Contacts of the helix formed by residues 741 - 745 (chain N) in PDB entry 1CZA
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 741 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487N VAL* 4.8 1.1 - - + -
491N MET* 3.5 19.7 - - + -
709N TRP* 3.2 37.9 - + - -
710N GLY 3.2 5.5 + - - +
712N PHE* 3.2 45.0 + + + +
718N LEU* 3.8 15.9 - - + +
740N ARG* 1.3 75.6 - - - +
742N GLU* 1.3 66.0 + - - +
744N MET* 3.0 20.0 + - - +
745N ILE* 3.4 35.0 + - + +
833N LEU* 2.7 45.6 + - + -
834N CYS* 3.7 4.7 + - - -
837N GLY* 3.4 18.5 + - - -
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Residues in contact with GLU 742 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620N THR* 4.5 1.9 - - - -
621N LYS* 4.4 7.1 + - - +
681N GLY* 3.1 10.3 - - - -
682N SER* 2.8 25.4 + - - +
710N GLY* 3.3 18.1 + - - -
739N GLN* 3.0 34.2 + - - +
741N TYR* 1.3 76.8 - - - +
743N LYS* 1.4 58.2 + - - +
745N ILE* 3.0 8.2 + - - -
746N SER* 2.8 48.4 + - - +
749N TYR* 3.9 15.4 + - + -
920N GLC 2.4 32.0 + - - -
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Residues in contact with LYS 743 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722N ARG* 5.9 1.8 - - - +
726N ASP* 4.7 1.8 - - - +
729N VAL* 4.9 7.6 - - + +
730N ASP* 2.7 36.9 + - + +
733N SER* 2.9 26.9 + - - -
735N ASN* 2.9 27.7 + - - +
738N LYS 2.7 28.5 + - - +
739N GLN* 3.0 13.6 + - + +
740N ARG* 3.6 10.8 - - - +
741N TYR 3.1 0.6 - - - -
742N GLU* 1.4 76.0 - - - +
744N MET* 1.3 59.4 + - + +
745N ILE 3.4 0.2 - - - -
749N TYR* 3.4 54.1 - - + +
753N ILE* 3.7 13.5 - - - +
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Residues in contact with MET 744 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718N LEU* 4.5 18.2 - - - -
721N ILE* 3.9 15.7 - - + +
722N ARG* 3.8 32.8 - - + +
726N ASP* 3.8 19.5 - - + +
740N ARG 3.5 14.6 - - - +
741N TYR* 3.0 10.8 + - + +
743N LYS* 1.3 78.2 - - - +
745N ILE* 1.3 59.0 + - - +
750N LEU* 3.6 9.1 - - - +
753N ILE* 4.4 1.1 - - - -
826N VAL 4.9 0.5 - - - +
829N ARG* 3.3 41.8 + - - +
830N ALA* 3.5 21.0 + - - +
833N LEU* 3.8 24.4 - - + +
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Residues in contact with ILE 745 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678N VAL* 4.1 13.9 - - + -
682N SER* 3.8 29.2 - - - +
709N TRP* 4.8 0.2 - - - +
741N TYR* 3.5 55.2 - - + +
742N GLU 3.0 2.0 + - - +
743N LYS 3.4 0.6 + - - -
744N MET* 1.3 84.1 - - + +
746N SER* 1.3 64.5 + - - +
750N LEU* 3.5 11.7 - - - +
830N ALA* 3.8 25.0 - - - +
833N LEU* 4.2 7.4 - - + -
834N CYS* 3.9 16.6 - - + +
864N LEU* 3.3 18.5 - - - +
871N PHE* 4.3 6.6 - - + -
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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