Contacts of the helix formed by residues 678 - 689 (chain B) in PDB entry 5WRZ
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 678 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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674B LYS 3.1 15.0 + - - +
675B MET* 3.7 9.6 + - - +
676B ILE 3.4 3.6 + - - -
677B PHE* 1.3 75.6 - - - +
679B VAL* 1.3 64.4 + - - +
680B GLU* 3.4 12.0 + - - +
681B SER* 2.8 43.8 + - - +
682B MET* 3.3 20.7 + - - +
867B THR* 5.4 0.2 - - - +
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Residues in contact with VAL 679 (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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677B PHE 3.2 2.3 + - - +
678B ASP* 1.3 72.3 + - - +
680B GLU* 1.3 62.7 + - + +
682B MET* 3.0 14.6 + - + +
683B LYS* 2.9 51.5 + - + +
698B LEU* 3.9 9.6 - - + -
775B TYR* 4.5 9.2 - - + -
778B LEU* 3.6 30.1 - - + -
779B ARG* 4.2 17.0 - - - +
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Residues in contact with GLU 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678B ASP* 3.4 12.7 + - - +
679B VAL* 1.3 76.9 - - + +
681B SER* 1.3 60.9 + - - +
683B LYS* 3.7 34.3 + - - +
684B LYS* 2.8 31.7 + - - +
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Residues in contact with SER 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675B MET 4.8 5.4 + - - -
678B ASP* 2.8 40.3 + - - +
679B VAL 3.3 0.2 - - - -
680B GLU* 1.3 69.3 - - - +
682B MET* 1.3 60.5 + - - +
684B LYS* 3.7 10.1 - - - +
685B ALA* 2.9 25.1 + - - +
866B THR* 5.3 5.2 - - - -
867B THR* 3.5 21.1 - - - +
914B ASP* 5.2 6.4 + - - -
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Residues in contact with MET 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B ILE 4.4 3.6 - - - +
677B PHE* 3.8 31.2 - - + +
678B ASP 3.3 10.7 + - - +
679B VAL* 3.0 12.4 + - - +
681B SER* 1.3 76.0 - - - +
683B LYS* 1.3 62.5 + - - +
685B ALA* 3.1 13.9 + - - +
686B MET* 3.2 20.2 + - - +
698B LEU* 3.9 21.5 - - + -
771B ILE* 4.0 27.9 - - + +
774B ALA* 4.0 21.8 - - + -
775B TYR* 4.2 20.0 - - - +
778B LEU* 4.4 11.9 - - + -
867B THR* 4.0 16.6 - - + +
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Residues in contact with LYS 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B VAL* 2.9 31.3 + - - +
680B GLU* 3.7 36.4 + - - +
682B MET* 1.3 73.2 - - - +
684B LYS* 1.3 63.1 + - - +
686B MET* 3.1 13.0 + - - +
687B VAL* 3.1 23.7 + - - +
693B LEU* 4.0 24.5 - - + +
698B LEU* 4.1 24.0 - - + +
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Residues in contact with LYS 684 (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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680B GLU 2.8 22.5 + - - +
681B SER* 3.7 9.4 - - - +
683B LYS* 1.3 73.1 - - - +
685B ALA* 1.3 60.0 + - - +
687B VAL* 3.4 15.9 + - + +
688B GLU* 3.2 40.5 + - + +
911B SER* 5.3 2.6 + - - -
913B GLY* 4.5 7.9 + - - -
914B ASP* 4.3 26.7 - - - +
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Residues in contact with ALA 685 (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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681B SER 2.9 17.1 + - - +
682B MET 3.1 8.9 + - - +
684B LYS* 1.3 70.0 - - - +
686B MET* 1.3 64.6 + - - +
688B GLU* 3.4 14.3 + - - +
689B TYR* 3.1 36.3 + - + -
771B ILE* 4.2 10.8 - - + -
865B ARG* 5.9 5.2 - - + +
867B THR* 4.1 21.1 - - + +
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Residues in contact with MET 686 (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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682B MET 3.2 9.8 + - - +
683B LYS* 3.1 8.7 + - - +
685B ALA* 1.3 78.0 - - - +
687B VAL* 1.3 60.5 + - - +
689B TYR* 3.4 4.4 + - - -
690B GLU 3.3 3.3 + - - -
691B ILE* 3.1 53.3 + - + +
693B LEU* 3.9 18.6 - - + -
696B MET* 3.6 30.3 - - + +
697B PRO 4.6 0.9 - - - -
698B LEU* 3.7 35.7 - - - -
701B LEU* 4.2 20.6 - - + -
768B LEU* 4.0 17.3 - - + -
771B ILE* 4.7 4.7 - - + -
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Residues in contact with VAL 687 (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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683B LYS 3.1 7.8 + - - +
684B LYS* 3.5 19.7 - - + +
685B ALA 3.3 0.2 - - - -
686B MET* 1.3 72.3 - - - +
688B GLU* 1.3 61.3 + - + +
689B TYR 3.1 1.6 - - - -
690B GLU* 2.7 29.4 + - - +
691B ILE 4.4 8.1 - - - +
693B LEU* 3.4 36.3 - - + -
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Residues in contact with GLU 688 (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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684B LYS* 3.2 38.2 + - + +
685B ALA* 3.4 13.3 + - - +
687B VAL* 1.3 78.1 - - + +
689B TYR* 1.3 63.1 + - + +
690B GLU* 3.2 8.5 + - - +
865B ARG* 4.2 17.7 + - - +
909B HIS 5.2 3.6 - - - +
911B SER* 5.5 4.3 + - - -
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Residues in contact with TYR 689 (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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685B ALA* 3.1 32.8 + - + -
686B MET* 3.6 10.3 - - - +
687B VAL 3.1 0.4 - - - -
688B GLU* 1.3 78.3 - - + +
690B GLU* 1.3 69.3 + - - +
691B ILE* 3.5 7.1 + - + -
742B HIS* 3.5 14.4 + - - -
744B PHE* 5.3 1.7 - - - -
761B LYS* 5.4 2.3 + - - -
764B MET* 3.9 50.2 - - + +
767B ASN* 2.7 40.9 + - + +
768B LEU* 4.9 6.7 - - + -
771B ILE* 5.7 1.8 - - + -
865B ARG* 2.8 28.0 + - - -
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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