Contacts of the strand formed by residues 886 - 895 (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 GLU 886 (chain v).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862v TRP 3.0 12.1 + - - +
864v SER* 3.4 13.4 + - - -
882v LEU* 4.2 9.1 - - + +
883v GLU* 3.8 27.0 + - + +
884v GLN 3.3 3.2 - - - -
885v ASN* 1.3 76.5 - - - +
887v ALA* 1.3 59.8 + - - +
909v VAL* 5.2 9.9 - - + -
910v ALA 3.3 7.9 - - - +
911v LYS* 4.8 4.7 - - + +
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Residues in contact with ALA 887 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802v THR* 4.8 7.4 - - - -
803v ASP 6.5 0.4 - - - -
862v TRP* 3.6 23.6 - - + +
863v ALA 5.2 0.4 - - - +
864v SER* 3.7 7.2 - - - -
886v GLU* 1.3 74.2 - - - +
888v ALA* 1.3 66.7 + - - +
889v PHE* 5.1 1.0 - - - +
908v GLY 3.7 0.3 - - - +
909v VAL* 3.1 6.4 - - - +
910v ALA* 2.8 40.4 + - + +
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Residues in contact with ALA 888 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1304u LEU 5.4 1.4 - - - +
786v ARG* 5.0 3.8 - - - +
800v ILE* 4.0 26.7 - - + +
801v GLU 5.4 0.2 - - - +
802v THR* 3.6 20.2 - - - -
864v SER* 3.6 16.6 - - - -
865v VAL 5.2 4.5 - - - +
866v ILE* 6.4 1.1 - - + -
887v ALA* 1.3 74.1 - - - +
889v PHE* 1.3 60.1 + - - +
890v SER 5.1 2.7 - - - +
907v VAL* 5.6 7.9 - - + -
908v GLY 3.3 9.4 - - - +
909v VAL* 4.5 2.5 - - + +
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Residues in contact with PHE 889 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1304u LEU 4.8 17.1 - - - +
786v ARG* 5.4 9.0 - - - +
787v LYS* 5.9 3.3 - - - +
800v ILE* 5.8 2.5 - - - -
887v ALA 5.1 1.6 - - - +
888v ALA* 1.3 75.0 - - - +
890v SER* 1.3 61.6 + - - +
908v GLY 2.9 9.9 + - - +
910v ALA* 6.2 3.1 - - + +
948v VAL* 6.3 2.9 - - + -
949v PRO 4.9 1.1 - - - +
950v ALA* 4.4 27.2 - - + +
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Residues in contact with SER 890 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787v LYS* 6.5 0.9 - - - -
800v ILE* 5.7 2.6 - - - +
888v ALA* 5.1 1.6 - - - +
889v PHE* 1.3 80.0 + - - +
891v VAL* 1.3 62.6 + - - +
906v LEU 3.7 1.2 - - - +
907v VAL* 3.4 5.2 - - - +
908v GLY* 2.9 27.8 + - - +
949v PRO 3.7 7.9 - - - -
950v ALA 3.6 28.9 - - - -
951v ALA* 3.6 10.3 - - - -
952v ILE* 4.0 10.3 - - - -
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Residues in contact with VAL 891 (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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787v LYS* 5.8 4.1 - - - +
788v PHE* 5.6 4.1 - - - -
789v VAL* 4.7 10.1 + - + +
798v ILE* 5.1 13.0 - - + +
799v ILE 6.0 0.4 - - - -
800v ILE* 5.0 15.5 - - + +
890v SER* 1.3 77.0 - - - +
892v ALA* 1.3 64.1 + - - +
906v LEU 3.4 9.6 - - - +
907v VAL* 5.0 6.7 - - + -
952v ILE* 4.6 2.8 - - - +
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Residues in contact with ALA 892 (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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789v VAL* 4.6 7.9 - - - -
891v VAL* 1.3 76.8 - - - +
893v VAL* 1.3 65.1 + - - +
894v CYS* 5.1 2.1 - - + +
904v TYR 3.8 0.7 - - - +
905v VAL* 3.7 5.0 - - - +
906v LEU* 3.3 30.2 + - + +
952v ILE* 3.9 29.4 - - + +
953v ALA 5.0 0.7 - - - +
954v PRO* 5.2 8.5 - - + -
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Residues in contact with VAL 893 (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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789v VAL* 4.5 14.6 - - + +
790v ILE 5.3 7.6 - - - +
791v HIS* 5.7 7.2 - - + -
798v ILE* 6.5 0.9 - - + -
892v ALA* 1.3 75.2 - - - +
894v CYS* 1.3 65.5 + - - +
903v TRP* 5.8 5.8 - - + -
904v TYR 3.5 8.3 - - - +
905v VAL* 4.8 4.3 - - + +
954v PRO* 4.4 8.1 - - - +
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Residues in contact with CYS 894 (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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182X LEU* 6.5 0.4 - - + -
183X VAL 3.5 4.0 - - - +
184X PRO* 1.1 110.6 + - + +
185X GLY 2.6 13.0 + - - +
892v ALA* 5.1 2.7 - - + +
893v VAL* 1.3 78.1 - - - +
895v ARG 1.3 35.2 - - - +
903v TRP* 3.5 1.4 - - - +
904v TYR 3.1 16.3 + - - +
954v PRO* 3.8 19.1 - - + -
958v ARG 5.4 2.9 - - - +
959v VAL* 6.1 3.4 - - + -
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Residues in contact with ARG 895 (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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184X PRO* 1.1 166.7 + - + +
185X GLY* 1.0 72.2 - - - +
894v CYS 1.3 10.7 - - - -
896v PHE* 1.3 60.1 + - - +
900v GLY 5.4 0.9 - - - +
957v GLY* 3.9 9.2 - - - -
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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