Contacts of the helix formed by residues 734 - 743 (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 GLY 734 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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733M LEU* 1.3 78.8 - - - +
735M LEU* 1.3 65.3 + - - -
736M ALA* 3.4 2.2 - - - -
737M THR* 2.4 40.9 + - - +
738M LEU* 3.2 7.4 - - - +
769M ARG* 5.3 0.2 - - - -
790M MET* 6.6 0.2 - - - -
13N G 3.9 20.0 - - - -
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Residues in contact with LEU 735 (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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734M GLY* 1.3 71.0 - - - -
736M ALA* 1.3 65.5 + - - +
737M THR 3.3 0.2 - - - -
738M LEU* 3.0 9.0 + - - +
739M TYR* 3.0 39.6 + - + -
769M ARG* 3.6 41.1 - - + +
772M ALA* 5.5 2.7 - - + +
773M ILE* 3.7 30.5 - - + -
786M ALA* 4.1 22.0 - - + +
787M GLU* 5.1 4.5 - - + +
790M MET* 3.7 34.9 - - + +
793M ARG* 5.9 1.6 - - - +
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Residues in contact with ALA 736 (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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574M HIS* 3.6 33.0 - - + +
599M THR* 3.9 18.4 - - + -
734M GLY 3.4 1.0 - - - -
735M LEU* 1.3 76.8 - - - +
737M THR* 1.3 59.3 + - + +
739M TYR* 3.6 15.0 + - - +
740M GLN* 2.9 38.1 + - + +
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Residues in contact with THR 737 (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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574M HIS* 6.1 2.0 - - + -
712M ILE* 3.8 29.6 - - + +
733M LEU* 4.2 10.6 - - + +
734M GLY* 2.4 36.0 + - - +
736M ALA* 1.3 76.8 - - + +
738M LEU* 1.3 62.9 + - - +
740M GLN* 3.6 4.0 - - - +
741M LEU* 2.8 37.7 + - - +
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Residues in contact with LEU 738 (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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727M ILE* 5.5 4.5 - - + -
730M ALA* 4.3 23.6 - - + +
733M LEU* 3.7 27.1 - - + -
734M GLY 3.2 23.1 + - - +
735M LEU* 3.0 13.3 + - - +
737M THR* 1.3 85.8 + - - +
739M TYR* 1.3 59.7 + - + +
741M LEU* 3.1 17.8 + - + +
742M ARG* 3.0 23.1 + - - +
756M LEU* 4.7 12.6 - - + -
769M ARG* 5.9 0.4 - - - +
770M LEU* 5.5 0.9 - - + -
773M ILE* 3.9 39.9 - - + -
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Residues in contact with TYR 739 (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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599M THR* 3.2 13.3 - - + +
735M LEU* 3.0 43.4 + - + -
736M ALA* 4.0 13.1 - - - -
738M LEU* 1.3 75.5 - - + +
740M GLN* 1.3 78.2 + - - +
742M ARG* 3.5 24.3 - - + +
743M GLY* 2.8 23.4 + - - -
773M ILE* 5.9 1.5 - - + +
776M LEU* 6.0 8.7 - - + -
779M LEU* 5.2 14.4 - - + -
782M GLY 5.8 1.3 - - - -
783M HIS* 3.2 34.1 + + + -
786M ALA* 5.9 3.8 - - + -
787M GLU* 2.4 36.3 + - + +
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Residues in contact with GLN 740 (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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471M ASP* 6.1 0.7 - - - +
575M ARG* 5.1 12.3 - - - +
712M ILE* 3.6 18.6 - - + -
736M ALA* 2.9 25.5 + - + +
737M THR* 3.6 6.3 - - - +
739M TYR* 1.3 99.4 + - + +
741M LEU* 1.3 62.2 + - - +
743M GLY* 3.4 6.8 + - - +
744M ARG* 2.9 41.2 + - - +
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Residues in contact with LEU 741 (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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655M PHE* 6.1 0.7 - - + -
657M VAL* 4.6 19.3 - - + -
712M ILE* 3.8 28.7 - - + +
715M ALA* 4.5 11.9 - - + -
725M ILE* 3.8 26.7 - - + +
727M ILE* 4.8 15.5 - - + -
733M LEU* 4.9 11.0 - - + -
737M THR* 2.8 28.5 + - - +
738M LEU* 3.1 19.3 + - + +
740M GLN* 1.3 77.2 - - - +
742M ARG* 1.3 62.1 + - - +
744M ARG* 3.0 12.9 + - + +
745M VAL* 3.1 18.6 + - - +
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Residues in contact with ARG 742 (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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627M PRO* 5.3 1.0 - - - +
628M ILE* 3.4 38.7 + - + +
630M THR* 3.5 26.7 - - + +
725M ILE* 5.8 0.7 - - - -
738M LEU 3.0 7.8 + - - +
739M TYR* 3.5 27.8 - - - +
740M GLN 3.3 0.4 - - - -
741M LEU* 1.3 77.2 - - - +
743M GLY* 1.3 57.6 + - - +
745M VAL* 3.3 23.2 - - + +
748M ARG* 5.6 0.2 + - - -
773M ILE* 2.9 42.8 + - - +
774M ALA* 4.2 4.6 - - - +
776M LEU* 2.8 31.3 + - - +
777M SER* 3.4 16.6 + - - +
778M ASP* 5.6 2.5 - - - +
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Residues in contact with GLY 743 (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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625M ARG* 5.5 4.7 + - - -
718M ASP* 2.9 13.9 - - - +
739M TYR 2.8 16.7 + - - -
740M GLN* 3.4 9.9 - - - -
741M LEU 3.2 0.2 - - - -
742M ARG* 1.3 74.8 - - - +
744M ARG* 1.3 65.2 + - - +
745M VAL 3.6 0.7 - - - -
748M ARG* 5.7 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