Contacts of the helix formed by residues 664 - 673 (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 664 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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658B CYS* 3.7 3.4 - - - -
662B GLY 5.0 3.4 - - - +
663B LEU* 1.3 76.7 - - - +
665B PRO* 1.3 73.0 - - + +
666B GLN* 3.4 15.5 + - - +
667B GLN* 3.0 36.0 + - - +
668B VAL* 3.0 23.7 + - - +
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Residues in contact with PRO 665 (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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627B HIS 4.9 9.6 - - - +
628B GLY 5.9 2.0 - - - +
629B LEU* 4.0 21.8 - - + -
633B GLN* 4.5 4.5 - - - +
654B LEU* 3.9 16.8 - - + -
658B CYS* 3.7 15.5 - - + -
663B LEU 4.5 0.4 - - - +
664B THR* 1.3 86.7 - - + +
666B GLN* 1.3 55.4 + - - +
668B VAL* 3.3 0.3 + - - +
669B VAL* 2.8 38.3 + - - +
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Residues in contact with GLN 666 (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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633B GLN* 4.3 14.1 - - - +
664B THR* 3.2 10.9 + - - +
665B PRO* 1.3 79.8 - - - +
667B GLN* 1.3 80.8 + - - +
669B VAL* 3.8 2.5 - - - +
670B ALA* 3.0 32.6 + - - +
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Residues in contact with GLN 667 (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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662B GLY 4.4 2.1 - - - +
663B LEU* 3.3 25.3 - - + +
664B THR* 3.0 37.0 + - - +
666B GLN* 1.3 92.5 - - - +
668B VAL* 1.3 67.0 + - - +
670B ALA* 3.2 5.2 + - - +
671B ILE* 3.0 30.2 + - - +
701B ASP* 3.6 24.9 + - - +
704B VAL* 4.3 23.7 - - + +
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Residues in contact with VAL 668 (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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650B VAL* 4.5 21.1 - - + -
653B LEU* 6.4 0.2 - - + -
654B LEU* 3.6 39.3 - - + -
657B LEU* 3.9 32.1 - - + -
658B CYS* 4.2 3.4 - - - -
663B LEU* 4.1 7.6 - - + -
664B THR 3.0 15.5 + - - +
665B PRO 3.8 3.1 - - - +
667B GLN* 1.3 74.1 - - - +
669B VAL* 1.3 58.9 + - + +
671B ILE* 3.3 10.3 + - - +
672B ALA* 2.9 27.2 + - - +
681B LEU* 3.9 15.8 - - + +
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Residues in contact with VAL 669 (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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629B LEU* 3.9 26.0 - - + -
633B GLN* 4.0 37.9 - - + +
636B ALA* 4.7 4.0 - - + -
637B ILE* 3.9 15.5 - - + -
650B VAL* 5.6 0.2 - - + -
665B PRO 2.8 24.2 + - - +
666B GLN* 3.8 4.7 - - - +
668B VAL* 1.3 75.3 - - + +
670B ALA* 1.3 56.8 + - - +
672B ALA* 3.2 5.8 + - - +
673B SER* 2.6 48.8 + - - +
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Residues in contact with ALA 670 (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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666B GLN* 3.0 29.8 + - - +
667B GLN* 3.2 6.9 + - - +
669B VAL* 1.3 78.1 - - - +
671B ILE* 1.3 63.8 + - - +
673B SER* 3.5 11.3 + - - -
674B ASN* 3.5 13.0 - - - +
704B VAL* 5.9 0.4 - - + -
708B CYS* 3.6 19.9 - - - +
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Residues in contact with ILE 671 (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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663B LEU* 4.1 19.7 - - + -
667B GLN 3.0 16.6 + - - +
668B VAL* 3.6 6.3 - - - +
670B ALA* 1.3 76.1 - - - +
672B ALA* 1.3 61.8 + - - +
673B SER 3.5 0.7 + - - -
674B ASN* 4.0 10.2 + - - +
677B GLY* 4.0 8.8 - - - -
680B ALA* 3.7 32.0 - - + +
681B LEU* 3.6 22.0 - - + -
684B ILE* 4.2 22.2 - - + -
704B VAL* 4.1 17.9 - - + -
707B ALA* 4.0 14.7 - - + +
708B CYS* 3.8 19.7 - - - +
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Residues in contact with ALA 672 (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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637B ILE* 4.1 16.2 - - + +
646B ALA* 3.7 17.9 - - + +
650B VAL* 3.5 30.3 - - + -
668B VAL 2.9 16.6 + - - +
669B VAL 3.9 3.1 - - - +
671B ILE* 1.3 75.1 - - - +
673B SER* 1.3 57.7 + - - +
674B ASN 3.0 18.9 + - - +
677B GLY* 3.8 9.5 - - - -
681B LEU* 3.6 11.7 - - + -
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Residues in contact with SER 673 (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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636B ALA* 3.6 18.5 - - - +
637B ILE* 3.6 18.3 + - - +
640B HIS* 2.9 28.0 + - - -
669B VAL* 2.6 31.9 + - - +
670B ALA* 3.5 6.5 + - - -
671B ILE 3.3 2.0 - - - -
672B ALA* 1.3 73.5 - - - +
674B ASN* 1.3 69.3 + - - +
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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