Contacts of the helix formed by residues 585 - 591 (chain B) in PDB entry 4OSI
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 LEU 585 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B THR* 2.9 25.5 + - + +
582B VAL* 2.8 6.1 + - - -
584B ARG* 1.3 98.2 - - - +
586B LEU* 1.3 61.4 + - - +
587B PRO* 2.8 9.1 - - - +
588B VAL* 3.3 15.6 + - + +
589B LEU* 2.8 30.3 + - + +
613B LEU* 4.6 7.4 - - + -
614B GLU* 4.4 21.1 - - + +
617B GLN* 3.0 43.7 - - + +
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Residues in contact with LEU 586 (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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559B HIS* 4.0 32.3 - - + +
561B LEU* 4.1 24.2 - - + -
582B VAL* 2.9 25.8 + - + +
585B LEU* 1.3 73.7 - - - +
587B PRO* 1.3 74.1 - - + +
589B LEU* 3.5 5.1 - - + +
590B CYS* 3.0 38.7 + - + +
591B GLN* 4.9 0.7 + - - -
597B PRO* 5.4 6.3 - - + -
600B VAL* 3.5 41.3 - - + +
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Residues in contact with PRO 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B HIS* 4.9 10.7 - - + +
582B VAL 4.3 0.9 - - - +
583B GLN 5.0 3.1 - - - +
584B ARG* 4.1 6.7 - - - +
585B LEU* 2.8 13.9 - - - +
586B LEU* 1.3 100.7 - - + +
588B VAL* 1.3 68.6 + - + +
589B LEU 2.9 0.2 + - - -
591B GLN* 3.3 42.5 + - - +
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Residues in contact with VAL 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B LEU* 3.3 18.8 + - + +
587B PRO* 1.3 82.8 - - + +
589B LEU* 1.3 64.4 + - - +
592B ALA* 3.2 27.9 + - + -
593B HIS* 3.2 32.9 + - + -
617B GLN* 5.0 8.5 - - + +
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Residues in contact with LEU 589 (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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585B LEU* 2.8 29.6 + - + +
586B LEU* 3.2 10.5 - - + +
587B PRO 2.9 1.0 - - - -
588B VAL* 1.3 84.6 - - - +
590B CYS* 1.3 68.4 + - - +
591B GLN 2.9 0.9 + - - -
593B HIS* 3.1 21.1 + - + +
594B GLY 3.5 2.9 + - - -
595B LEU* 3.5 28.5 - - + -
600B VAL* 3.5 39.0 - - + -
603B ILE* 5.0 4.9 - - + -
613B LEU* 5.1 13.0 - - + -
616B VAL* 4.8 15.0 - - + -
617B GLN* 4.6 22.0 - - + +
620B LEU* 6.2 1.6 - - + -
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Residues in contact with CYS 590 (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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586B LEU* 3.0 31.8 + - + +
589B LEU* 1.3 77.6 - - - +
591B GLN* 1.3 69.2 + - - +
594B GLY* 3.2 19.4 - - - -
595B LEU 3.0 26.2 - - - +
596B THR 3.4 3.1 - - - -
597B PRO* 3.2 37.9 - - - -
600B VAL* 3.7 3.6 - - - -
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Residues in contact with GLN 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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586B LEU 4.9 1.4 + - - -
587B PRO* 3.3 31.6 + - - +
589B LEU 2.9 3.6 + - - -
590B CYS* 1.3 82.3 - - - +
592B ALA* 1.3 58.2 + - + +
593B HIS 2.8 16.3 + - - -
594B GLY* 2.9 8.7 + - - -
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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