Contacts of the strand formed by residues 724 - 731 (chain B) in PDB entry 3ZNS
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 724 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B K 2.6 27.2 - - - -
689B CYS* 3.5 19.3 - - - -
693B GLN* 3.4 30.1 - - - +
701B ILE 3.3 9.9 - - - +
703B ILE* 4.0 19.7 - - + -
718B PHE* 3.5 43.7 - - + -
721B ASP* 3.2 6.8 + - - +
722B PRO 3.2 0.9 - - - -
723B SER* 1.3 80.7 + - - +
725B LEU* 1.3 65.0 + - - +
726B TYR* 4.7 1.3 - - - +
755B PHE* 3.6 5.9 - - - +
789B PHE* 4.2 2.0 - - - -
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Residues in contact with LEU 725 (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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701B ILE 2.9 7.1 + - - -
702B LEU* 3.4 23.1 - - + +
703B ILE* 2.7 34.0 + - - +
724B VAL* 1.3 73.3 - - - +
726B TYR* 1.3 57.7 + - - +
727B ILE* 4.0 15.9 - - + -
755B PHE* 3.4 30.1 - - + +
757B VAL* 4.3 7.6 - - + -
785B ILE* 3.9 18.8 - - + +
786B ALA* 4.5 2.2 - - - -
789B PHE* 3.5 49.5 - - + -
895B TRP* 4.1 12.1 - - + -
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Residues in contact with TYR 726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B ILE* 3.4 19.3 - - + -
705B ASP* 2.7 42.3 + - + +
710B HIS* 4.0 6.3 - - - -
711B GLY* 3.2 23.0 + - - -
714B THR* 3.5 31.9 - - + +
715B GLN* 4.0 21.8 - - + -
718B PHE* 5.5 5.6 - - + -
724B VAL* 4.0 5.3 - - + -
725B LEU* 1.3 72.1 - - - +
727B ILE* 1.3 57.9 + - - +
728B SER* 3.5 24.0 - - - -
755B PHE 3.2 8.7 + - - +
756B ASN* 3.4 27.6 - - - +
757B VAL 2.8 32.4 + - - +
758B ASN* 4.5 1.3 - - - -
797B SER* 5.7 0.2 - - - -
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Residues in contact with ILE 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B LEU* 3.9 24.0 - - + -
703B ILE 2.8 11.1 + - - +
704B VAL* 3.3 9.4 - - + +
705B ASP 2.8 25.6 + - - +
725B LEU* 4.0 18.2 - - + -
726B TYR* 1.3 79.2 - - - +
728B SER* 1.3 62.8 + - - +
729B LEU* 4.2 2.9 + - + -
757B VAL* 3.3 24.2 - - + +
759B VAL* 4.6 8.7 - - + -
781B VAL* 5.0 1.1 - - + +
782B VAL* 3.9 52.0 - - + +
785B ILE* 4.4 10.8 - - + -
786B ALA* 4.7 1.1 - - + +
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Residues in contact with SER 728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B K 2.8 23.7 - - - -
705B ASP* 3.5 4.3 - - - -
710B HIS* 3.7 4.2 - - - -
726B TYR* 3.5 31.8 + - - -
727B ILE* 1.3 75.0 - - - +
729B LEU* 1.3 57.2 + - - +
730B HIS* 3.0 20.0 - - - -
757B VAL 2.9 6.9 + - - -
758B ASN* 3.6 8.4 - - - -
759B VAL* 2.7 33.5 + - - +
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Residues in contact with LEU 729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B K 2.8 18.7 - - - -
704B VAL* 4.5 13.0 - - + -
705B ASP 3.1 15.2 + - - +
706B TRP* 4.3 10.5 - - + +
707B ASP 3.0 9.0 - - - +
708B VAL* 4.7 0.3 - - - -
727B ILE* 4.7 3.4 - - + +
728B SER* 1.3 74.1 - - - +
730B HIS* 1.3 61.4 + - - +
759B VAL* 3.5 16.8 - - + +
761B TRP* 4.2 11.2 - - + +
774B TYR* 4.1 35.2 + - + -
777B ALA* 3.4 33.2 - - + -
778B PHE* 4.5 13.7 - - + -
782B VAL* 4.2 20.9 - - + -
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Residues in contact with HIS 730 (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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201B K 3.8 0.7 - - - -
708B VAL* 3.2 17.7 - - - +
709B HIS 3.7 2.5 - - - -
710B HIS* 3.4 34.3 - + + +
728B SER* 3.0 29.8 - - - -
729B LEU* 1.3 74.3 - - - +
731B ARG* 1.3 73.9 + - - +
732B HIS* 3.5 18.1 - + - -
741B SER 3.8 8.0 + - - -
742B GLY 3.0 27.7 + - - -
758B ASN* 3.6 8.3 + - - +
759B VAL 3.2 6.6 + - - +
760B ALA* 3.9 9.7 - - + +
761B TRP* 3.0 31.9 + - - -
774B TYR* 5.0 1.1 - - - -
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Residues in contact with ARG 731 (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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708B VAL* 3.0 15.4 + - + +
710B HIS 5.3 0.7 + - - -
730B HIS* 1.3 77.0 + - - +
732B HIS* 1.3 58.2 + - - +
733B ASP* 2.7 32.8 + - - +
736B ASN 5.8 1.2 + - - -
737B PHE* 3.3 57.9 - - + +
738B PHE 5.1 1.0 - - - +
761B TRP* 4.0 3.9 - - - -
764B GLY* 5.4 0.4 - - - -
765B LEU* 3.1 31.8 - - - +
808B ALA* 2.9 29.1 + - - +
811B GLY 2.9 24.0 + - - -
813B TYR* 3.3 28.7 - - + +
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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