Contacts of the strand formed by residues 724 - 731 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C K 2.9 20.8 - - - -
689C CYS* 3.7 20.0 - - - -
693C GLN* 3.3 27.8 - - - +
701C ILE* 3.3 9.0 - - + +
703C ILE* 4.4 8.3 - - + -
718C PHE* 3.6 49.4 - - + -
721C ASP* 3.2 13.8 + - + +
723C SER* 1.3 79.8 + - - +
725C LEU* 1.3 68.7 + - - +
726C TYR* 4.7 1.8 - - + +
755C PHE* 3.5 8.0 - - - +
789C PHE* 4.3 1.6 - - - -
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Residues in contact with LEU 725 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701C ILE 2.9 9.4 + - - +
702C LEU* 3.5 19.9 - - + +
703C ILE* 2.8 32.6 + - - +
724C VAL* 1.3 73.6 - - - +
726C TYR* 1.3 58.7 + - - +
727C ILE* 4.0 15.5 - - + -
755C PHE* 3.5 30.3 - - + +
756C ASN 4.5 0.2 - - - +
757C VAL* 4.5 4.5 - - + -
785C ILE* 3.8 20.4 - - + +
786C ALA* 4.3 3.8 - - - -
789C PHE* 3.6 51.1 - - + -
895C TRP* 4.0 13.0 - - + -
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Residues in contact with TYR 726 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C K 4.0 6.6 - - - -
703C ILE* 3.6 17.3 - - + -
705C ASP* 2.7 41.4 + - + +
710C HIS* 4.1 6.5 - - - -
711C GLY* 3.3 24.3 + - - -
714C THR* 3.4 31.8 - - + +
715C GLN* 4.1 20.2 - - + -
718C PHE* 5.8 1.8 - - + -
724C VAL* 5.3 3.6 - - + -
725C LEU* 1.3 72.9 - - - +
727C ILE* 1.3 57.7 + - - +
728C SER* 3.5 24.8 - - - -
755C PHE 3.2 7.3 + - - -
756C ASN* 3.4 29.6 - - - +
757C VAL 2.7 32.7 + - - +
758C ASN* 4.2 3.8 - - - -
797C SER* 5.9 0.2 - - - -
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Residues in contact with ILE 727 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702C LEU* 4.0 11.2 - - + -
703C ILE 2.9 9.0 + - - +
704C VAL* 3.4 7.7 - - - +
705C ASP 2.9 24.8 + - - +
725C LEU* 4.0 30.3 - - + -
726C TYR* 1.3 77.7 - - - +
728C SER* 1.3 62.9 + - - +
729C LEU* 4.3 3.5 + - + +
757C VAL* 3.2 24.0 - - + +
759C VAL* 4.6 7.0 - - + -
782C VAL* 3.7 59.0 - - + +
785C ILE* 4.2 10.5 - - + -
786C ALA* 4.6 1.6 - - + +
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Residues in contact with SER 728 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C K 2.7 23.6 - - - -
705C ASP 3.5 4.5 - - - -
710C HIS* 3.8 3.6 - - - -
726C TYR* 3.5 33.1 + - - -
727C ILE* 1.3 74.8 - - - +
729C LEU* 1.3 56.7 + - - +
730C HIS* 3.3 15.7 - - - -
757C VAL 2.9 7.1 + - - -
758C ASN* 3.5 11.0 - - - -
759C VAL* 2.6 35.9 + - - +
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Residues in contact with LEU 729 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C K 3.3 1.1 - - - -
704C VAL* 4.3 20.9 - - + -
705C ASP 3.2 12.8 + - - +
706C TRP* 4.1 11.8 - - + +
707C ASP 3.2 18.9 - - - +
727C ILE* 4.6 2.7 - - + +
728C SER* 1.3 75.9 - - - +
730C HIS* 1.3 60.1 + - - +
759C VAL* 3.5 15.9 - - + -
761C TRP* 4.2 11.9 - - + +
774C TYR* 3.9 36.8 + - + -
777C ALA* 3.7 30.1 - - + -
778C PHE* 4.2 15.0 - - + -
782C VAL* 4.4 13.9 - - + -
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Residues in contact with HIS 730 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C K 3.9 1.1 - - - -
708C VAL* 3.2 16.2 - - - +
709C HIS 3.8 14.1 - - - -
710C HIS* 3.5 21.3 - + + +
728C SER* 3.3 27.8 - - - -
729C LEU* 1.3 73.3 - - - +
731C ARG* 1.3 69.1 + - - +
732C HIS* 3.4 19.8 + + - +
741C SER 3.6 8.9 + - - -
742C GLY* 2.9 29.3 + - - -
758C ASN* 3.9 6.9 - - - +
759C VAL 3.1 6.1 + - - +
760C ALA* 3.9 9.2 - - + +
761C TRP* 2.8 40.4 + - - -
774C TYR* 5.0 0.4 - - - -
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Residues in contact with ARG 731 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708C VAL* 3.0 18.1 + - + +
709C HIS* 5.4 0.2 - - - -
710C HIS 5.5 0.2 + - - -
730C HIS* 1.3 78.4 + - - +
732C HIS* 1.3 59.2 + - - +
733C ASP* 3.0 29.2 + - - +
737C PHE* 3.2 62.1 - - + +
738C PHE 5.0 1.0 - - - +
761C TRP* 4.0 1.1 - - - -
764C GLY* 5.5 0.6 - - - -
765C LEU* 3.2 32.7 - - + +
808C ALA* 3.9 18.4 - - - +
809C PRO* 5.6 0.4 - - - +
811C GLY 2.6 38.3 + - - +
813C TYR* 3.3 30.0 + - + +
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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
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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