 13.0 - - - -
573B ARG 4.1 4.7 - - - +
574B THR 3.5 22.4 - - - -
575B LEU* 3.6 33.9 - - + -
590B ALA 3.5 8.1 + - - +
591B CYS 3.3 2.3 - - - +
593B HIS* 1.3 98.7 - - + +
595B GLU* 1.3 62.6 + - - +
596B ASP 3.3 1.0 + - - +
597B ILE* 3.9 12.7 - - + +
650B ARG* 3.1 25.2 + - - +
676B ASP* 4.0 1.6 - - + -
677B ALA* 3.6 27.8 - - + -
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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