Contacts of the helix formed by residues 693 - 701 (chain A) in PDB entry 3H0G
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 ARG 693 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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689A VAL* 3.5 3.6 + - - +
690A LYS* 3.4 28.7 - - + +
692A ALA* 1.3 75.0 - - - +
694A ARG* 1.3 51.4 + - - +
695A GLN 2.9 3.6 - - - -
696A VAL* 2.5 32.3 + - - +
697A ALA* 2.8 15.5 + - - -
800A PRO* 5.4 11.7 - - - +
801A GLU* 3.2 53.7 + - - +
805A PHE* 5.6 4.9 - - - -
807A GLU* 2.8 36.7 + - - +
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Residues in contact with ARG 694 (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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690A LYS 4.1 4.2 + - - +
691A GLU* 4.5 18.3 - - - +
693A ARG* 1.3 78.2 - - - +
695A GLN* 1.3 59.8 + - + +
696A VAL 3.2 0.2 - - - -
697A ALA* 3.7 11.3 - - + +
698A GLU* 3.2 30.9 + - + +
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Residues in contact with GLN 695 (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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691A GLU* 3.6 27.7 + - - +
692A ALA* 3.5 23.3 + - - +
693A ARG 2.8 1.2 + - - -
694A ARG* 1.3 79.7 - - + +
696A VAL* 1.3 60.4 + - - +
698A GLU* 3.5 28.7 - - - +
699A CYS* 3.7 13.5 - - - -
727A ILE* 4.2 24.1 - - + +
731A ALA* 4.9 4.0 - - - +
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Residues in contact with VAL 696 (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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692A ALA 3.5 8.7 - - - +
693A ARG* 2.5 17.0 + - - +
695A GLN* 1.3 70.8 - - - +
697A ALA* 1.3 54.4 + - - +
698A GLU 3.0 1.6 - - - -
699A CYS* 2.5 28.4 + - + -
700A ILE* 2.6 44.5 + - + +
724A VAL* 4.1 13.2 - - + -
727A ILE* 3.1 28.5 - - + -
728A LEU* 4.3 1.8 - - + -
798A ASP 4.6 1.3 - - - +
799A SER* 5.1 0.7 - - - -
800A PRO* 4.0 35.0 - - + -
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Residues in contact with ALA 697 (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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693A ARG 2.8 10.6 + - - +
694A ARG* 3.7 15.7 - - + +
696A VAL* 1.3 76.5 - - - +
698A GLU* 1.3 57.1 + - - +
699A CYS 2.9 5.7 + - - -
700A ILE* 3.4 17.8 - - + +
701A GLN* 3.4 24.6 + - - +
702A ASP 4.4 0.2 + - - -
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Residues in contact with GLU 698 (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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694A ARG* 3.2 17.1 + - + +
695A GLN* 3.5 30.8 - - - +
696A VAL 3.0 1.4 - - - -
697A ALA* 1.3 76.9 - - - +
699A CYS* 1.3 62.9 + - - +
702A ASP* 3.5 24.3 - - + +
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Residues in contact with CYS 699 (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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695A GLN 3.7 15.9 - - - +
696A VAL* 2.5 19.9 + - + +
697A ALA 2.9 0.6 + - - -
698A GLU* 1.3 84.2 - - - +
700A ILE* 1.3 65.8 + - - +
701A GLN 3.2 1.6 - - - -
702A ASP* 3.9 3.4 - - - +
703A ALA* 3.3 27.6 + - - +
708A LEU* 6.1 4.9 - - + -
720A PHE* 3.6 19.7 - - + -
723A LYS* 5.0 21.8 - - - -
724A VAL* 5.1 5.6 - - + -
727A ILE* 5.9 2.9 - - + -
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Residues in contact with ILE 700 (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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696A VAL* 2.6 37.2 + - + +
697A ALA* 3.4 20.6 - - + +
699A CYS* 1.3 72.9 - - - +
701A GLN* 1.3 64.3 + - + +
703A ALA 4.7 0.7 - - - -
704A GLN* 3.3 28.9 + - - +
720A PHE* 4.4 11.7 - - + -
798A ASP* 3.5 32.5 - - + +
799A SER* 4.8 10.3 - - - -
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Residues in contact with GLN 701 (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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697A ALA 3.4 11.5 + - - +
700A ILE* 1.3 82.6 - - + +
702A ASP* 1.3 62.2 - - - +
703A ALA 3.2 2.5 - - - -
704A GLN* 3.3 21.0 + - - +
705A HIS* 2.8 43.4 + - + +
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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