Contacts of the strand formed by residues 792 - 796 (chain A) in PDB entry 4AY6
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 PHE 792 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730A ASP* 4.2 9.4 - - + -
733A ALA* 3.6 21.5 - - + -
734A PHE* 3.6 53.8 - + + -
737A SER* 4.0 15.7 - - - -
788A THR* 3.3 5.1 - - - -
789A ILE 2.7 45.2 + - - +
790A ASN* 3.4 10.1 - - + -
791A GLY* 1.3 73.0 - - - +
793A SER* 1.3 63.5 + - - +
794A ILE* 3.5 3.7 + - + +
817A ILE* 4.3 12.3 - - + -
1000D LYS* 4.6 15.5 - - + +
1004D MET* 3.5 33.0 - - + -
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Residues in contact with SER 793 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786A GLN* 5.3 2.7 - - - -
787A ILE 3.6 7.0 - - - -
791A GLY 3.9 0.6 + - - -
792A PHE* 1.3 72.0 - - - +
794A ILE* 1.3 66.4 + - - +
795A SER* 4.1 2.9 - - - -
815A ARG 5.4 0.2 + - - -
816A THR* 3.9 18.9 - - - +
817A ILE* 3.5 24.6 + - - +
571D HIS 4.7 0.5 + - - -
572D ASN* 3.0 32.8 + - - +
573D PRO* 3.4 21.0 - - - +
574D ASP* 5.4 0.4 - - - -
1000D LYS* 5.0 9.9 + - - +
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Residues in contact with ILE 794 (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 LEU* 5.5 1.3 - - + -
734A PHE* 4.0 20.4 - - + -
776A VAL* 4.4 11.9 - - + -
779A MET* 3.7 5.7 - - + +
786A GLN* 3.2 4.3 - - - +
787A ILE* 2.8 56.8 + - + +
789A ILE* 4.0 23.3 - - + -
792A PHE* 4.1 8.7 - - + +
793A SER* 1.3 82.6 - - - +
795A SER* 1.3 59.8 - - - +
817A ILE* 3.7 33.7 - - + +
819A VAL* 3.5 30.7 - - + -
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Residues in contact with SER 795 (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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779A MET* 3.8 4.3 - - - -
785A ILE 4.0 2.9 - - - -
786A GLN* 4.3 8.2 + - - +
793A SER* 4.7 1.2 - - - -
794A ILE* 1.3 76.0 + - - +
796A ASN* 1.3 62.1 + - - +
797A GLY 3.2 0.3 + - - -
800A THR* 5.4 0.9 - - - -
803A ILE* 3.7 24.7 - - - +
816A THR* 2.8 34.5 + - - +
817A ILE 2.8 11.8 + - - -
818A ILE* 3.4 9.4 - - - -
819A VAL* 2.9 29.5 + - - +
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Residues in contact with ASN 796 (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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779A MET* 3.5 12.4 - - + +
780A ILE* 4.0 18.5 + - - +
783A GLY* 4.1 10.5 - - - -
784A GLN 3.1 29.7 + - - +
785A ILE* 2.9 23.7 + - - +
795A SER* 1.3 69.6 - - - +
797A GLY* 1.3 58.7 + - - +
798A LEU* 2.8 25.8 + - - +
799A ALA* 3.1 17.6 + - + +
800A THR* 3.9 6.1 + - - +
803A ILE* 4.1 4.2 - - - +
819A VAL 4.5 0.9 - - - -
824A GLN* 2.6 29.6 + - - +
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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