Contacts of the helix formed by residues 732 - 737 (chain N) in PDB entry 4G7Z
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 VAL 732 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639N LEU* 3.8 25.4 - - + -
714N GLN* 3.4 26.9 - - - +
716N PHE* 3.6 29.8 - - + -
728N LEU* 3.6 15.7 - - + -
729N HIS* 3.1 17.5 - - + +
731N LEU* 1.3 73.0 - - - +
733N CYS* 1.3 64.9 + - - +
734N GLU 3.1 3.7 + - - -
735N ALA* 3.2 15.5 + - - +
736N PHE* 3.1 24.5 + - + -
765N SER* 4.1 3.6 - - - +
779N ALA* 5.6 4.5 - - + -
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Residues in contact with CYS 733 (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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684M PHE* 4.1 13.0 - - + -
685M GLU* 5.4 2.0 - - + -
728N LEU* 3.7 22.0 - - - -
729N HIS 3.7 10.1 - - - -
730N PRO* 3.2 19.5 - - - +
731N LEU 3.1 0.4 - - - -
732N VAL* 1.3 79.6 - - - +
734N GLU* 1.3 60.3 + - - +
736N PHE 3.7 0.2 + - - -
737N ASN* 3.2 1.9 + - - -
738N ALA* 2.8 46.7 + - - +
740N PHE* 3.6 32.5 - - - -
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Residues in contact with GLU 734 (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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730N PRO 4.6 0.4 + - - -
731N LEU 3.8 10.1 + - - +
732N VAL 3.1 0.4 - - - -
733N CYS* 1.3 77.6 - - - +
735N ALA* 1.3 65.6 + - - +
737N ASN* 3.0 17.9 + - - +
777N PRO 5.2 0.2 - - - +
778N LEU* 3.2 32.7 - - + +
780N LYS* 3.2 44.0 + - - +
782N SER* 4.6 15.3 + - - +
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Residues in contact with ALA 735 (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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709N HIS* 2.9 27.6 + - - -
711N LEU* 4.2 8.5 - - + +
714N GLN* 3.7 21.1 - - - +
731N LEU 4.7 0.8 + - - +
732N VAL* 3.2 12.5 + - - +
734N GLU* 1.3 80.5 - - - +
736N PHE* 1.3 61.1 + - - +
737N ASN* 3.2 2.3 + - - +
778N LEU* 4.1 35.1 + - + +
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Residues in contact with PHE 736 (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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702N LEU* 3.4 15.3 - - + -
704N ARG* 3.2 25.6 + - + +
706N PRO 4.9 4.9 - - - +
711N LEU 3.6 4.3 - - - -
712N GLY* 3.1 41.7 - - - -
714N GLN* 3.5 46.0 - - + -
716N PHE* 4.2 8.5 - + - -
728N LEU* 4.6 2.2 - - + -
732N VAL* 3.1 40.3 + - + +
735N ALA* 1.3 77.6 - - - +
737N ASN* 1.3 67.7 + - - +
738N ALA* 4.0 9.2 - - + +
745N MET* 3.5 35.4 - - + -
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Residues in contact with ASN 737 (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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704N ARG* 2.9 26.8 + - - +
708N LEU* 6.1 5.6 - - + -
733N CYS 3.2 4.2 + - - -
734N GLU* 3.0 12.1 + - - +
735N ALA 3.0 6.7 - - - +
736N PHE* 1.3 79.7 - - - +
738N ALA* 1.3 60.1 + - - +
739N ASP* 4.1 4.3 + - - +
743N ASP* 4.3 0.5 - - - +
1231N GLU* 6.2 0.4 - - - +
1235N GLN* 6.0 1.8 - - - +
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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