Contacts of the helix formed by residues 664 - 676 (chain B) in PDB entry 5VOT
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 ILE 664 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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662B SER* 3.4 2.4 + - - +
663B LYS* 1.3 79.2 - - - +
665B ALA* 1.3 55.9 + - - +
666B VAL* 4.7 5.2 - - + +
667B PHE* 3.4 36.7 - - + +
668B ASP* 2.7 34.5 + - - +
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Residues in contact with ALA 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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663B LYS 3.5 3.7 + - - -
664B ILE* 1.3 70.5 - - - +
666B VAL* 1.3 63.5 + - - +
668B ASP* 3.0 9.7 + - - +
669B LYS* 2.9 23.7 + - - +
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Residues in contact with VAL 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636B ALA* 3.9 19.5 - - + +
637B GLU* 4.4 5.6 - - + +
640B SER* 3.7 30.0 - - - +
664B ILE* 4.7 6.3 - - + -
665B ALA* 1.3 78.5 - - - +
667B PHE* 1.3 79.6 + - + +
669B LYS* 3.4 6.3 + - - +
670B MET* 2.9 38.4 + - - +
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Residues in contact with PHE 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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636B ALA* 4.4 9.2 - - + -
658B PHE* 4.4 19.1 - + - -
659B PHE* 4.2 14.9 - + + +
662B SER* 3.1 34.8 - - - +
664B ILE* 3.2 19.3 + - + +
665B ALA 3.2 1.0 - - - -
666B VAL* 1.3 90.6 - - + +
668B ASP* 1.3 60.5 + - - +
670B MET* 3.3 22.1 + - - +
671B TRP* 2.9 28.2 + - - +
727B LEU* 3.6 42.6 - - + -
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Residues in contact with ASP 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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659B PHE 5.7 0.9 - - - -
662B SER* 4.9 10.7 + - - +
663B LYS 5.4 2.5 - - - +
664B ILE 2.7 17.3 + - - +
665B ALA* 3.2 12.8 - - - +
667B PHE* 1.3 72.5 - - - +
669B LYS* 1.3 62.2 + - - +
671B TRP* 3.0 13.9 + - - +
672B THR* 2.9 29.1 + - - -
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Residues in contact with LYS 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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640B SER* 3.2 39.0 - - - +
665B ALA 2.9 12.4 + - - +
666B VAL* 3.8 9.2 - - - +
668B ASP* 1.3 75.8 - - - +
670B MET* 1.3 57.5 + - - +
672B THR* 3.3 7.7 + - - +
673B TYR* 2.9 31.5 + - + +
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Residues in contact with MET 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B ILE* 6.1 1.1 - - + -
636B ALA* 3.7 33.4 - - + +
639B LEU* 4.2 11.7 - - + -
640B SER* 4.8 8.1 - - - +
647B TYR* 3.3 41.1 - - + +
659B PHE* 4.6 15.0 - - + -
666B VAL* 2.9 28.2 + - + +
667B PHE* 3.5 21.3 - - + +
669B LYS* 1.3 76.6 - - - +
671B TRP* 1.3 57.3 + - - +
673B TYR* 3.3 2.5 + - - +
674B MET* 2.9 43.3 + - + +
703B LEU* 4.7 9.4 - - + -
727B LEU* 5.9 1.3 - - + -
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Residues in contact with TRP 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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656B LYS* 3.7 43.1 - - + -
659B PHE* 4.0 22.0 - - + +
660B ARG* 3.5 52.8 + - + +
667B PHE 2.9 13.9 + - - +
668B ASP* 3.0 15.0 + - - +
670B MET* 1.3 75.7 - - - +
672B THR* 1.3 69.1 + - - +
674B MET* 3.2 15.5 + - + +
675B ARG* 2.9 75.3 + - + +
682B PHE* 5.4 8.7 - + - -
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Residues in contact with THR 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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668B ASP* 2.9 24.2 + - - -
669B LYS* 3.8 8.4 - - - -
671B TRP* 1.3 79.7 - - - +
673B TYR* 1.3 52.5 + - - +
675B ARG* 3.3 18.0 - - - +
676B SER* 2.7 34.2 + - - +
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Residues in contact with TYR 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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642B GLN* 5.3 4.0 - - - -
643B THR* 4.2 35.2 + - + -
645B ILE 5.0 1.1 + - - -
646B ALA* 4.7 21.5 - - + +
647B TYR* 4.1 34.8 - + - +
669B LYS* 2.9 19.4 + - + +
670B MET* 3.6 4.5 - - - +
672B THR* 1.3 75.6 - - - +
674B MET* 1.3 72.1 + - + +
676B SER* 3.0 19.2 + - - -
677B ALA* 3.1 23.4 + - + +
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Residues in contact with MET 674 (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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647B TYR* 3.6 47.1 - - + +
648B GLY* 4.5 6.5 - - - -
649B THR* 4.7 8.5 - - + -
659B PHE* 4.5 23.6 - - + -
670B MET* 2.9 41.2 + - + +
671B TRP* 3.7 19.3 - - + +
673B TYR* 1.3 79.4 - - + +
675B ARG* 1.3 62.4 + - - +
676B SER 3.1 1.4 + - - -
677B ALA* 3.3 13.0 + - - +
681B VAL* 3.7 25.8 - - + +
682B PHE* 4.6 10.9 - - + -
703B LEU* 4.4 10.8 - - + -
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Residues in contact with ARG 675 (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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660B ARG* 5.9 1.0 - - - +
671B TRP* 2.9 68.8 + - + +
672B THR* 3.3 20.4 - - + +
674B MET* 1.3 76.8 - - - +
676B SER* 1.3 59.4 + - - +
677B ALA 3.6 2.6 - - - +
682B PHE* 5.4 7.6 - - - -
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Residues in contact with SER 676 (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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672B THR* 2.7 26.0 + - - +
673B TYR* 3.0 11.6 + - - -
675B ARG* 1.3 80.7 - - - +
677B ALA* 1.3 61.6 + - - +
678B GLU* 4.0 4.8 + - - +
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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