Contacts of the strand formed by residues 795 - 798 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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789Q LEU* 4.1 21.3 - - + +
792Q GLU* 3.0 30.4 + - + +
793Q VAL 4.2 4.2 - - - +
794Q PHE* 1.3 80.6 - - - +
796Q GLU* 1.3 64.5 + - - +
324R PHE 3.6 4.5 - - - -
326R PHE* 3.9 20.0 - - + -
346R ILE* 4.1 3.4 - - + -
347R ILE* 4.0 4.0 - - + +
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Residues in contact with GLU 796 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765Q PHE 5.8 0.2 - - - +
767Q GLU* 3.8 44.9 - - + +
768Q SER* 5.6 2.5 + - - +
789Q LEU* 4.6 4.7 - - - -
795Q ALA* 1.3 77.6 - - - +
797Q TRP* 1.3 64.8 + - - +
323R ILE* 3.6 43.3 - - + +
324R PHE 3.0 6.7 + - - +
325R VAL* 3.5 9.7 - - + +
326R PHE* 2.9 29.1 + - - -
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Residues in contact with TRP 797 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764Q VAL* 3.4 35.2 - - + -
765Q PHE 3.7 20.0 + - - +
766Q CYS* 3.8 14.4 - - + -
767Q GLU 3.8 19.4 + - - -
768Q SER* 4.8 1.7 + - - -
774Q PHE* 3.5 33.9 - + - -
779Q VAL* 4.0 17.0 - - + -
781Q LEU* 4.0 15.3 - - + +
789Q LEU* 4.1 21.7 - - + +
796Q GLU* 1.3 81.6 - - - +
798Q CYS* 1.3 80.2 + - - +
799Q CYS* 3.6 19.5 - - + -
325R VAL* 5.0 0.6 - - - +
326R PHE* 3.4 13.5 - - - -
327R SER 4.2 1.1 - - - -
328R THR* 3.1 34.9 + - - +
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Residues in contact with CYS 798 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766Q CYS* 4.1 4.9 - - - -
768Q SER* 3.4 29.4 - - - +
797Q TRP* 1.3 93.3 + - - +
799Q CYS* 1.3 76.4 + - - +
800Q ASP* 5.0 0.2 - - - +
802Q CYS* 3.8 11.9 - - - -
803Q VAL* 3.8 17.9 - - + -
325R VAL* 3.6 23.8 - - + -
326R PHE 3.0 8.4 + - - +
327R SER* 3.7 13.4 - - - +
328R THR 4.0 1.6 + - - -
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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