Contacts of the strand formed by residues 701 - 705 (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 ILE 701 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689B CYS* 3.8 33.7 - - - +
692B LEU* 3.8 39.7 - - + -
693B GLN* 4.0 16.4 - - + +
699B SER* 4.1 7.2 + - - +
700B LYS* 1.3 79.0 - - - +
702B LEU* 1.3 71.6 - - - +
703B ILE* 4.5 1.6 - - + -
723B SER 3.0 7.3 + - - -
724B VAL* 3.3 7.2 - - + +
725B LEU 2.9 23.7 + - - -
789B PHE* 3.9 3.8 - - - -
792B ASP* 5.6 0.7 - - + -
793B LEU* 3.5 20.6 - - + +
795B LEU* 4.1 16.6 - - + -
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Residues in contact with LEU 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701B ILE* 1.3 74.6 - - - +
703B ILE* 1.3 63.5 + - - +
704B VAL* 3.7 24.0 - - + -
725B LEU* 3.4 43.3 - - + +
727B ILE* 3.9 16.6 - - + -
786B ALA* 3.7 26.9 - - + -
789B PHE* 4.6 2.9 - - + -
791B PRO* 3.8 19.5 - - + +
793B LEU 3.1 8.3 + - - +
794B VAL* 3.4 9.2 - - + -
795B LEU 2.8 27.0 + - - +
827B LEU* 4.8 0.4 - - + -
830B LEU* 3.8 16.4 - - + -
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Residues in contact with ILE 703 (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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685B VAL* 4.0 20.6 - - + +
686B ALA* 4.9 0.2 - - - -
689B CYS* 4.3 10.8 - - + -
701B ILE* 4.5 2.7 - - + -
702B LEU* 1.3 76.2 - - - +
704B VAL* 1.3 67.7 + - - +
714B THR* 3.6 15.0 - - + -
718B PHE* 3.6 33.7 - - + -
724B VAL* 4.0 13.9 - - + -
725B LEU 2.7 11.6 + - - +
726B TYR* 3.4 25.4 - - + -
727B ILE 2.8 27.7 + - - +
795B LEU* 3.2 20.6 - - + +
797B SER* 4.8 5.6 - - - +
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Residues in contact with VAL 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B LEU* 3.7 33.4 - - + -
703B ILE* 1.3 73.1 - - - +
705B ASP* 1.3 65.6 + - - +
706B TRP* 4.6 11.4 - - + -
727B ILE* 3.3 10.1 - - + +
729B LEU* 4.5 16.4 - - + -
778B PHE* 4.7 2.9 - - + -
782B VAL* 4.6 15.7 - - + -
794B VAL* 4.2 5.4 - - + -
795B LEU 2.9 8.6 + - - +
796B VAL* 3.1 8.6 - - + +
797B SER 2.8 23.9 + - - -
827B LEU* 4.0 31.2 - - + -
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Residues in contact with ASP 705 (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 2.9 30.9 - - - -
669B HIS* 2.7 24.8 + - - +
703B ILE* 5.0 0.2 - - + -
704B VAL* 1.3 74.3 - - - +
706B TRP* 1.3 56.8 + - - +
707B ASP* 3.2 21.3 + - - +
711B GLY* 3.5 2.8 - - - -
726B TYR* 2.7 39.5 + - + +
727B ILE 2.8 10.7 + - - +
728B SER* 4.2 0.7 - - - +
729B LEU* 3.1 17.7 + - - +
797B SER* 3.4 21.6 + - - -
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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