Contacts of the helix formed by residues 708 - 712 (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 GLU 708 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509N VAL* 4.3 7.3 - - - +
510N LYS* 3.6 20.2 + - + +
512N LEU* 3.8 11.2 - - + -
605N PRO* 3.3 32.2 - - + +
683N ASN* 2.7 15.9 + - - -
706N ASN* 3.0 28.0 + - - +
707N MET* 1.3 75.3 - - - +
709N TRP* 1.3 62.7 - - - +
710N GLY 3.1 7.3 + - - -
711N ALA* 3.5 15.0 + - + +
739N GLN* 4.7 5.4 + - - +
920N GLC 2.4 48.4 + - - -
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Residues in contact with TRP 709 (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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491N MET* 3.8 20.0 - - + -
509N VAL* 4.2 11.9 - - - -
676N LEU* 3.6 28.7 - - + -
682N SER* 3.1 24.7 + - - -
683N ASN* 3.0 27.5 + - - +
684N ALA* 3.7 20.2 - - + -
707N MET* 3.9 24.2 - - + -
708N GLU* 1.3 76.3 - - - +
710N GLY* 1.4 69.2 + - - +
711N ALA 3.1 0.7 - - - -
712N PHE* 3.1 13.7 + - - +
741N TYR* 3.2 37.1 - + - -
745N ILE* 4.8 0.2 - - - +
834N CYS* 3.8 20.0 - - - -
837N GLY* 3.5 23.8 - - - -
838N MET* 3.6 22.9 - - + -
841N VAL* 4.2 4.5 - - + -
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Residues in contact with GLY 710 (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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682N SER 3.9 9.8 + - - -
683N ASN* 5.2 0.2 - - - +
708N GLU* 3.1 3.4 + - - +
709N TRP* 1.4 82.6 - - - +
711N ALA* 1.3 56.0 + - - +
739N GLN* 3.1 38.1 - - - +
741N TYR 3.2 13.5 + - - -
742N GLU* 3.3 25.1 + - - -
920N GLC 4.8 0.8 + - - -
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Residues in contact with ALA 711 (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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508N VAL* 3.4 28.4 - - + +
510N LYS* 4.7 8.3 - - - +
708N GLU 3.5 7.9 + - - +
709N TRP 3.1 0.8 - - - -
710N GLY* 1.3 74.2 - - - +
712N PHE* 1.3 66.8 + - - +
714N ASP* 2.9 44.4 + - + +
739N GLN* 3.6 16.3 + - - +
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Residues in contact with PHE 712 (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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487N VAL* 3.8 19.1 - - + -
490N ARG* 3.8 16.8 - - + -
491N MET* 3.4 56.3 - - + -
494N GLU* 3.8 14.4 - - + -
508N VAL* 4.3 1.8 - - - -
509N VAL* 3.8 18.9 - - + +
709N TRP 3.1 17.4 + - - +
711N ALA* 1.3 79.8 - - - +
713N GLY* 1.3 58.3 + - - +
714N ASP 3.4 0.2 + - - -
717N CYS* 3.5 26.9 - - - -
718N LEU* 3.8 23.6 - - + -
740N ARG* 3.9 0.3 - - - +
741N TYR* 3.2 43.5 + + + +
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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