Contacts of the strand formed by residues 718 - 723 (chain A) in PDB entry 2ZNS
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 TYR 718 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527A TYR* 3.3 16.0 - - - -
528A ARG* 3.7 1.2 - - - +
665A ILE* 4.3 0.2 - - - -
666A GLU* 3.1 38.4 - - - -
667A TYR 3.6 16.8 - - - -
668A GLY 3.3 19.8 - - - -
669A ALA 3.6 1.2 + - - -
701A ALA* 2.7 27.4 + - - -
703A VAL* 3.7 12.9 - - + +
709A GLY* 4.1 4.7 - - - -
712A ARG* 3.6 35.2 - - + +
713A VAL* 3.6 26.3 - - + +
716A THR* 3.1 23.0 + - + -
717A ASP* 1.3 77.9 + - - +
719A ALA* 1.3 72.8 + - - +
720A LEU* 3.8 15.9 - - + +
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Residues in contact with ALA 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A ILE* 3.9 18.4 - - + -
526A LEU 3.3 11.2 - - - +
527A TYR* 3.8 15.5 - - + -
659A LEU* 3.9 25.6 - - + -
665A ILE* 4.2 0.6 - - + +
666A GLU 3.0 6.9 + - - -
667A TYR* 3.1 25.3 - - + +
668A GLY 3.2 5.7 + - - -
718A TYR* 1.3 77.8 - - - +
720A LEU* 1.3 60.7 + - - +
721A LEU* 4.4 0.4 - - - +
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Residues in contact with LEU 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A ILE* 3.4 1.8 - - - -
526A LEU* 2.7 47.2 + - + +
668A GLY 3.6 15.5 - - - +
669A ALA* 3.9 9.9 - - - -
670A VAL* 4.6 3.1 - - + +
703A VAL* 4.3 6.5 - - + -
706A SER* 4.6 7.2 - - - +
709A GLY* 4.0 31.2 - - - +
710A ILE 4.3 1.8 - - - +
713A VAL* 3.7 16.5 - - + +
718A TYR* 3.8 16.8 - - + +
719A ALA* 1.3 73.7 - - - +
721A LEU* 1.3 73.5 + - - +
722A MET* 3.5 43.2 + - + -
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Residues in contact with LEU 721 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A GLU* 4.5 2.3 - - - +
523A ILE* 4.0 6.5 - - + -
524A SER 3.4 13.9 - - - +
525A ILE* 3.9 15.3 - - + -
659A LEU* 4.7 6.7 - - + -
667A TYR* 4.3 9.4 - - + -
668A GLY 2.8 34.2 + - - +
669A ALA* 4.1 5.0 - - + +
670A VAL* 4.9 1.9 + - - +
675A THR* 3.6 28.5 - - + +
679A PHE* 3.5 33.0 - - + -
690A MET* 4.1 17.9 - - + -
694A MET* 4.3 6.7 - - + -
719A ALA 4.4 0.4 - - - +
720A LEU* 1.3 83.6 - - - +
722A MET* 1.3 59.3 + - - +
744A ILE* 4.0 6.1 - - + -
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Residues in contact with MET 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A GLU* 4.6 5.2 - - - +
523A ILE* 4.4 2.8 - - - +
524A SER 2.8 30.3 + - - +
526A LEU* 4.1 13.7 - - + -
675A THR* 4.9 0.9 - - - -
706A SER* 3.9 26.0 - - - +
710A ILE* 3.9 20.0 - - + -
720A LEU* 3.8 36.6 - - + +
721A LEU* 1.3 76.9 - - - +
723A GLU* 1.3 76.0 + - - +
726A SER* 3.9 18.6 - - - +
727A ILE* 3.4 36.4 - - + +
730A VAL* 4.4 3.1 - - + -
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Residues in contact with GLU 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A GLU* 2.8 40.1 + - + +
503A THR* 2.6 23.0 + - - +
521A LEU* 3.5 29.0 - - + +
522A GLY 3.5 5.8 - - - +
523A ILE* 4.8 5.8 - - + -
674A SER* 3.3 12.6 + - - -
675A THR* 3.9 7.6 + - - +
722A MET* 1.3 76.4 - - - +
724A SER* 1.3 58.8 + - - +
725A THR* 3.2 2.2 - - - +
726A SER* 3.0 23.3 + - - +
727A ILE* 3.0 10.0 + - - +
747A LYS* 4.2 2.8 - - - -
749A TYR* 2.6 29.9 + - - +
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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