Contacts of the helix formed by residues 788 - 797 (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 788 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660B HIS* 3.7 17.6 - - - +
661B MET* 4.7 2.6 - - - +
662B LYS* 2.7 50.1 - - - +
663B SER* 3.5 15.8 - - - +
670B GLN* 4.9 1.7 - - - +
787B LYS* 1.3 72.9 - - - +
789B PRO* 1.3 77.2 - - - +
790B ILE* 2.9 25.3 + - - +
791B ASP* 2.9 20.6 + - - +
792B VAL* 3.1 8.5 + - - +
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Residues in contact with PRO 789 (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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660B HIS* 4.0 16.8 - - + +
787B LYS 3.2 7.4 - - - +
788B ASP* 1.3 89.5 - - - +
790B ILE* 1.3 60.8 + - + +
792B VAL* 3.0 12.2 + - + +
793B ASN* 2.9 38.1 + - - +
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Residues in contact with ILE 790 (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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663B SER* 4.2 7.0 - - - +
665B LEU* 4.2 7.4 - - + -
670B GLN* 3.6 49.8 - - + +
673B ILE* 4.0 20.8 - - + +
674B LYS* 3.5 37.7 - - + +
788B ASP* 2.9 20.1 + - - +
789B PRO* 1.3 77.0 - - + +
791B ASP* 1.3 57.9 + - - +
793B ASN* 3.9 3.1 - - - +
794B TYR* 3.0 26.9 + - - +
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Residues in contact with ASP 791 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661B MET* 5.6 2.8 - - - +
663B SER* 2.6 46.1 + - - -
664B LYS 4.5 0.9 + - - -
665B LEU* 3.3 16.8 - - - +
787B LYS* 5.2 8.0 - - + +
788B ASP* 2.9 17.4 + - - +
790B ILE* 1.3 77.2 - - - +
792B VAL* 1.3 64.8 + - - +
794B TYR* 3.4 6.0 + - - +
795B GLU* 3.2 28.0 + - + +
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Residues in contact with VAL 792 (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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782B SER 4.5 13.7 - - - +
784B ASP* 4.7 9.9 - - + +
787B LYS* 3.8 30.3 - - + +
788B ASP 3.1 11.6 + - - +
789B PRO* 3.0 14.2 + - + +
791B ASP* 1.3 75.9 - - - +
793B ASN* 1.3 63.0 + - - +
795B GLU* 3.3 10.2 + - - +
796B LYS* 3.1 46.2 + - - +
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Residues in contact with ASN 793 (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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673B ILE* 3.6 21.3 - - + +
677B PHE* 3.6 28.8 - - + +
778B LEU* 3.8 30.2 - - - +
789B PRO* 2.9 27.2 + - - +
790B ILE* 5.0 2.0 - - - +
792B VAL* 1.3 78.2 - - - +
794B TYR* 1.3 66.8 + - - +
796B LYS* 3.1 26.8 + - - +
797B LEU* 3.4 15.1 + - - +
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Residues in contact with TYR 794 (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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665B LEU* 3.9 29.5 - - + +
669B VAL* 4.2 15.0 - - + -
673B ILE* 3.9 25.4 - - + +
790B ILE 3.0 19.3 + - - +
791B ASP* 3.4 5.1 + - - +
793B ASN* 1.3 74.9 - - - +
795B GLU* 1.3 82.2 + - - +
797B LEU* 3.2 19.5 + - - +
798B LYS 4.0 2.3 + - - -
799B THR 3.4 20.6 + - - +
800B ASP* 3.5 10.7 + - - -
801B ILE* 3.1 47.3 + - + -
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Residues in contact with GLU 795 (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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787B LYS* 6.3 0.7 - - - +
791B ASP* 3.2 16.9 + - + +
792B VAL* 3.4 11.2 - - - +
793B ASN 3.2 0.2 - - - -
794B TYR* 1.3 98.5 - - - +
796B LYS* 1.3 63.3 + - + +
798B LYS* 3.1 20.1 + - - +
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Residues in contact with LYS 796 (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* 4.6 9.2 - - + -
777B LEU* 3.1 55.9 + - + +
778B LEU* 3.2 21.1 + - - +
780B GLY 3.3 16.1 + - - -
781B GLY* 4.9 5.6 - - - -
782B SER 5.1 4.6 + - - +
792B VAL* 3.1 35.2 + - - +
793B ASN* 3.1 23.5 + - - +
795B GLU* 1.3 75.6 - - + +
797B LEU* 1.3 61.3 + - - +
798B LYS* 3.3 10.4 + - - +
874B SER* 4.3 5.2 - - - -
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Residues in contact with LEU 797 (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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673B ILE* 3.4 33.7 - - + -
676B ILE* 4.0 13.2 - - + -
677B PHE* 3.6 25.1 - - + -
777B LEU* 4.9 1.8 - - + -
793B ASN 3.6 7.9 - - - +
794B TYR 3.2 10.1 + - - +
795B GLU 3.1 1.0 - - - -
796B LYS* 1.3 75.4 - - - +
798B LYS* 1.3 59.8 + - - +
799B THR* 2.7 31.5 + - - +
801B ILE* 4.4 8.3 - - + -
870B ALA* 3.8 30.1 - - - +
873B LEU* 3.4 28.3 - - + +
874B SER* 3.6 6.9 - - - -
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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