Contacts of the strand formed by residues 856 - 866 (chain A) in PDB entry 1VDV
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 856 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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848A VAL* 4.1 12.6 - - + -
849A GLY 3.6 10.8 - - - +
850A PHE* 4.0 4.0 - - + -
854A GLY 3.1 9.0 - - - +
855A THR* 1.3 80.2 - - - +
857A VAL* 1.3 64.7 + - - +
858A ALA 3.7 9.9 - - - +
859A LEU* 4.8 2.0 - - + -
889A TYR* 6.2 0.7 - - + -
890A LYS 4.6 3.8 - - - +
891A ILE* 3.7 34.3 - - + -
892A PRO* 3.7 16.5 - - - +
926A TRP* 3.7 19.5 - - + -
927A MET* 3.8 17.0 - - + -
930A VAL* 4.4 7.0 - - + -
945A ASN* 2.9 43.1 + - - +
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Residues in contact with VAL 857 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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722A GLY* 3.5 20.4 - - - +
725A GLU* 3.3 29.6 - - + +
726A ALA* 5.0 1.1 - - + -
849A GLY 2.8 10.3 + - - +
850A PHE* 4.7 0.4 - - - -
851A MET* 3.7 37.2 - - + -
855A THR* 4.0 6.1 - - + +
856A ILE* 1.3 80.0 - - - +
858A ALA* 1.3 61.0 + - - +
892A PRO* 4.5 8.2 - - + +
893A ASN* 2.8 41.3 + - - +
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Residues in contact with ALA 858 (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 LEU* 4.5 2.2 - - + +
722A GLY* 3.7 3.8 - - - -
723A PHE* 3.6 50.9 - - + +
848A VAL* 3.4 5.4 - - - +
849A GLY* 2.7 32.8 + - - +
856A ILE* 3.7 3.5 - - - +
857A VAL* 1.3 83.5 - - - +
859A LEU* 1.3 63.8 + - - +
893A ASN* 3.3 10.1 - - + +
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Residues in contact with LEU 859 (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 LEU* 3.7 2.7 - - - +
723A PHE* 4.2 1.0 - - - -
846A TYR* 4.9 0.7 - - + -
847A LYS 3.4 13.5 - - - +
848A VAL* 3.9 12.6 - - + -
856A ILE* 4.8 0.4 - - + -
858A ALA* 1.3 77.9 - - - +
860A GLU* 1.3 66.2 + - - +
861A VAL* 3.5 23.3 - - + -
885A MET* 3.9 24.0 - - + +
891A ILE* 3.4 27.8 - - + -
893A ASN 3.2 5.9 + - - -
894A ILE* 3.2 6.0 - - + +
895A ARG 2.9 24.4 + - - -
926A TRP* 3.4 48.9 - - + +
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Residues in contact with GLU 860 (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 LEU* 2.8 39.4 - - + +
723A PHE* 3.4 26.1 - - + -
845A ARG 4.6 0.4 - - - -
846A TYR* 3.2 1.9 - - - -
847A LYS* 2.9 58.1 + - + +
859A LEU* 1.3 73.4 - - - +
861A VAL* 1.3 66.3 - - - +
862A ASP* 4.4 3.8 - - - +
895A ARG* 3.2 17.3 - - + +
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Residues in contact with VAL 861 (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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844A ALA* 4.5 3.6 - - + -
845A ARG 3.5 7.2 - - - +
846A TYR* 3.9 10.1 - - + -
859A LEU* 3.5 27.8 - - + -
860A GLU* 1.3 80.0 - - - +
862A ASP* 1.3 67.2 + - - +
863A HIS* 3.3 36.8 + - + +
885A MET* 4.0 14.1 - - + +
895A ARG 2.9 8.3 + - - -
896A GLY* 3.2 3.5 - - - -
897A THR 2.9 24.4 + - - -
922A ILE* 4.0 16.4 - - + -
926A TRP* 4.4 7.2 - - + +
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Residues in contact with ASP 862 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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843A LEU 3.7 0.9 - - - +
844A ALA* 3.4 5.4 - - - +
845A ARG* 2.9 44.9 + - + +
860A GLU* 5.5 2.3 - - - +
861A VAL* 1.3 75.0 + - - +
863A HIS* 1.3 62.0 + - - +
864A TYR* 3.8 25.1 + - + +
895A ARG* 3.7 11.7 + - - -
897A THR* 2.6 35.4 + - - +
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Residues in contact with HIS 863 (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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842A PHE* 4.1 13.2 - + + -
843A LEU 3.7 3.4 - - - -
861A VAL* 3.3 34.6 + - + +
862A ASP* 1.3 73.4 - - - +
864A TYR* 1.3 67.7 + - - +
878A MET* 3.8 20.9 - - + -
881A ALA* 5.1 2.2 + - + -
882A LEU* 3.8 19.8 - - + +
885A MET* 4.3 21.5 - - + +
897A THR* 2.8 31.0 + - - +
898A GLY* 3.4 1.7 - - - -
899A ARG* 2.9 24.2 + - - +
919A ALA* 4.5 12.1 + - + +
922A ILE* 3.5 31.2 - - + +
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Residues in contact with TYR 864 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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698A ILE* 3.5 21.9 - - + +
702A ILE* 3.7 37.6 - - + +
707A PHE* 4.5 5.4 - + - -
842A PHE* 3.3 4.9 - - - +
843A LEU* 2.8 52.6 + - + +
845A ARG* 4.3 24.2 + - - -
862A ASP* 3.8 32.7 + - + +
863A HIS* 1.3 76.2 - - - +
865A SER* 1.3 59.9 + - - +
878A MET* 4.3 1.3 - - - -
897A THR* 5.8 0.7 - - - -
899A ARG* 3.5 33.2 - - + -
901A CYS* 4.2 6.3 - - - -
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Residues in contact with SER 865 (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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698A ILE* 4.1 3.4 - - - -
840A HIS* 4.0 17.2 - - - -
841A PRO 3.3 5.6 - - - -
842A PHE* 3.5 29.2 - - - -
864A TYR* 1.3 74.4 - - - +
866A ASN* 1.3 60.1 + - - +
867A ALA* 3.4 1.4 + - - +
874A SER 5.2 0.3 + - - -
877A ILE* 6.2 0.2 - - - -
878A MET* 3.7 6.2 - - - +
899A ARG 3.1 5.7 + - - -
900A LEU* 3.6 27.2 - - - +
901A CYS* 2.8 29.6 + - - +
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Residues in contact with ASN 866 (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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696A ILE 3.1 24.4 + - - -
697A THR* 3.9 1.8 - - - +
698A ILE* 3.8 30.4 - - + +
840A HIS* 3.5 7.6 - - - -
841A PRO* 3.1 28.5 + - + +
865A SER* 1.3 70.1 - - - +
867A ALA* 1.3 52.6 + - - +
868A GLY* 3.5 3.5 + - - -
901A CYS* 4.2 2.9 - - - -
903A THR* 2.7 27.4 + - - +
905A LEU* 3.8 15.8 - - - +
908A ASN* 2.8 33.1 + - - -
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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