Contacts of the strand formed by residues 923 - 928 (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 GLY 923 (chain v).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909v VAL 3.4 11.7 - - - -
910v ALA* 4.3 6.7 - - - -
911v LYS* 4.4 2.7 - - - -
922v GLY* 1.3 74.9 - - - -
924v PHE* 1.3 59.9 + - - +
944v PRO* 3.6 5.0 - - - +
945v VAL* 2.9 35.0 + - - +
946v GLU 4.5 1.8 - - - -
947v GLU 4.5 9.6 - - - +
948v VAL* 5.2 0.9 - - - -
949v PRO 6.0 0.2 - - - -
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Residues in contact with PHE 924 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213X THR* 5.7 0.4 - - - -
908v GLY* 3.9 1.9 - - - -
909v VAL* 2.8 41.7 + - + +
923v GLY* 1.3 75.2 - - - +
925v VAL* 1.3 64.6 + - - +
926v TYR 4.2 0.4 - - - -
942v LYS* 5.6 6.7 - - + -
943v THR 3.3 13.7 - - - +
944v PRO* 4.9 1.1 - - + -
945v VAL* 4.7 4.0 - - - +
949v PRO* 5.0 5.4 - - - +
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Residues in contact with VAL 925 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166X MET* 5.4 7.2 - - + -
906v LEU* 6.2 2.7 - - + -
907v VAL 3.3 9.4 - - - +
908v GLY* 5.3 1.8 - - - -
924v PHE* 1.3 75.7 - - - +
926v TYR* 1.3 61.7 + - - +
927v THR* 4.1 0.5 + - - -
941v HIS 4.0 0.7 - - - +
942v LYS* 3.5 4.2 - - - -
943v THR* 2.9 39.8 + - - +
945v VAL* 5.7 0.2 - - - +
949v PRO* 5.5 7.0 - - + -
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Residues in contact with TYR 926 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905v VAL 3.5 1.1 - - - +
906v LEU* 3.4 5.7 - - - +
907v VAL* 2.9 46.7 + - + +
909v VAL* 5.7 4.4 - - + +
924v PHE* 4.2 1.0 - - - +
925v VAL* 1.3 74.5 - - - +
927v THR* 1.3 62.6 + - - +
928v TYR* 5.9 0.4 - - + -
941v HIS 3.7 5.8 - - - +
942v LYS* 4.7 3.8 - - + +
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Residues in contact with THR 927 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188X ASP* 4.7 10.1 - - - -
904v TYR* 6.2 1.1 - - - -
905v VAL 3.3 5.4 - - - -
906v LEU* 4.9 1.6 - - - +
925v VAL 4.1 0.4 + - - -
926v TYR* 1.3 76.8 - - - +
928v TYR* 1.3 61.2 + - - +
939v PHE* 4.1 2.1 - - - -
940v LEU* 2.9 32.5 + - - +
941v HIS* 3.0 24.7 + - - +
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Residues in contact with TYR 928 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187X HIS* 2.8 31.0 - - - +
188X ASP* 3.3 7.0 + - - -
904v TYR* 3.3 0.3 - - - -
905v VAL* 2.9 31.5 + - + +
926v TYR* 6.4 0.4 - - + -
927v THR* 1.3 74.6 - - - +
929v LYS* 1.3 54.4 + - - +
930v LEU* 3.7 3.8 - - + +
937v LEU* 5.1 9.4 - - + -
938v GLU 3.4 15.7 - - - +
939v PHE* 5.2 1.1 - - - -
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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
------------------------------------------------------------
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