Contacts of the helix formed by residues 725 - 730 (chain A) in PDB entry 5A7R
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 THR 725 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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724A GLY* 1.3 78.4 - - - +
726A ILE* 1.3 60.2 + - - +
727A GLU* 3.3 18.9 + - - +
728A GLU* 3.1 26.2 + - - +
729A ASN* 2.9 34.8 + - - +
900A PHE* 3.8 9.3 - - - -
902A PHE* 4.1 6.7 - - + -
1964A AR6 3.7 16.6 - - - +
1988A PPI 4.0 3.4 - - - +
1990A PPI 3.7 37.4 - - + +
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Residues in contact with ILE 726 (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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725A THR* 1.3 74.7 - - - +
727A GLU* 1.3 61.4 + - - +
730A GLY* 3.1 26.7 + - - -
735A GLN* 3.6 34.2 + - + -
736A VAL 4.0 10.5 - - - +
738A PHE* 3.8 24.9 - - + -
754A GLN* 3.8 13.7 - - - +
758A ARG* 4.4 5.4 - - - +
866A ALA* 3.8 13.0 - - + +
867A THR* 3.8 28.0 - - - +
900A PHE* 3.9 11.4 - - + -
1964A AR6 3.3 28.6 + - + +
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Residues in contact with GLU 727 (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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725A THR* 3.3 16.3 + - - +
726A ILE* 1.3 77.1 - - - +
728A GLU* 1.3 60.0 + - + +
730A GLY 4.6 0.6 + - - -
731A GLN* 5.5 1.2 + - - +
735A GLN* 4.5 1.5 + - - -
757A ILE* 6.2 0.2 - - - -
758A ARG* 3.5 40.2 - - - +
761A ILE* 4.3 17.3 - - + -
788A GLN* 4.6 11.5 - - - +
792A TYR* 2.7 35.6 + - + -
1964A AR6 2.9 24.5 + - - -
1974A GOL 3.5 25.0 + - - -
1990A PPI 4.8 0.5 - - - +
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Residues in contact with GLU 728 (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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725A THR* 3.1 17.9 + - - +
727A GLU* 1.3 81.4 - - + +
729A ASN* 1.3 76.2 + - - +
730A GLY 3.6 0.9 - - - -
731A GLN* 3.3 24.8 + - - +
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Residues in contact with ASN 729 (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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458A ILE* 4.1 14.7 - - + +
463A ARG* 4.0 6.8 + - - -
724A GLY* 3.1 15.4 - - - -
725A THR 2.9 34.2 + - - +
728A GLU* 1.3 95.3 + - - +
730A GLY* 1.3 56.5 + - - +
731A GLN* 3.1 15.1 - - - +
733A MET* 4.7 1.0 - - - +
900A PHE* 3.6 25.1 - - + -
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Residues in contact with GLY 730 (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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463A ARG* 4.1 0.7 - - - -
726A ILE 3.1 18.5 + - - -
727A GLU 4.6 0.4 - - - -
728A GLU 3.6 0.6 - - - -
729A ASN* 1.3 77.4 - - - +
731A GLN* 1.4 65.7 + - - +
733A MET* 3.0 23.8 + - - +
735A GLN* 3.0 20.8 + - - -
866A ALA* 4.1 18.2 - - - -
900A PHE* 5.0 0.9 - - - -
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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