Contacts of the strand formed by residues 806 - 811 (chain A) in PDB entry 2VGE
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 GLN 806 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777A LEU* 3.7 19.3 - - + +
801A ALA 3.6 0.2 - - - +
802A ALA* 3.1 6.1 - - - -
803A LEU 2.9 38.1 + - - +
804A HIS* 4.2 8.6 + - + +
805A GLY* 1.3 84.6 + - - +
807A GLU* 1.3 61.2 + - - +
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Residues in contact with GLU 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775A ASP* 5.3 2.3 - - - -
776A GLU 5.2 1.0 - - - +
777A LEU* 4.1 5.9 - - - +
788A LEU* 3.6 25.8 - - + +
800A TRP* 2.9 35.8 + - + +
801A ALA 3.1 3.8 - - - +
802A ALA* 4.3 5.1 - - + +
805A GLY 3.9 6.8 + - - +
806A GLN* 1.3 78.6 + - - +
808A GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775A ASP 3.5 12.1 - - - -
776A GLU 4.2 1.8 - - - -
777A LEU* 4.0 17.0 - - - +
799A TRP 3.6 0.2 - - - +
800A TRP* 3.7 15.6 - - - -
801A ALA* 2.7 39.4 + - - +
807A GLU* 1.3 76.4 - - - +
809A TYR* 1.3 62.5 + - - -
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Residues in contact with TYR 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769A TYR* 4.9 0.2 - - - -
775A ASP* 3.0 33.9 + - - +
776A GLU* 3.4 13.2 - - + +
777A LEU 2.9 22.2 + - - +
789A ARG* 4.3 11.2 + - + -
792A GLY* 6.1 1.9 - - - -
794A GLU* 3.5 28.4 - - - +
795A GLU* 4.0 25.8 - - + -
798A TRP* 3.8 30.6 - - + -
799A TRP* 3.3 17.0 - - - -
800A TRP* 3.6 42.4 - + + -
808A GLY* 1.3 72.4 - - - -
810A VAL* 1.3 60.5 + - - +
811A PRO* 4.7 0.2 - - - +
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Residues in contact with VAL 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763A VAL* 6.2 0.2 - - + -
777A LEU* 3.6 27.8 - - + -
779A PHE* 3.6 21.3 - - + -
785A VAL* 4.7 2.0 - - + -
787A VAL* 6.0 0.2 - - + -
798A TRP* 3.3 6.5 - - - -
799A TRP* 3.0 47.0 + - + +
801A ALA* 3.9 15.0 - - + -
808A GLY 4.2 1.3 - - - +
809A TYR* 1.3 80.5 - - - +
811A PRO* 1.3 69.0 - - + +
812A ARG 3.5 0.2 + - - -
815A PHE* 3.6 29.2 - - + -
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Residues in contact with PRO 811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769A TYR* 4.2 20.2 - - + -
779A PHE* 4.3 3.1 - - + -
797A ASP 3.8 8.1 - - - +
798A TRP* 3.5 31.6 - - + -
810A VAL* 1.3 84.7 - - + +
812A ARG* 1.3 65.9 + - - +
813A ASN* 3.3 15.3 - - - +
814A TYR* 3.2 39.1 + - + -
815A PHE* 3.2 13.3 - - - -
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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