Contacts of the helix formed by residues 735 - 745 (chain A) in PDB entry 1WER
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 735 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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730A ILE 4.2 5.4 - - - +
732A GLN* 3.0 25.8 + - - +
733A LYS 3.8 9.2 - - - +
734A GLU* 1.3 79.8 - - - +
736A HIS* 1.3 64.4 + - - +
737A VAL* 3.3 2.2 - - - -
738A VAL* 3.2 15.2 + - + +
739A TYR* 3.0 33.0 + - + +
760A PHE* 4.0 31.0 - - + -
768A LEU* 4.2 12.8 - - + +
769A LEU* 4.2 19.3 - - + +
772A THR* 3.6 32.3 - - + +
773A LEU* 4.6 8.3 - - + -
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Residues in contact with HIS 736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732A GLN* 6.1 0.6 - - - +
734A GLU* 3.5 37.8 + - + +
735A LEU* 1.3 75.7 - - - +
737A VAL* 1.3 62.5 + - - +
739A TYR* 3.4 12.8 + + + +
740A ALA* 3.0 24.1 + - - +
776A ARG* 6.1 0.7 - - - -
1018A ALA* 3.5 33.2 + - + +
1019A GLN* 3.6 36.2 + - + +
1022A VAL* 3.9 26.7 - - + +
1023A LEU* 4.3 4.8 - - + +
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Residues in contact with VAL 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726A PHE* 5.3 1.3 - - + -
729A LEU* 4.0 29.4 + - + +
730A ILE* 4.4 24.7 - - + +
735A LEU 3.3 0.4 - - - -
736A HIS* 1.3 72.3 - - - +
738A VAL* 1.3 62.4 + - + +
740A ALA* 3.3 6.1 + - - +
741A LEU* 2.9 46.3 + - + +
1022A VAL* 3.4 26.9 - - + +
1023A LEU* 4.6 3.4 - - + -
1026A LEU* 4.0 30.7 - - + -
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Residues in contact with VAL 738 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730A ILE* 4.3 10.3 - - + +
735A LEU* 3.2 31.5 + - + +
737A VAL* 1.3 77.4 - - - +
739A TYR* 1.3 57.0 + - - +
741A LEU* 3.4 8.7 + - - +
742A SER* 2.9 28.4 + - - -
756A LEU* 4.0 37.0 - - + -
760A PHE* 4.2 13.5 - - + -
769A LEU* 4.2 12.8 - - + -
773A LEU* 4.5 13.9 - - + -
793A LEU* 4.2 12.6 - - + +
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Residues in contact with TYR 739 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734A GLU 3.6 18.2 - - - -
735A LEU* 3.0 29.7 + - + +
736A HIS* 3.7 13.9 - + + +
738A VAL* 1.3 73.4 - - - +
740A ALA* 1.3 64.3 + - - +
742A SER* 2.9 22.5 + - - -
743A HIS* 3.1 11.6 + - - +
772A THR* 3.6 22.3 + - + +
773A LEU* 3.2 29.8 - - + +
776A ARG* 3.3 64.9 + - + +
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Residues in contact with ALA 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736A HIS 3.0 10.3 + - - +
737A VAL 3.7 3.8 - - - +
739A TYR* 1.3 75.8 - - - +
741A LEU* 1.3 62.6 + - - +
743A HIS* 3.2 4.8 + - - +
744A VAL* 3.0 26.9 + - - +
1009A LEU* 3.6 17.0 - - + -
1012A LEU* 4.0 14.8 - - + -
1023A LEU* 3.5 35.4 - - + -
1026A LEU* 5.3 0.4 - - + -
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Residues in contact with LEU 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730A ILE* 5.9 0.2 - - + -
737A VAL* 2.9 36.6 + - + +
738A VAL* 3.6 8.5 - - + +
740A ALA* 1.3 75.0 - - - +
742A SER* 1.3 61.1 + - - +
744A VAL* 3.8 4.0 - - + -
745A CYS* 2.9 35.5 + - - -
752A LEU* 3.7 16.6 - - + -
756A LEU* 4.8 3.4 - - + -
998A LEU* 3.9 36.8 - - + -
1001A ILE* 4.1 18.6 - - + -
1002A CYS* 3.8 23.8 - - - +
1009A LEU* 4.3 17.9 - - + -
1026A LEU* 5.3 0.9 - - + -
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Residues in contact with SER 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738A VAL 2.9 10.6 + - - -
739A TYR* 2.9 27.2 + - - -
741A LEU* 1.3 75.0 - - - +
743A HIS* 1.3 56.5 + - - +
745A CYS 2.7 24.7 - - - +
752A LEU* 3.7 9.8 - - - +
773A LEU* 6.0 0.3 - - - +
793A LEU* 3.5 37.2 - - - -
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Residues in contact with HIS 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739A TYR 3.1 13.9 + - - +
740A ALA* 3.3 9.9 - - - +
741A LEU 3.2 0.2 - - - -
742A SER* 1.3 81.5 + - - +
744A VAL* 1.3 66.7 + - - +
745A CYS 3.3 4.0 + - - +
746A GLY* 4.4 3.1 + - - -
1008A GLU* 4.5 11.3 + - - +
1012A LEU* 3.8 34.0 - - + +
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Residues in contact with VAL 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740A ALA 3.4 13.0 - - - +
741A LEU* 3.4 20.6 - - + +
743A HIS* 1.3 77.0 - - - +
745A CYS* 1.3 66.9 + - - +
746A GLY 3.4 3.3 + - - -
1005A HIS* 3.4 35.9 + - + +
1008A GLU* 3.2 53.3 - - + +
1009A LEU* 3.9 14.1 - - + -
1012A LEU* 3.8 18.8 - - + -
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Residues in contact with CYS 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741A LEU 2.9 24.3 + - - +
742A SER* 2.7 21.0 - - - +
743A HIS 4.0 0.7 - - - -
744A VAL* 1.3 77.9 - - - +
746A GLY* 1.3 65.2 + - - +
748A ASP* 4.4 22.4 - - + +
749A ARG* 4.8 4.9 + - - +
752A LEU* 4.1 24.5 - - + -
1001A ILE* 3.5 34.3 - - - -
1005A HIS* 4.1 12.3 - - - -
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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