Contacts of the strand formed by residues 1992 - 1995 (chain A) in PDB entry 3PZD
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 GLU1992 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1967A PHE* 3.5 28.3 - - + -
1980A VAL 4.8 0.2 - - - -
1981A SER* 3.3 4.6 + - - -
1982A VAL* 2.8 39.4 + - + +
1990A PRO* 4.0 0.5 - - - +
1991A LEU* 1.3 86.2 - - - +
1993A VAL* 1.3 68.5 + - - +
1994A PHE* 3.3 39.3 - - + -
2017A ARG* 2.9 28.5 + - - -
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Residues in contact with VAL1993 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1979A ALA* 4.2 16.6 - - + -
1980A VAL 3.9 0.2 - - - -
1981A SER* 3.5 20.2 - - - +
1990A PRO* 3.8 23.8 - - + +
1991A LEU 5.8 0.2 - - - -
1992A GLU* 1.3 80.9 + - - +
1994A PHE* 1.3 66.2 + - - +
1995A GLN* 3.9 9.2 + - + +
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Residues in contact with PHE1994 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1967A PHE* 5.4 0.4 - + - -
1973A LEU* 6.2 0.2 - - + -
1979A ALA* 3.9 1.8 - - - -
1980A VAL* 2.7 50.1 + - + +
1982A VAL* 4.0 17.0 - - + -
1992A GLU* 3.3 47.6 - - + -
1993A VAL* 1.3 74.6 - - - +
1995A GLN* 1.3 61.3 + - - +
1998A HIS* 6.0 0.7 - - - -
1999A ILE* 3.8 21.4 - - + +
2012A ILE* 4.6 12.6 - - + -
2014A VAL* 3.6 34.1 - - + -
2017A ARG* 3.7 4.9 - - - -
2019A LEU* 3.6 30.7 - - + -
2021A PHE* 5.6 2.0 - + - -
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Residues in contact with GLN1995 (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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1978A ASP* 3.4 36.0 + - - +
1979A ALA* 3.8 7.8 - - + +
1993A VAL* 3.9 10.5 + - + +
1994A PHE* 1.3 73.7 - - - +
1996A TYR* 1.3 59.2 + - - +
1997A GLU* 4.1 15.5 - - + +
1998A HIS* 3.0 49.5 + - + +
1999A ILE* 3.2 15.3 + - - +
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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
------------------------------------------------------------
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