Contacts of the helix formed by residues 630 - 639 (chain B) in PDB entry 4OSV
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 THR 630 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624B CYS* 3.9 2.0 - - - -
628B GLY 5.0 3.4 - - - +
629B LEU* 1.3 77.2 - - - +
631B PRO* 1.3 67.8 - - - +
632B GLU* 3.5 15.2 + - - +
633B GLN* 2.9 42.4 + - - +
634B VAL* 3.0 26.2 + - - +
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Residues in contact with PRO 631 (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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593B HIS 5.4 5.6 - - - +
594B GLY 6.3 0.7 - - - -
595B LEU* 4.2 19.1 - - + -
620B LEU* 4.3 13.1 - - + +
624B CYS* 3.9 19.7 - - - -
629B LEU 4.3 0.2 - - - +
630B THR* 1.3 87.2 - - - +
632B GLU* 1.3 72.1 + - - +
634B VAL* 3.1 2.1 + - - +
635B VAL* 2.8 36.1 + - - +
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Residues in contact with GLU 632 (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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599B GLN* 3.5 27.1 + - - +
630B THR* 3.2 17.7 - - - +
631B PRO* 1.3 89.1 - - - +
633B GLN* 1.3 59.0 + - + +
635B VAL* 3.6 3.6 + - - +
636B ALA* 3.0 28.5 + - - +
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Residues in contact with GLN 633 (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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628B GLY 4.4 1.4 - - - +
629B LEU* 3.3 20.3 - - + +
630B THR* 2.9 49.8 + - - +
632B GLU* 1.3 75.7 - - + +
634B VAL* 1.3 64.8 + - - +
636B ALA* 3.3 6.9 + - - +
637B ILE* 3.1 30.0 + - - +
665B PRO* 4.5 2.7 + - - +
666B GLN* 4.3 21.0 - - - +
669B VAL* 4.0 29.9 - - + +
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Residues in contact with VAL 634 (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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616B VAL* 4.5 14.6 - - + -
620B LEU* 3.5 33.9 - - + +
623B LEU* 3.9 33.4 - - + -
624B CYS* 4.1 6.7 - - - -
629B LEU* 4.2 9.0 - - + -
630B THR 3.0 17.4 + - - +
631B PRO 3.1 6.9 + - - +
633B GLN* 1.3 76.8 - - - +
635B VAL* 1.3 56.4 + - + +
637B ILE* 3.2 10.6 + - - +
638B ALA* 3.0 26.6 + - - +
647B LEU* 3.7 16.4 - - + +
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Residues in contact with VAL 635 (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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595B LEU* 4.0 18.6 - - + -
599B GLN* 3.9 41.7 - - + +
602B ALA* 5.1 4.0 - - + -
603B ILE* 4.1 20.4 - - + -
616B VAL* 5.8 0.4 - - + -
620B LEU* 5.8 0.4 - - + -
631B PRO 2.8 23.9 + - - +
632B GLU* 3.8 5.2 - - - +
634B VAL* 1.3 73.0 - - + +
636B ALA* 1.3 61.6 + - - +
638B ALA* 3.2 7.3 + - - +
639B SER* 2.5 42.1 + - - +
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Residues in contact with ALA 636 (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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632B GLU 3.0 19.2 + - - +
633B GLN* 3.6 9.0 - - - +
634B VAL 3.3 0.2 - - - -
635B VAL* 1.3 77.1 - - - +
637B ILE* 1.3 62.8 + - - +
639B SER* 3.3 6.6 + - - -
640B HIS* 3.0 27.9 + - - +
669B VAL* 4.7 4.0 - - + -
673B SER* 3.6 16.9 + - - +
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Residues in contact with ILE 637 (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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623B LEU* 5.4 0.4 - - + -
629B LEU* 4.0 17.5 - - + -
633B GLN 3.1 17.5 + - - +
634B VAL* 3.2 8.5 + - - +
636B ALA* 1.3 76.3 - - - +
638B ALA* 1.3 61.1 + - - +
639B SER 3.4 0.3 + - - -
640B HIS* 3.9 9.5 + - - +
643B GLY* 4.0 9.7 - - - -
646B ALA* 3.8 17.1 - - + +
647B LEU* 3.7 37.0 - - + +
650B VAL* 3.9 22.7 - - + -
669B VAL* 3.9 23.6 - - + -
672B ALA* 4.1 10.8 - - + +
673B SER* 3.7 17.7 - - - +
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Residues in contact with ALA 638 (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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603B ILE* 4.2 17.1 - - + +
612B ALA* 3.7 17.2 - - + +
616B VAL* 3.4 33.9 - - + -
634B VAL 3.0 12.9 + - - +
635B VAL 3.2 4.9 + - - +
637B ILE* 1.3 76.4 - - - +
639B SER* 1.3 56.7 + - - +
640B HIS 3.0 16.2 + - - +
643B GLY* 3.7 9.3 - - - -
647B LEU* 3.9 9.9 - - + -
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Residues in contact with SER 639 (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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602B ALA* 3.9 16.8 - - - +
603B ILE* 3.7 14.5 + - - +
606B ASN* 3.4 20.7 + - - +
635B VAL* 2.5 36.4 + - - +
636B ALA* 3.3 7.4 + - - -
637B ILE 3.2 2.8 - - - -
638B ALA* 1.3 74.0 - - - +
640B HIS* 1.3 73.1 + - - +
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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