Contacts of the strand formed by residues 862 - 869 (chain v) in PDB entry 6FF7
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 862 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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803v ASP 3.6 5.8 - - - -
804v HIS* 4.6 3.1 - - + +
860v GLY 4.2 2.2 + - - +
861v GLN* 1.3 77.4 - - - +
863v ALA* 1.3 61.2 + - - +
883v GLU 4.1 0.3 - - - +
884v GLN 2.9 20.5 + - - +
885v ASN* 4.1 16.0 - - - +
886v GLU 3.0 18.6 + - - +
887v ALA* 3.6 25.1 - - + -
913v LEU* 6.3 2.5 - - + -
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Residues in contact with ALA 863 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802v THR* 3.3 1.2 - - - -
803v ASP* 2.9 35.8 + - + +
806v ALA* 3.4 31.2 + - + +
807v TYR 3.6 23.1 - - - +
808v THR* 4.1 6.1 - - - +
862v TRP* 1.3 71.4 - - - +
864v SER* 1.3 65.0 + - - +
883v GLU 4.9 3.1 - - - -
884v GLN 4.4 3.1 - - - -
887v ALA* 5.2 0.5 - - - +
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Residues in contact with SER 864 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801v GLU 2.9 13.5 - - - -
802v THR* 4.3 2.2 - - - -
808v THR* 5.8 1.8 - - - -
862v TRP 3.8 1.6 + - - -
863v ALA* 1.3 77.3 - - - +
865v VAL* 1.3 61.6 + - - +
881v GLN* 4.6 0.2 - - - -
882v LEU* 3.3 29.9 + - - +
883v GLU 4.9 2.0 + - - +
886v GLU 3.4 19.1 + - - -
887v ALA* 3.7 2.2 - - - -
888v ALA* 3.6 27.6 - - - -
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Residues in contact with VAL 865 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782v GLN* 6.5 0.7 - - + -
800v ILE* 3.8 2.9 - - - +
801v GLU* 2.9 39.9 + - + +
864v SER* 1.3 76.4 - - - +
866v ILE* 1.3 64.2 + - - +
867v ARG* 4.3 1.3 - - + -
879v LEU* 6.1 2.2 - - + -
880v VAL 3.5 14.6 - - - +
881v GLN* 4.4 7.6 - - + -
882v LEU* 4.8 1.3 - - - +
888v ALA* 5.2 1.9 - - - +
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Residues in contact with ILE 866 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799v ILE 3.5 7.4 - - - +
800v ILE* 4.7 3.4 - - + +
865v VAL* 1.3 75.7 - - - +
867v ARG* 1.3 61.9 + - - +
868v VAL 4.2 0.2 - - - -
878v ASP 4.0 0.3 - - - +
879v LEU* 3.5 4.2 - - - +
880v VAL* 2.9 45.6 + - + +
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Residues in contact with ARG 867 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797v LEU 3.7 1.2 - - - +
798v ILE* 3.6 2.0 - - - -
799v ILE* 2.9 48.8 + - + +
801v GLU* 6.1 4.9 - - + +
865v VAL* 4.3 1.5 - - + -
866v ILE* 1.3 74.7 - - - +
868v VAL* 1.3 62.5 + - - +
869v MET* 3.9 6.0 + - + +
878v ASP 3.4 7.0 - - - +
879v LEU* 5.3 3.6 - - + -
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Residues in contact with VAL 868 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796v ASN* 6.0 2.5 - - + -
797v LEU 3.2 8.7 - - - +
798v ILE* 4.5 7.6 - - + +
866v ILE 4.2 0.4 - - - -
867v ARG* 1.3 71.8 - - - +
869v MET* 1.3 58.5 + - - +
876v THR* 4.4 0.9 - - - -
877v LEU* 3.3 11.5 + - + +
878v ASP* 2.9 52.3 + - + +
934v GLY 4.7 13.5 - - - +
935v GLU 5.7 0.4 - - - -
936v LYS 5.8 2.0 - - - +
937v LEU* 5.8 4.0 - - + -
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Residues in contact with MET 869 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796v ASN* 3.6 6.0 - - - +
797v LEU* 2.9 40.3 + - + +
867v ARG* 3.9 7.6 + - + +
868v VAL* 1.3 73.9 - - - +
870v ASN* 1.3 65.8 + - - +
871v PRO* 3.5 2.1 - - + -
874v GLY* 5.7 2.2 - - - -
875v ASN 3.9 13.9 - - - +
876v THR* 6.0 0.4 - - - -
877v LEU* 4.8 1.3 - - - -
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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