Contacts of the strand formed by residues 869 - 876 (chain B) 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 TYR 869 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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836B VAL 3.4 1.2 - - - +
837B GLN* 3.3 5.1 - - - -
838B ALA* 2.9 32.7 + - - +
861B ALA 3.3 14.8 - - - +
862B PRO* 3.7 16.6 - - + -
863B ILE* 3.8 9.0 - - - +
867B PRO 3.5 6.5 + - - +
868B LEU* 1.3 75.9 - - - +
870B THR* 1.3 62.4 + - - +
871B ILE* 5.6 0.3 - - - +
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Residues in contact with THR 870 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835B GLU* 6.1 3.6 - - - -
836B VAL 3.1 9.0 - - - -
837B GLN* 4.6 1.8 - - - +
859B GLN 3.7 0.6 - - - +
860B ASP* 3.6 3.1 - - - +
861B ALA* 2.9 48.1 + - - -
863B ILE* 5.4 5.6 - - - +
869B TYR* 1.3 74.4 - - - +
871B ILE* 1.3 62.0 + - - +
872B LYS* 4.2 0.9 - - - -
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Residues in contact with ILE 871 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834B VAL 3.3 5.4 - - - +
835B GLU* 3.4 2.1 - - - -
836B VAL* 2.8 48.4 + - + +
846B VAL* 5.9 5.6 - - + -
859B GLN 3.4 5.8 - - - +
860B ASP* 4.8 4.3 - - + +
870B THR* 1.3 75.6 - - - +
872B LYS* 1.3 59.9 + - - +
873B ALA* 4.0 4.5 + - + +
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Residues in contact with LYS 872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834B VAL 3.3 6.5 - - - +
835B GLU* 4.7 4.7 - - + +
857B VAL* 4.3 0.9 - - - +
858B THR* 2.9 27.9 + - - -
859B GLN* 2.8 35.5 + - + +
870B THR* 4.2 1.1 - - - -
871B ILE* 1.3 72.1 - - - +
873B ALA* 1.3 59.3 + - - +
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Residues in contact with ALA 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833B PHE* 3.4 6.6 - - - +
834B VAL* 2.9 38.4 + - + +
850B LEU* 5.6 9.4 - - + -
856B HIS 3.8 6.3 - - - +
857B VAL* 3.8 22.7 - - + +
858B THR* 4.1 2.9 - - - +
871B ILE* 5.2 4.5 - - + +
872B LYS* 1.3 75.0 - - - +
874B PHE* 1.3 63.5 + - - +
875B ILE* 6.3 0.4 - - + -
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Residues in contact with PHE 874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831B TYR* 4.8 12.6 - - + -
832B TYR 3.6 5.4 - - - +
833B PHE* 4.8 0.9 - - - +
854B ARG 4.1 1.2 - - - +
855B GLY* 3.4 6.4 - - - -
856B HIS* 3.1 40.7 + - + +
873B ALA* 1.3 77.2 - - - +
875B ILE* 1.3 60.6 + - - +
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Residues in contact with ILE 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831B TYR* 3.2 6.9 - - - -
832B TYR* 2.8 38.8 + - + +
834B VAL* 5.7 6.7 - - + +
850B LEU* 5.9 5.6 - - + -
853B ARG* 4.9 9.9 - - + +
854B ARG 4.5 5.6 - - - -
855B GLY* 5.1 3.6 - - - -
873B ALA* 6.3 0.7 - - + -
874B PHE* 1.3 74.8 - - - +
876B PRO* 1.3 67.2 - - - +
879B ASP* 5.9 2.5 - - + +
880B SER* 6.0 2.9 - - - -
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Residues in contact with PRO 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829B GLU* 6.0 4.5 - - + -
830B PRO 3.9 7.0 - - - +
831B TYR* 4.5 1.3 - - + -
832B TYR 4.8 0.2 - - - -
853B ARG 4.5 9.1 - - - +
854B ARG* 4.6 7.7 - - + +
875B ILE* 1.3 77.8 - - - +
877B ALA* 1.3 65.0 + - - +
878B ILE* 3.3 5.8 - - + +
879B ASP* 3.2 26.0 + - + +
880B SER* 3.2 12.2 + - - -
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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