Contacts of the helix formed by residues 673 - 682 (chain A) in PDB entry 2ZNT
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 GLY 673 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A DYH 3.4 24.9 - - - -
474A TYR* 5.1 5.2 - - - -
475A GLY 5.6 0.4 - - - -
508A ARG* 4.8 3.4 - - - -
670A VAL* 3.7 5.8 + - - -
671A ARG 3.3 5.8 + - - -
672A ASP* 1.3 77.1 - - - +
674A SER* 1.3 60.3 + - - -
675A THR 3.2 3.1 - - - -
676A MET* 3.2 2.1 + - - +
677A THR* 2.9 32.2 + - - -
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Residues in contact with SER 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A DYH 2.8 38.5 + - - -
503A THR* 3.3 22.5 + - - +
505A THR* 4.1 18.8 - - - -
508A ARG* 4.2 6.2 - - - +
673A GLY* 1.3 68.6 - - - -
675A THR* 1.3 61.2 + - - +
677A THR* 3.8 7.5 - - - -
678A PHE* 2.9 29.3 + - - +
723A GLU* 3.3 5.5 + - - -
747A LYS* 4.3 8.2 + - - -
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Residues in contact with THR 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A DYH 2.6 32.6 + - - -
523A ILE* 3.7 32.3 - - + +
669A ALA* 4.1 7.2 - - + -
670A VAL 5.6 1.6 - - - -
674A SER* 1.3 76.1 + - - +
676A MET* 1.3 65.8 + - - +
678A PHE* 3.2 10.7 + - - +
679A PHE* 3.3 21.4 - - + -
721A LEU* 3.6 42.0 - - + +
722A MET 4.3 0.2 - - - +
723A GLU* 3.7 9.7 + - - +
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Residues in contact with MET 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A ALA* 4.2 9.9 - - + +
670A VAL 3.5 18.2 + - - +
671A ARG* 3.9 9.2 - - - +
672A ASP* 3.3 39.7 - - - +
673A GLY 3.2 6.8 + - - +
675A THR* 1.3 77.6 - - - +
677A THR* 1.3 72.2 + - - +
679A PHE* 3.1 8.4 + - - +
680A LYS* 3.0 31.1 + - + +
691A TRP* 3.6 27.9 - - + -
694A MET* 5.2 0.7 - - - -
702A LEU* 3.8 36.6 - - + -
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Residues in contact with THR 677 (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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476A ALA* 5.1 7.1 - - - +
507A VAL* 5.3 13.2 - - + -
672A ASP 4.7 3.3 + - - -
673A GLY 2.9 18.6 + - - -
674A SER* 3.8 8.7 - - - -
676A MET* 1.3 84.2 - - - +
678A PHE* 1.3 65.3 + - - +
680A LYS* 3.2 9.3 + - + +
681A LYS* 2.9 45.2 + - + +
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Residues in contact with PHE 678 (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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523A ILE* 3.6 17.7 - - + -
674A SER 2.9 14.4 + - - +
675A THR 3.4 9.2 - - - +
676A MET 3.2 0.2 - - - -
677A THR* 1.3 76.2 - - - +
679A PHE* 1.3 75.3 + + - +
681A LYS* 3.8 3.6 - - - +
682A SER* 3.0 26.1 + - - -
684A ILE* 6.1 1.1 - - + -
687A TYR* 3.7 31.9 - + + -
744A ILE* 3.5 33.4 - - + -
745A ASP* 3.7 28.7 - - + +
747A LYS* 4.9 1.8 - - - +
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Residues in contact with PHE 679 (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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523A ILE* 4.2 8.7 - - + -
669A ALA* 5.4 0.4 - - + -
675A THR* 3.3 23.6 - - + -
676A MET* 3.1 8.4 + - - +
678A PHE* 1.3 88.1 - + - +
680A LYS* 1.3 66.5 + - - +
681A LYS 3.2 0.9 + - - -
682A SER* 3.3 16.1 + - - +
687A TYR* 3.8 42.1 - + + +
688A GLU* 5.1 1.0 + - - -
690A MET* 3.7 20.9 - - + -
691A TRP* 3.4 30.6 - - + +
694A MET* 4.0 19.7 - - + -
721A LEU* 3.6 42.6 - - + -
744A ILE* 4.4 10.8 - - + -
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Residues in contact with LYS 680 (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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477A GLN 5.5 4.6 + - - -
479A ASP* 4.8 11.1 + - - -
676A MET* 3.0 24.2 + - + +
677A THR* 3.6 12.1 - - + +
679A PHE* 1.3 76.7 - - - +
681A LYS* 1.3 86.8 + - + +
682A SER 3.8 2.1 + - - +
691A TRP* 3.6 48.8 - - + +
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Residues in contact with LYS 681 (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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507A VAL* 6.5 0.7 - - + -
677A THR* 2.9 35.5 + - + +
678A PHE* 3.8 2.5 - - - +
680A LYS* 1.3 105.2 - - - +
682A SER* 1.3 65.9 + - - +
683A LYS* 3.6 15.2 + - - +
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Residues in contact with SER 682 (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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678A PHE* 3.0 21.6 + - - -
679A PHE 3.3 9.9 + - - +
680A LYS 4.6 2.3 - - - +
681A LYS* 1.3 80.4 - - - +
683A LYS* 1.3 66.7 + - - +
684A ILE* 3.1 20.4 + - - +
687A TYR* 3.3 36.7 - - - +
688A GLU* 3.3 17.0 - - - +
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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