Contacts of the strand formed by residues 725 - 728 (chain A) in PDB entry 1CEZ
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 VAL 725 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703A ALA* 4.2 22.0 - - + -
706A LEU* 3.5 30.5 - - + -
723A CYS 5.1 0.2 - - - +
724A ALA* 1.3 71.3 - - - +
726A HIS* 1.3 59.0 + - - +
727A TRP* 3.5 12.0 - - + -
736A TRP* 4.6 0.4 - - - -
737A GLN* 2.7 43.5 + - + +
774A GLN* 4.4 15.3 - - + -
778A ILE* 3.7 13.0 - - + -
845A PHE* 3.5 37.0 - - + -
849A PHE* 5.9 0.4 - - + -
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Residues in contact with HIS 726 (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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706A LEU* 5.5 0.4 - - - +
724A ALA 3.4 5.5 + - - +
725A VAL* 1.3 75.0 - - - +
727A TRP* 1.3 78.2 + - - +
728A VAL* 4.0 17.0 - - + +
734A PRO* 3.9 10.3 - - - +
735A VAL 2.9 27.1 - - - -
736A TRP* 3.4 46.1 + + + +
845A PHE* 3.8 9.9 - - - -
848A GLN* 4.0 30.2 + - + +
849A PHE* 5.4 2.7 + - - +
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Residues in contact with TRP 727 (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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422A TRP* 5.1 0.4 - - - -
725A VAL* 3.5 30.1 - - + -
726A HIS* 1.3 83.1 - - - +
728A VAL* 1.3 78.6 + - - +
729A THR* 4.6 0.7 - - - -
735A VAL* 3.0 65.6 + - + +
737A GLN* 3.9 13.7 - - + -
778A ILE* 3.8 23.6 - - + -
781A ASN* 3.7 33.7 - - + -
782A PHE* 3.4 29.6 - + + -
785A SER* 3.1 20.4 + - - -
786A GLN* 5.1 2.2 - - - -
845A PHE* 3.3 26.5 - + + -
848A GLN* 4.6 7.0 - - - +
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Residues in contact with VAL 728 (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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726A HIS* 4.0 17.5 - - + +
727A TRP* 1.3 87.1 - - - +
729A THR* 1.3 74.4 + - - +
730A PRO* 3.8 1.9 - - - +
732A GLY* 4.1 16.8 - - - +
733A PHE 3.7 9.2 - - - +
734A PRO* 4.4 7.0 - - + -
841A VAL* 6.1 0.7 - - - +
844A ASP* 5.7 5.2 - - - +
848A GLN* 3.2 28.3 - - - +
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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
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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