Contacts of the strand formed by residues 724 - 728 (chain B) 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 ILE 724 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710B VAL* 3.3 18.9 - - - +
711B ILE* 3.3 53.0 + - + +
713B PHE* 4.0 42.8 - - + -
723B ARG* 1.3 83.5 - - - +
725B VAL* 1.3 63.8 + - - +
726B LEU* 5.0 0.4 - - + -
776B VAL* 5.5 1.1 - - + -
777B ILE* 4.3 20.4 - - + -
819B VAL* 4.3 18.4 - - + -
820B THR 3.6 4.0 - - - -
821B THR* 4.0 15.9 - - + -
829B GLU* 4.7 3.8 - - - +
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Residues in contact with VAL 725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708B LYS* 3.9 26.9 - - + -
709B ALA 3.6 4.7 - - - +
710B VAL* 4.3 0.9 - - + -
721B ASP 4.0 19.7 - - - +
722B ASN* 4.2 7.4 - - - -
724B ILE* 1.3 79.7 - - - +
726B LEU* 1.3 80.5 + - - +
727B ASN* 3.7 16.8 - - - +
818B ILE 3.6 0.6 - - - +
819B VAL* 3.3 0.9 - - - +
820B THR* 2.7 44.7 + - - +
906B GLN* 3.8 22.0 - - + +
907B LEU* 4.2 17.9 - - + -
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Residues in contact with LEU 726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708B LYS* 3.4 4.7 - - - -
709B ALA* 2.8 44.0 + - + +
711B ILE* 4.5 20.0 - - + -
724B ILE* 5.0 0.7 - - + -
725B VAL* 1.3 85.5 - - - +
727B ASN* 1.3 63.5 + - - +
731B LEU* 3.4 22.1 - - + +
734B PHE* 4.6 14.1 - - + -
767B ILE* 3.6 31.0 - - + -
776B VAL* 4.8 4.5 - - + -
794B ILE* 5.5 2.0 - - + -
817B ILE* 4.6 7.2 - - + -
818B ILE 3.5 3.1 - - - +
819B VAL* 3.4 36.8 - - + -
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Residues in contact with ASN 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704B HIS* 3.2 19.7 - - + +
705B LEU* 3.7 20.5 - - + +
707B LYS 3.1 21.1 + - - -
708B LYS* 3.5 6.1 - - - +
725B VAL* 3.7 4.0 - - - +
726B LEU* 1.3 77.0 - - - +
728B GLY* 1.3 58.7 + - - +
731B LEU* 4.2 6.5 - - - -
817B ILE* 3.3 6.5 - - - +
818B ILE* 2.7 38.4 + - + +
820B THR* 4.2 5.2 + - - -
903B ARG* 4.3 4.4 - - - -
906B GLN* 3.0 42.4 + - - +
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Residues in contact with GLY 728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704B HIS* 3.8 19.3 + - - +
707B LYS 5.1 0.2 + - - -
727B ASN* 1.3 78.8 - - - +
729B ILE* 1.3 68.3 + - - +
730B ASP 3.2 3.5 + - - -
731B LEU* 3.3 21.4 + - - +
816B THR 3.7 15.5 - - - -
817B ILE* 4.2 3.8 - - - -
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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