Contacts of the helix formed by residues 733 - 738 (chain B) in PDB entry 6WCZ
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 GLN 733 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333B TRP* 3.5 23.2 - - - +
731B ARG 3.4 4.5 + - - -
732B HIS* 1.3 71.7 - - - +
734B ASP* 1.3 62.2 + - - +
736B LEU* 3.4 11.3 + - - +
737B ILE* 3.2 28.5 + - + +
771B ARG* 3.7 15.6 + - - +
773B ASP* 2.7 44.6 + - - +
774B LEU* 4.1 20.7 - - + +
846B ASP* 4.6 0.3 - - - +
849B CYS 2.9 16.9 + - - +
850B GLY 2.9 23.0 - - - +
851B SER* 3.3 7.4 - - - -
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Residues in contact with ASP 734 (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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176A ARG* 5.1 6.4 + - - +
198A ILE* 5.6 6.3 - - + +
333B TRP* 5.7 2.5 - - - +
336B VAL* 3.9 14.5 - - - +
338B GLY* 3.2 26.1 + - - -
339B VAL* 3.2 30.1 + - - +
342B ILE* 4.4 1.4 - - - +
732B HIS* 3.1 24.7 + - + +
733B GLN* 1.3 78.9 - - - +
735B GLU* 1.3 60.6 + - + +
737B ILE* 3.8 5.8 - - - -
738B GLY* 3.0 28.9 + - - -
850B GLY 5.1 0.6 + - - +
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Residues in contact with GLU 735 (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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194A LYS* 5.7 4.2 + - - +
198A ILE* 5.8 5.9 - - + +
342B ILE* 3.7 30.7 - - + +
712B SER* 5.6 0.7 - - - -
731B ARG* 3.4 35.4 + - - +
732B HIS* 3.2 20.2 + - - +
734B ASP* 1.3 80.3 - - + +
736B LEU* 1.3 57.0 + - - +
739B ARG* 3.8 12.0 - - - +
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Residues in contact with LEU 736 (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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731B ARG* 3.8 34.3 - - + +
732B HIS 4.1 2.8 + - - +
733B GLN* 3.4 14.4 - - - +
734B ASP 3.1 0.6 - - - -
735B GLU* 1.3 78.3 - - - +
737B ILE* 1.3 68.9 + - - +
738B GLY 3.1 1.6 - - - -
739B ARG* 2.7 29.5 + - - +
740B ALA 3.4 5.2 + - - -
763B MET* 6.2 1.1 - - + -
764B TRP* 3.5 29.0 + - + +
768B TYR* 3.6 31.2 - - + -
771B ARG* 5.4 3.4 - - - +
774B LEU* 3.8 38.6 - - + -
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Residues in contact with ILE 737 (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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326B VAL* 6.0 3.1 - - + +
330B SER* 5.5 1.1 - - - -
333B TRP* 3.8 45.3 - - + +
339B VAL* 4.0 5.8 - - + +
733B GLN* 3.2 24.3 + - + +
734B ASP* 3.4 12.6 - - - +
736B LEU* 1.3 80.0 - - + +
738B GLY* 1.3 63.0 + - - +
739B ARG 3.5 0.3 + - - -
740B ALA* 3.9 3.2 + - + +
741B ARG* 3.7 23.9 + - - +
764B TRP* 3.6 32.3 - - + -
774B LEU* 4.0 11.0 - - + -
777B MET* 3.8 23.3 - - + -
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Residues in contact with GLY 738 (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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339B VAL* 4.3 15.6 - - - +
342B ILE* 3.3 34.7 - - - +
734B ASP 3.0 13.4 + - - -
737B ILE* 1.3 78.4 - - - +
739B ARG* 1.3 58.6 + - - +
741B ARG* 4.0 12.9 - - - +
742B VAL* 3.8 14.6 - - - +
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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