Contacts of the strand formed by residues 733 - 735 (chain A) in PDB entry 3AR2
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 MET 733 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A MET* 4.6 12.6 - - - -
331A ALA* 4.4 17.7 - - + -
332A ILE 3.4 15.9 - - - +
333A VAL* 4.5 15.7 - - - -
334A ARG* 4.3 2.0 - - - +
338A SER* 4.4 10.1 - - - +
339A VAL* 5.4 1.1 - - - +
342A LEU* 3.6 19.1 - - + -
716A ILE* 3.4 28.9 - - + -
717A GLY 3.1 3.7 + - - +
718A ILE* 3.1 28.1 - - + +
719A ALA 2.9 23.9 + - - -
731A SER* 3.3 2.1 - - - -
732A GLU* 1.3 84.1 - - + +
734A VAL* 1.3 68.5 + - - +
735A LEU* 4.9 3.8 - - + -
742A THR* 5.8 0.2 - - - -
743A ILE* 6.0 1.1 - - - -
746A ALA* 4.5 3.1 - - + -
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Residues in contact with VAL 734 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ALA* 3.4 3.1 - - - +
332A ILE* 3.0 46.7 + - + +
334A ARG* 3.6 26.2 - - + +
719A ALA* 3.3 12.6 - - + +
720A MET 4.4 0.2 - - - +
721A GLY* 3.8 22.4 - - - +
728A LYS* 4.1 34.8 - - + +
733A MET* 1.3 73.7 - - - +
735A LEU* 1.3 63.7 + - - +
736A ALA* 3.2 10.7 + - + +
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Residues in contact with LEU 735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ASN 4.2 2.5 - - - +
331A ALA* 3.9 17.3 - - + -
701A THR* 5.3 0.2 - - + -
718A ILE* 3.7 19.1 - - + -
719A ALA 2.7 13.3 + - - +
720A MET* 4.5 14.4 - - - -
721A GLY 2.8 20.3 + - - -
733A MET* 4.2 5.1 + - + -
734A VAL* 1.3 68.8 - - - +
736A ALA* 1.3 54.7 + - - +
737A ASP* 3.0 3.4 - - + +
738A ASP* 2.7 31.7 + - - +
739A ASN 3.3 23.8 - - - +
740A PHE* 4.3 1.8 - - - -
742A THR* 3.8 25.8 - - + +
743A ILE* 3.7 31.0 - - + +
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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