Contacts of the strand formed by residues 903 - 911 (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 903 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184X PRO 4.5 0.7 - - - +
185X GLY 1.3 38.9 - - - +
186X ARG* 1.8 0.8 - - - +
187X HIS* 0.9 95.1 + - + +
893v VAL* 5.8 4.7 - - + -
894v CYS 4.0 5.2 - - - +
901v GLU 3.5 1.4 + - - -
902v ASP* 1.3 62.4 - - - +
904v TYR 1.3 47.8 - - - +
929v LYS 2.9 8.6 + - - +
930v LEU* 4.5 19.1 + - + +
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Residues in contact with TYR 904 (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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183X VAL 3.0 22.4 - - - +
185X GLY 2.7 2.6 + - - -
186X ARG 4.0 0.2 - - - +
187X HIS* 1.2 80.2 - - + +
188X ASP* 2.6 14.1 - - - +
189X ILE 4.5 1.6 - - - +
892v ALA 3.8 1.2 - - - +
893v VAL* 3.5 5.2 - - - +
894v CYS* 3.1 29.3 + - + +
903v TRP* 1.3 64.0 - - - +
905v VAL* 1.3 58.2 + - - +
927v THR* 6.2 1.1 - - - -
930v LEU* 5.8 0.2 - - - -
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Residues in contact with VAL 905 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187X HIS* 2.9 3.8 - - + +
892v ALA 3.7 8.7 - - - +
893v VAL* 5.3 3.8 - - + -
904v TYR* 1.3 74.3 - - - +
906v LEU* 1.3 60.1 + - - +
907v VAL* 4.0 1.9 + - + +
926v TYR 3.5 1.4 - - - +
927v THR* 3.3 7.1 - - - -
928v TYR* 2.9 45.4 + - + +
930v LEU* 5.6 6.3 - - + -
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Residues in contact with LEU 906 (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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890v SER 3.7 1.7 - - - +
891v VAL* 3.4 22.5 - - - +
892v ALA* 3.3 13.7 + - + +
904v TYR 4.2 0.6 - - - -
905v VAL* 1.3 72.7 - - - +
907v VAL* 1.3 60.4 + - - +
925v VAL* 6.2 2.5 - - + -
926v TYR 3.4 5.8 - - - +
927v THR* 4.9 1.8 - - - +
952v ILE* 4.4 15.5 - - + +
959v VAL* 5.6 9.9 - - + -
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Residues in contact with VAL 907 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888v ALA* 5.6 7.4 - - + -
890v SER 3.4 7.0 - - - +
891v VAL* 4.7 6.5 - - + +
905v VAL* 5.4 2.0 - - + +
906v LEU* 1.3 73.1 - - - +
908v GLY* 1.3 63.5 + - - +
909v VAL* 3.7 3.1 + - + +
925v VAL* 3.3 7.0 - - - +
926v TYR* 2.9 48.0 + - + +
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Residues in contact with GLY 908 (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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888v ALA* 3.3 5.2 - - - +
889v PHE* 2.9 30.9 + - - +
890v SER* 2.9 14.8 + - - -
906v LEU 4.2 0.2 - - - -
907v VAL* 1.3 71.2 - - - +
909v VAL* 1.3 60.3 + - - -
924v PHE 3.9 4.3 - - - -
925v VAL* 4.8 1.8 - - - -
949v PRO* 3.6 31.6 - - - -
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Residues in contact with VAL 909 (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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886v GLU* 5.2 8.3 - - + -
887v ALA 3.1 13.9 - - - +
888v ALA* 5.0 2.0 - - + -
907v VAL* 3.7 4.5 + - + +
908v GLY* 1.3 74.2 - - - +
910v ALA* 1.3 62.0 + - - +
923v GLY* 3.4 2.6 - - - -
924v PHE* 2.8 47.3 + - + +
926v TYR* 5.7 4.3 - - + +
949v PRO* 5.1 6.7 - - - +
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Residues in contact with ALA 910 (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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862v TRP* 5.4 0.2 - - - +
885v ASN 3.2 4.6 - - - +
886v GLU* 3.3 3.6 - - - -
887v ALA* 2.8 38.9 + - + +
889v PHE* 6.2 3.3 - - + +
909v VAL* 1.3 74.1 - - - +
911v LYS* 1.3 61.4 + - - +
913v LEU* 4.7 17.5 - - + -
922v GLY 5.3 0.7 - - - +
923v GLY* 4.3 5.4 - - - -
948v VAL* 3.8 26.7 - - + -
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Residues in contact with LYS 911 (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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885v ASN* 3.3 13.5 - - + +
886v GLU* 5.1 3.8 - - + -
910v ALA* 1.3 75.3 - - - +
912v ASP* 1.3 72.9 + - + +
913v LEU* 3.6 2.3 - - - -
920v VAL* 5.1 1.0 - - - +
921v ALA 3.6 10.6 + - - +
922v GLY 3.1 25.3 + - - +
923v GLY* 4.4 2.4 - - - -
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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