Contacts of the helix formed by residues 681 - 687 (chain B) in PDB entry 2NVT
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 TRP 681 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B VAL* 3.7 27.4 - - + -
36B ALA* 3.7 10.4 - - + +
37B PHE* 3.3 52.7 - + + +
40B GLU* 3.2 34.1 - - + +
41B LYS* 3.8 13.9 - - + +
542B MET* 5.6 1.3 - - + -
636B PRO* 3.6 28.9 - - + -
680B THR* 1.3 68.1 - - - +
682B SER* 1.3 52.9 - - - +
684B LEU* 2.5 46.2 + - + +
685B LEU* 2.7 24.3 + - + +
690B VAL* 3.9 25.1 - - + -
692B TYR* 3.1 29.4 + + - -
743B ILE* 4.9 5.6 - - + -
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Residues in contact with SER 682 (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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40B GLU* 2.9 24.4 + - - -
680B THR* 2.5 6.1 + - - -
681B TRP* 1.3 76.7 - - - +
683B SER* 1.3 52.2 - - - -
685B LEU* 3.9 13.7 - - - +
686B ASN* 2.6 47.3 + - - +
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Residues in contact with SER 683 (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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678B GLU 4.4 2.6 + - - -
679B TYR* 3.3 36.1 - - - -
680B THR 2.3 46.0 + - - -
682B SER* 1.3 68.3 - - - +
684B LEU* 1.3 56.0 + - - -
686B ASN* 3.6 3.6 - - - +
687B GLU* 2.9 39.6 + - - +
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Residues in contact with LEU 684 (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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33B VAL* 4.3 17.3 - - + -
36B ALA* 5.0 1.6 - - + -
638B PHE* 5.9 0.7 - - + -
653B VAL* 4.1 15.7 - - + -
657B HIS* 5.0 1.6 - - + -
661B LEU* 4.3 26.0 - - + -
679B TYR* 4.2 16.6 - - + +
681B TRP* 2.5 48.0 + - + +
683B SER* 1.3 72.5 - - - +
685B LEU* 1.3 65.0 + - - +
687B GLU* 3.1 7.7 + - - -
689B LEU* 3.1 54.9 + - + -
690B VAL* 3.8 14.0 + - + -
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Residues in contact with LEU 685 (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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604B ARG 4.9 2.3 - - - +
605B ARG* 4.2 8.1 - - - +
607B GLY 5.3 0.2 + - - -
611B PRO* 3.8 35.0 - - + +
681B TRP* 2.7 24.6 + - + +
682B SER* 3.5 16.4 - - - +
684B LEU* 1.3 76.5 - - - +
686B ASN* 1.3 66.2 + - - +
687B GLU 3.4 0.5 + - - -
688B GLY* 3.4 10.2 + - - -
690B VAL* 3.7 28.9 - - + +
691B GLU* 4.8 3.6 - - - -
692B TYR* 3.6 46.7 - - + +
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Residues in contact with ASN 686 (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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605B ARG 3.7 8.6 - - - +
606B LYS* 3.9 28.0 + - - +
607B GLY* 4.6 10.4 - - - +
611B PRO* 5.0 5.0 - - - +
682B SER* 2.6 31.7 + - - +
683B SER* 3.6 4.0 - - - +
685B LEU* 1.3 82.9 - - - +
687B GLU* 1.3 60.3 + - + +
688B GLY 3.4 0.4 - - - -
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Residues in contact with GLU 687 (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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605B ARG 3.7 3.8 - - - +
657B HIS* 4.5 13.7 + - - -
660B LYS* 5.7 0.5 + - - -
679B TYR* 3.2 38.5 + - - -
683B SER* 2.9 22.4 + - - +
684B LEU* 3.1 6.2 + - - +
686B ASN* 1.3 78.7 - - + +
688B GLY* 1.3 64.1 + - - +
689B LEU* 3.5 10.8 + - + +
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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