Contacts of the strand formed by residues 795 - 798 (chain U) in PDB entry 3ZPV
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 ALA 795 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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789U LEU* 4.1 20.0 - - + +
792U GLU* 3.0 26.0 + - + +
793U VAL 3.3 4.5 - - - +
794U PHE* 1.3 79.1 - - - +
796U GLU* 1.3 63.7 + - - +
324V PHE 3.5 4.9 - - - -
326V PHE* 3.8 21.8 - - + -
346V ILE* 4.2 3.1 - - + -
347V ILE* 3.9 10.0 - - + +
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Residues in contact with GLU 796 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765U PHE 5.7 0.4 - - - +
767U GLU* 3.6 36.0 - - + +
768U SER* 4.0 11.3 + - - -
789U LEU* 4.6 4.3 - - - -
795U ALA* 1.3 76.4 - - - +
797U TRP* 1.3 63.9 + - - +
323V ILE* 3.7 37.0 - - + +
324V PHE 2.9 6.9 + - - +
325V VAL* 3.4 20.0 - - + +
326V PHE* 2.8 34.1 + - - +
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Residues in contact with TRP 797 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764U VAL* 3.4 36.1 - - + -
765U PHE 3.7 19.2 + - - +
766U CYS* 3.8 12.1 - - + -
767U GLU 3.8 19.2 + - - -
768U SER* 4.8 0.5 + - - -
774U PHE* 3.5 36.6 - + - -
779U VAL* 4.0 16.2 - - + -
781U LEU* 4.0 7.0 - - + +
789U LEU* 4.1 29.1 - - + +
796U GLU* 1.3 82.0 - - - +
798U CYS* 1.3 74.0 + - - +
799U CYS* 3.6 18.6 - - + -
800U ASP 5.3 0.2 - - - -
325V VAL* 4.8 0.4 - - - -
326V PHE* 3.3 18.6 - - - +
327V SER 4.1 1.1 - - - -
328V THR* 3.1 38.2 + - - +
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Residues in contact with CYS 798 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766U CYS* 4.1 5.2 - - - -
768U SER* 3.4 28.7 - - - +
797U TRP* 1.3 91.0 + - - +
799U CYS* 1.3 77.0 + - - +
800U ASP* 5.0 0.3 - - - +
802U CYS* 3.8 12.3 - - - -
803U VAL* 3.8 18.4 - - + -
325V VAL* 3.6 24.2 - - + -
326V PHE 2.9 9.6 + - - +
327V SER* 3.6 13.7 - - - -
328V THR 4.1 1.2 + - - -
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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