Contacts of the helix formed by residues 664 - 676 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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662D SER* 3.4 2.2 + - - +
663D LYS* 1.3 79.9 + - - +
665D ALA* 1.3 54.2 + - - +
666D VAL* 4.7 5.4 - - + +
667D PHE* 3.4 36.1 - - + +
668D ASP* 2.7 34.0 + - - +
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Residues in contact with ALA 665 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663D LYS 3.5 3.5 + - - -
664D ILE* 1.3 71.5 - - - +
666D VAL* 1.3 64.3 + - - +
668D ASP* 3.0 9.4 + - - +
669D LYS* 2.9 23.2 + - - +
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Residues in contact with VAL 666 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636D ALA* 3.9 19.5 - - + +
637D GLU* 4.4 5.8 - - + +
640D SER* 3.7 29.4 - - - +
664D ILE* 4.7 6.5 - - + -
665D ALA* 1.3 77.7 - - - +
667D PHE* 1.3 79.2 + - + +
669D LYS* 3.4 7.0 + - - +
670D MET* 2.9 38.0 + - - +
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Residues in contact with PHE 667 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636D ALA* 4.4 14.8 - - + -
658D PHE* 4.4 19.3 - + - -
659D PHE* 4.2 14.9 - + + +
662D SER* 3.1 34.5 - - - +
664D ILE* 3.2 19.2 + - + +
665D ALA 3.2 0.4 - - - -
666D VAL* 1.3 89.0 - - + +
668D ASP* 1.3 60.8 + - - +
670D MET* 3.3 16.8 + - - +
671D TRP* 2.9 28.6 + - - +
727D LEU* 3.6 43.5 - - + -
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Residues in contact with ASP 668 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659D PHE 5.7 1.1 - - - -
662D SER* 4.9 10.3 + - - +
663D LYS 5.4 2.2 - - - +
664D ILE 2.7 17.0 + - - +
665D ALA* 3.2 12.3 - - - +
667D PHE* 1.3 73.8 - - - +
669D LYS* 1.3 64.9 + - - +
671D TRP* 3.0 13.2 + - - +
672D THR* 2.9 30.0 + - - -
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Residues in contact with LYS 669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640D SER* 3.2 37.9 - - - +
665D ALA 2.9 11.5 + - - +
666D VAL* 3.8 9.4 - - - +
668D ASP* 1.3 75.3 - - - +
670D MET* 1.3 57.6 + - - +
672D THR* 3.3 8.0 + - - +
673D TYR* 2.9 31.1 + - + +
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Residues in contact with MET 670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502D ILE* 6.1 0.7 - - + -
636D ALA* 3.7 33.7 - - + +
639D LEU* 4.1 11.2 - - + -
640D SER* 4.8 8.1 - - - +
647D TYR* 3.3 40.6 - - + +
659D PHE* 4.6 14.4 - - + -
666D VAL* 2.9 28.2 + - + +
667D PHE* 3.5 21.3 - - + +
668D ASP 3.2 0.2 - - - -
669D LYS* 1.3 75.7 - - - +
671D TRP* 1.3 57.3 + - - +
673D TYR* 3.3 2.0 + - - +
674D MET* 2.9 42.4 + - + +
703D LEU* 4.7 10.1 - - + -
727D LEU* 5.9 1.3 - - + -
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Residues in contact with TRP 671 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656D LYS* 3.7 44.4 - - + -
659D PHE* 4.0 21.1 - - + +
660D ARG* 3.5 53.4 + - + +
667D PHE 2.9 14.2 + - - +
668D ASP* 3.3 14.8 - - - +
670D MET* 1.3 75.6 - - - +
672D THR* 1.3 69.8 + - - +
674D MET* 3.2 15.3 + - + +
675D ARG* 2.9 77.1 + - + +
682D PHE* 5.4 8.3 - + - -
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Residues in contact with THR 672 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668D ASP* 2.9 25.1 + - - -
669D LYS* 3.8 7.8 - - - -
671D TRP* 1.3 79.3 - - - +
673D TYR* 1.3 53.6 + - - +
675D ARG* 3.3 18.9 - - + +
676D SER* 2.7 34.8 + - - +
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Residues in contact with TYR 673 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642D GLN* 5.3 4.7 - - - -
643D THR* 4.2 35.5 + - + -
645D ILE 5.0 1.3 + - - -
646D ALA* 4.8 19.3 - - + +
647D TYR* 4.0 36.8 - + - +
669D LYS* 2.9 19.5 + - + +
670D MET 3.6 4.3 - - - +
672D THR* 1.3 75.2 - - - +
674D MET* 1.3 69.9 + - + +
676D SER* 3.0 20.6 + - - -
677D ALA* 3.1 24.0 + - + +
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Residues in contact with MET 674 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647D TYR* 3.6 46.4 - - + +
648D GLY* 4.5 6.7 - - - -
649D THR* 4.7 7.6 - - + -
659D PHE* 4.5 24.5 - - + -
670D MET* 2.9 41.4 + - + +
671D TRP* 3.7 18.8 - - + +
673D TYR* 1.3 78.6 - - + +
675D ARG* 1.3 62.6 + - - +
676D SER 3.1 1.2 + - - -
677D ALA* 3.3 13.2 + - - +
681D VAL* 3.7 26.3 - - + +
682D PHE* 4.6 10.6 - - + -
703D LEU* 4.3 10.8 - - + -
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Residues in contact with ARG 675 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660D ARG* 5.9 1.0 - - - +
671D TRP* 2.9 69.8 + - + +
672D THR* 3.3 20.2 - - + +
674D MET* 1.3 77.3 - - - +
676D SER* 1.3 59.2 + - - +
677D ALA 3.6 2.0 + - - +
682D PHE* 5.4 8.0 - - - -
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Residues in contact with SER 676 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672D THR* 2.7 25.4 + - - +
673D TYR* 3.0 11.8 + - - -
675D ARG* 1.3 81.2 - - - +
677D ALA* 1.3 61.6 + - - +
678D GLU* 4.0 6.0 + - - +
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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