Contacts of the helix formed by residues 685 - 695 (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 THR 685 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402B GLU* 5.7 3.6 - - - -
448B GLY 5.8 3.1 - - - +
650B LEU* 3.9 6.1 - - - -
683B VAL* 3.2 5.5 - - - +
684B ARG* 1.3 88.4 - - + +
686B THR* 1.3 65.5 + - - +
687B ALA* 4.0 9.8 - - - +
688B GLU* 3.0 36.8 + - - +
689B GLY 3.1 8.1 + - - -
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Residues in contact with THR 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B GLU* 4.5 21.2 + - - +
450B TYR* 5.6 1.7 + - - -
650B LEU* 3.4 22.0 - - - +
685B THR* 1.3 72.0 - - - +
687B ALA* 1.3 56.2 + - - +
689B GLY* 2.7 21.0 + - - -
690B VAL* 2.9 19.6 + - + +
702B TYR* 3.6 28.7 + - + +
704B LEU* 4.8 14.1 - - + -
708B MET* 5.2 11.4 - - + +
712B ILE* 6.4 1.6 - - + -
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Residues in contact with ALA 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B GLU* 5.6 1.0 + - - -
685B THR* 4.0 9.3 - - - +
686B THR* 1.3 77.6 - - - +
688B GLU* 1.3 62.2 + - - +
690B VAL* 3.1 12.2 + - - +
691B ALA* 2.9 23.8 + - - +
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Residues in contact with GLU 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B PHE 5.3 0.3 - - - +
683B VAL* 3.5 22.3 - - + +
684B ARG* 3.1 26.7 + - - +
685B THR* 3.0 27.3 + - - +
687B ALA* 1.3 75.8 - - - +
689B GLY* 1.3 55.2 + - - +
691B ALA* 3.9 6.1 - - + +
692B ARG* 2.9 29.5 + - + +
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Residues in contact with GLY 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683B VAL* 4.1 5.8 - - - +
685B THR 3.1 6.9 + - - -
686B THR 2.7 16.7 + - - -
688B GLU* 1.3 69.6 - - - +
690B VAL* 1.3 64.2 + - - -
692B ARG* 3.2 6.6 + - - +
693B VAL* 2.9 28.3 + - - +
702B TYR* 3.4 32.7 - - - -
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Residues in contact with VAL 690 (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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503B MET* 5.0 11.9 - - + -
686B THR* 2.9 23.0 + - + +
687B ALA* 3.1 11.4 + - - +
689B GLY* 1.3 74.6 - - - +
691B ALA* 1.3 64.0 + - - +
693B VAL* 3.1 8.9 + - - +
694B ARG* 2.9 59.0 + - + +
702B TYR* 5.2 1.8 - - + -
704B LEU* 6.4 0.7 - - + -
712B ILE* 4.5 33.7 - - + -
720B THR* 5.0 4.7 - - + -
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Residues in contact with ALA 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687B ALA 2.9 15.4 + - - +
688B GLU* 3.9 7.2 - - + +
690B VAL* 1.3 77.5 - - - +
692B ARG* 1.3 58.2 + - - +
694B ARG* 3.2 10.5 + - - +
695B LYS* 2.9 32.3 + - - +
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Residues in contact with ARG 692 (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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646B ALA* 5.5 1.6 - - - +
679B PRO* 5.5 2.2 + - - +
680B SER 3.3 20.7 + - - -
681B VAL* 3.3 35.8 + - - +
682B PHE 3.9 2.0 + - - +
683B VAL* 4.0 22.1 - - + +
688B GLU* 2.9 21.2 + - + +
689B GLY* 3.2 5.4 + - - +
691B ALA* 1.3 75.9 - - - +
693B VAL* 1.3 53.8 + - - +
695B LYS* 3.2 5.8 + - - +
696B SER* 2.3 44.2 + - - +
700B TYR* 3.3 49.5 + - + -
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Residues in contact with VAL 693 (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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503B MET* 5.2 10.3 - - + +
504B ILE* 4.3 6.5 - - - +
505B LYS* 4.1 34.3 - - + +
689B GLY 2.9 19.3 + - - +
690B VAL* 3.6 8.5 - - - +
692B ARG* 1.3 75.1 - - - +
694B ARG* 1.3 66.5 + - + +
695B LYS 3.2 0.9 + - - -
696B SER* 3.2 17.1 + - - -
697B LYS 4.1 3.6 + - - -
698B GLY* 4.6 4.2 + - - -
700B TYR* 4.1 24.7 - - + +
702B TYR* 3.6 29.6 - - + +
720B THR* 5.5 6.3 - - + -
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Residues in contact with ARG 694 (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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505B LYS* 5.4 11.3 + - + +
690B VAL* 2.9 43.6 + - + +
691B ALA* 3.7 8.1 - - - +
693B VAL* 1.3 79.7 - - + +
695B LYS* 1.3 57.7 + - - +
696B SER 3.5 0.2 - - - -
697B LYS* 4.7 4.4 + - - +
712B ILE* 4.5 11.9 - - - +
715B ARG* 5.1 2.0 + - - +
716B LYS 3.3 11.1 + - - -
717B PRO* 3.3 33.5 - - - +
719B ASP* 2.8 33.5 + - - +
720B THR* 4.7 2.9 - - + +
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Residues in contact with LYS 695 (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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691B ALA 2.9 17.2 + - - +
692B ARG* 3.5 5.6 - - - +
693B VAL 3.1 0.2 - - - -
694B ARG* 1.3 78.4 - - - +
696B SER* 1.3 57.2 + - - +
697B LYS* 3.4 7.7 + - - +
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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