Contacts of the strand formed by residues 958 - 962 (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 ARG 958 (chain v).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180X VAL 4.1 9.9 - - - +
181X ARG* 4.6 0.9 - - - -
182X LEU* 3.9 14.1 - - - +
184X PRO* 5.5 2.6 - - - +
954v PRO* 3.5 6.2 - - - +
955v PHE 2.9 32.5 + - - +
956v GLN* 3.3 3.1 - - + +
957v GLY* 1.3 80.4 - - - +
959v VAL* 1.3 63.3 + - - +
969v VAL* 5.9 3.4 - - + -
970v TYR 3.5 17.3 - - - +
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Residues in contact with VAL 959 (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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164X GLU* 3.2 3.9 - - - +
182X LEU* 4.2 11.3 - - + +
906v LEU* 5.6 10.1 - - + -
952v ILE* 6.1 2.0 - - + -
953v ALA 3.4 11.4 - - - +
954v PRO* 5.1 0.9 - - + -
955v PHE* 5.5 1.1 - - - -
958v ARG* 1.3 78.7 - - - +
960v LEU* 1.3 63.0 + - - +
961v ILE* 6.2 0.9 - - + -
969v VAL* 3.5 4.9 - - - +
970v TYR* 2.9 38.4 + - + +
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Residues in contact with LEU 960 (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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951v ALA 3.8 1.0 - - - +
952v ILE* 3.7 2.9 - - - -
953v ALA* 2.9 44.6 + - + +
955v PHE* 5.3 8.7 - - + +
959v VAL* 1.3 75.3 - - - +
961v ILE* 1.3 60.2 + - - +
962v GLY 4.3 0.2 - - - -
967v LEU* 6.4 2.0 - - + -
968v ARG 3.5 8.3 - - - +
969v VAL* 4.6 3.8 - - + +
993v ILE* 5.2 5.8 - - + +
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Residues in contact with ILE 961 (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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164X GLU 4.1 16.4 - - - +
165X MET* 6.3 0.2 - - + -
949v PRO* 5.1 11.7 - - + -
951v ALA 3.4 10.3 - - - +
952v ILE* 5.4 2.0 - - + -
959v VAL* 4.2 1.1 - - + -
960v LEU* 1.3 75.1 - - - +
962v GLY* 1.3 61.4 + - - +
963v VAL* 3.5 5.5 + - + +
966v LEU 3.6 0.2 - - - +
967v LEU* 3.6 2.0 - - - -
968v ARG* 2.9 39.8 + - + +
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Residues in contact with GLY 962 (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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948v VAL 4.0 0.3 - - - +
949v PRO* 3.9 3.5 - - - +
950v ALA* 3.7 19.9 + - - +
951v ALA* 3.4 17.9 + - - +
960v LEU 4.3 0.4 - - - -
961v ILE* 1.3 68.6 - - - +
963v VAL* 1.3 64.1 + - - -
964v GLY 3.2 3.3 + - - -
966v LEU 3.6 5.8 - - - -
967v LEU* 4.5 5.6 - - - -
990v ILE* 4.0 23.6 - - - +
993v ILE* 5.7 2.6 - - - +
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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