Contacts of the helix formed by residues 931 - 938 (chain B) in PDB entry 5V4R
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 ASP 931 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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898B GLN* 2.9 25.1 + - + +
902B VAL* 4.7 9.5 - - + +
929B ASP 4.2 0.2 + - - -
930B ILE* 1.3 72.3 - - - +
932B PRO* 1.3 79.2 - - - +
933B LYS* 2.8 24.7 + - - +
934B LEU* 3.0 20.0 + - + +
935B GLN* 2.9 19.9 + - - +
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Residues in contact with PRO 932 (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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930B ILE 3.2 5.8 - - - +
931B ASP* 1.3 90.7 - - - +
933B LYS* 1.3 61.7 + - - +
935B GLN* 3.1 17.8 + - - +
936B GLU* 3.0 20.3 + - - +
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Residues in contact with LYS 933 (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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902B VAL* 3.7 21.0 - - - +
906B GLU* 2.9 25.3 + - - +
931B ASP* 2.8 18.6 + - - +
932B PRO* 1.3 74.0 - - - +
934B LEU* 1.3 61.6 + - - +
936B GLU* 3.1 15.9 + - - +
937B TYR* 3.1 45.1 + - + +
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Residues in contact with LEU 934 (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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898B GLN* 3.8 33.0 - - + +
901B THR* 3.9 13.0 - - + +
902B VAL* 4.0 15.1 - - + +
913B LEU* 3.8 25.6 - - + -
916B PHE* 3.7 33.2 - - + -
930B ILE* 4.3 7.0 - - + -
931B ASP* 3.0 19.2 + - + +
933B LYS* 1.3 76.3 - - - +
935B GLN* 1.3 65.1 + - - +
937B TYR* 3.0 12.0 + - + -
938B LEU* 2.9 32.8 + - + +
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Residues in contact with GLN 935 (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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930B ILE* 3.7 39.0 - - + +
931B ASP 2.9 7.2 + - - +
932B PRO* 3.3 17.7 - - + +
934B LEU* 1.3 75.7 - - - +
936B GLU* 1.3 61.8 + - - +
938B LEU* 3.3 20.3 + - + +
939B GLY* 3.3 10.4 + - - -
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Residues in contact with GLU 936 (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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932B PRO 3.0 11.3 + - - +
933B LYS* 3.1 16.8 + - - +
935B GLN* 1.3 78.5 - - - +
937B TYR* 1.3 78.6 + - + +
939B GLY* 3.0 14.5 + - - -
940B LYS 4.5 1.0 + - - -
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Residues in contact with TYR 937 (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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902B VAL* 4.1 11.9 - - + -
905B TYR* 3.4 55.5 + + + -
906B GLU* 2.8 36.9 + - + +
913B LEU* 3.8 26.6 - - + +
933B LYS* 3.1 33.4 + - + +
934B LEU* 3.0 19.6 + - + +
936B GLU* 1.3 94.7 - - + +
938B LEU* 1.3 58.9 + - - +
939B GLY 3.1 4.3 + - - -
940B LYS* 3.7 13.3 + - - +
941B PHE 4.8 0.3 + - - -
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Residues in contact with LEU 938 (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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913B LEU* 3.6 31.6 - - + +
916B PHE* 3.9 20.2 - - + -
917B TRP* 3.8 40.3 - - + -
920B LEU* 3.8 24.9 - - + -
930B ILE* 4.6 4.5 - - + -
934B LEU* 2.9 24.7 + - + +
935B GLN* 3.7 14.1 - - + +
936B GLU 3.2 0.4 - - - -
937B TYR* 1.3 74.4 - - - +
939B GLY* 1.3 63.8 + - - +
940B LYS 3.3 0.7 - - - -
941B PHE* 3.3 17.1 + - + +
942B ARG* 3.5 9.7 + - - +
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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