Contacts of the helix formed by residues 729 - 733 (chain M) in PDB entry 6M6A
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 729 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657M VAL* 5.6 1.0 - - - +
659M ASP* 3.0 37.7 - - - +
660M ARG* 2.6 43.9 - - + +
727M ILE* 4.2 2.7 - - - +
728M GLU* 1.3 120.3 + - - +
730M ALA* 1.3 53.2 + - - -
731M ASP* 2.6 43.9 + - - -
732M ARG* 3.1 29.8 + - + +
733M LEU* 3.3 14.9 - - - +
757M PHE 4.3 5.1 + - - -
758M HIS* 4.7 1.6 - - - +
759M PRO* 4.4 5.3 - - - +
760M PRO* 3.9 30.3 - - - +
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Residues in contact with ALA 730 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727M ILE* 3.7 18.2 - - + +
729M ARG* 1.3 73.9 - - - +
731M ASP* 1.3 64.6 + - - +
732M ARG 3.2 0.2 - - - -
733M LEU* 3.5 23.7 + - + +
738M LEU* 4.3 16.0 - - + +
756M LEU* 4.9 4.0 - - + -
758M HIS* 3.0 25.1 + - + +
769M ARG* 3.1 14.2 + - - -
770M LEU* 3.4 16.3 - - + +
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Residues in contact with ASP 731 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729M ARG* 2.6 44.9 + - - -
730M ALA* 1.3 74.1 + - - +
732M ARG* 1.3 76.7 + - - +
733M LEU 3.2 1.1 + - - -
758M HIS* 3.5 15.1 + - + -
760M PRO* 4.6 7.1 - - - +
763M THR* 4.3 24.4 - - + +
766M ALA* 4.1 7.2 - - + +
767M GLU* 5.4 0.9 - - - +
769M ARG* 2.9 21.9 + - - +
770M LEU* 4.0 9.8 - - + +
14N C 3.3 14.9 - - - +
15N T 5.7 0.8 + - - +
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Residues in contact with ARG 732 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659M ASP* 4.2 8.2 - - - +
660M ARG* 5.9 3.2 - - - +
729M ARG* 3.1 22.8 + - + +
731M ASP* 1.3 100.7 + - - +
733M LEU* 1.3 69.2 + - - +
13N G 4.7 9.1 + - - +
14N C 3.3 45.0 + - - +
15N T 3.4 49.6 + - - -
26T G 4.2 4.2 - - - +
27T C 5.9 0.2 + - - -
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Residues in contact with LEU 733 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657M VAL* 6.2 1.1 - - + -
659M ASP* 3.6 20.4 - - + +
727M ILE* 4.6 10.3 - - + -
729M ARG 3.3 13.5 - - - +
730M ALA* 3.6 23.6 - - + +
731M ASP 3.2 4.4 + - - -
732M ARG* 1.3 83.8 - - - +
734M GLY* 1.3 59.9 + - - +
737M THR* 4.2 9.2 - - + +
738M LEU* 3.7 20.0 - - + -
741M LEU* 4.9 9.4 - - + -
769M ARG* 3.3 15.1 + - - -
13N G 2.9 30.0 - - - +
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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