Contacts of the strand formed by residues 810 - 817 (chain A) in PDB entry 2VJ0
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 810 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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806A ARG* 3.4 8.1 + - - +
807A TYR* 2.7 53.7 + - + +
809A GLY* 1.3 84.9 - - - +
811A PHE* 1.3 66.2 + - - +
812A GLN* 3.0 25.3 + - - +
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Residues in contact with PHE 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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805A PHE 3.7 4.3 - - - -
806A ARG* 3.7 41.5 - - + -
809A GLY 4.2 14.4 - - - -
810A THR* 1.3 77.0 - - - +
812A GLN* 1.3 69.9 + - - +
813A ASN* 4.4 0.6 + - - +
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Residues in contact with GLN 812 (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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719A ASN* 5.2 4.7 + - - -
721A LEU* 3.5 25.6 - - + +
803A ILE 4.3 1.1 - - - -
804A GLN* 3.2 24.5 - - - +
805A PHE* 2.9 54.2 + - + +
807A TYR* 4.2 4.6 - - + -
810A THR* 3.0 32.6 + - - +
811A PHE* 1.3 79.7 + - - +
813A ASN* 1.3 64.2 + - - +
814A VAL* 5.5 4.2 - - + +
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Residues in contact with ASN 813 (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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693A ILE* 2.9 38.8 + - - +
694A LEU 4.2 0.2 - - - -
695A ALA* 2.9 38.3 + - + +
802A ASN* 2.9 20.4 + - - -
803A ILE 3.3 4.2 + - - -
804A GLN* 3.4 18.3 + - - -
811A PHE 5.5 0.4 - - - +
812A GLN* 1.3 77.9 + - - +
814A VAL* 1.3 64.3 + - - +
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Residues in contact with VAL 814 (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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695A ALA* 4.1 1.3 - - - -
698A ALA* 4.8 2.7 - - + -
717A PHE* 3.7 50.0 - - + -
719A ASN* 4.8 7.9 - - - +
722A LEU* 5.0 7.9 - - + -
802A ASN* 3.2 4.8 + - - -
803A ILE* 2.7 56.8 + - + +
805A PHE* 5.2 6.5 - - + -
812A GLN* 5.5 3.8 - - + +
813A ASN* 1.3 84.1 + - - +
815A SER* 1.3 65.6 + - - +
816A VAL* 4.3 7.0 - - + -
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Residues in contact with SER 815 (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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694A LEU* 4.4 2.8 - - - +
695A ALA* 2.7 33.0 + - - +
696A PRO 3.9 8.0 + - - -
697A LEU* 3.4 11.6 - - - -
698A ALA* 3.0 26.4 + - - +
800A VAL* 4.3 8.9 - - - +
801A LEU 3.4 4.7 - - - -
802A ASN* 3.0 23.4 + - - +
814A VAL* 1.3 73.2 - - - +
816A VAL* 1.3 65.8 + - - +
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Residues in contact with VAL 816 (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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697A LEU* 4.0 5.6 - - - +
698A ALA* 4.1 8.3 - - + -
701A SER* 4.0 14.4 - - - +
716A LEU* 3.7 33.4 - - + +
717A PHE* 3.8 37.5 - - + -
724A ILE* 4.9 0.7 - - + -
800A VAL* 3.5 1.5 - - - +
801A LEU* 2.8 52.6 + - + +
803A ILE* 4.7 6.1 - - + -
814A VAL* 4.3 2.9 - - + -
815A SER* 1.3 81.2 - - - +
817A LYS* 1.3 61.3 + - - +
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Residues in contact with LYS 817 (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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697A LEU* 3.9 25.5 - - + +
701A SER* 3.3 17.2 + - - +
702A GLU* 2.7 29.9 + - - +
705A PHE* 3.6 34.9 - - + +
716A LEU* 3.9 13.9 - - - +
798A ALA* 3.6 28.3 - - + +
799A PRO 3.7 4.7 - - - +
800A VAL* 4.5 7.0 - - + +
816A VAL* 1.3 74.3 - - - +
818A LEU* 1.3 60.0 + - - +
819A PRO* 3.7 7.1 - - - +
929A ARG* 6.1 0.2 - - - +
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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