Contacts of the helix formed by residues 938 - 945 (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 LEU 938 (chain B).
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Specific contacts
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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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Residues in contact with GLY 939 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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935B GLN 3.3 6.6 + - - -
936B GLU* 3.0 15.3 + - - -
938B LEU* 1.3 77.9 - - - +
940B LYS* 1.3 62.4 + - - +
942B ARG* 3.2 20.2 + - - +
943B ARG* 3.7 10.8 + - - +
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Residues in contact with LYS 940 (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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833A GLN* 5.3 16.6 - - + +
837A THR* 5.9 5.6 - - + -
905B TYR* 5.9 2.0 - - + +
936B GLU 4.5 1.2 + - - -
937B TYR 3.7 10.1 + - - +
938B LEU 3.3 0.6 - - - -
939B GLY* 1.3 75.7 - - - +
941B PHE* 1.3 70.8 + - + +
942B ARG 3.3 0.5 + - - -
943B ARG* 3.3 13.2 + - - +
944B LEU* 2.8 27.3 - - + +
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Residues in contact with PHE 941 (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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833A GLN* 5.9 1.1 - - - -
840A ARG* 6.3 0.9 - - - -
872A TYR* 5.7 0.7 - - - -
910B LEU* 4.4 18.4 - - + -
913B LEU* 3.9 30.3 - - + -
914B GLU* 3.5 53.8 - - + -
917B TRP* 3.8 43.8 + + + +
937B TYR 5.3 0.2 - - - -
938B LEU* 3.3 11.0 + - + +
939B GLY 3.2 1.0 - - - -
940B LYS* 1.3 86.7 - - + +
942B ARG* 1.3 62.7 + - - +
944B LEU* 3.2 28.6 + - + +
945B GLU* 3.4 12.1 + - - +
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Residues in contact with ARG 942 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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917B TRP* 4.6 18.1 - - + -
938B LEU 3.5 7.5 + - - +
939B GLY* 3.2 13.9 + - - +
941B PHE* 1.3 78.6 - - - +
943B ARG* 1.3 62.5 + - + +
944B LEU 3.3 0.5 + - - -
945B GLU* 3.4 18.6 + - - +
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Residues in contact with ARG 943 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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795A MET* 3.5 38.8 + - + +
796A GLN* 4.1 7.1 + - - -
797A HIS* 3.8 56.7 + - + +
798A PRO* 4.6 3.8 - - - +
800A HIS* 4.7 2.4 - - - +
834A GLU* 5.5 2.0 + - - -
939B GLY 4.0 12.3 - - - +
940B LYS* 3.3 10.2 + - - +
941B PHE 3.2 0.8 - - - -
942B ARG* 1.3 78.1 - - + +
944B LEU* 1.3 65.1 + - + +
945B GLU 3.7 5.7 - - - +
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Residues in contact with LEU 944 (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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797A HIS* 4.7 15.5 - - + +
799A SER* 4.4 10.5 - - - +
800A HIS* 3.1 28.7 - - + +
837A THR* 4.7 23.3 - - + -
840A ARG* 3.3 59.1 + - - +
940B LYS* 2.8 32.8 - - + +
941B PHE* 3.2 20.5 + - + +
943B ARG* 1.3 84.2 - - + +
945B GLU* 1.3 57.4 + - - +
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Residues in contact with GLU 945 (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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800A HIS* 4.5 4.3 - - - -
840A ARG* 5.8 0.7 - - - +
917B TRP* 5.0 13.9 - - + +
941B PHE 3.4 7.7 + - - +
942B ARG* 3.4 18.6 + - - +
943B ARG 3.4 6.5 - - - +
944B LEU* 1.3 81.4 - - - +
946B ASP* 1.3 67.9 + - - +
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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