Contacts of the helix formed by residues 763 - 775 (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 THR 763 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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731M ASP* 4.3 18.3 - - + +
760M PRO* 4.9 5.4 - - + +
761M ARG 3.6 1.8 - - - -
762M LEU* 1.3 82.6 - - - +
764M GLU* 1.3 55.2 - - - +
765M ALA* 2.8 2.4 + - - -
766M ALA* 2.6 46.9 + - + +
767M GLU* 2.9 30.4 + - + +
15N T 2.8 27.0 + - - +
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Residues in contact with GLU 764 (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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594D PRO* 2.9 58.3 - - + +
595D GLY* 4.0 1.6 + - - -
761M ARG 5.3 0.4 + - - -
762M LEU 3.8 2.1 - - - +
763M THR* 1.3 80.1 - - - +
765M ALA* 1.3 61.2 + - + +
767M GLU* 3.4 12.5 - - - +
768M LYS* 2.9 32.8 + - - +
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Residues in contact with ALA 765 (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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763M THR 2.8 5.4 + - - +
764M GLU* 1.3 83.2 + - + +
766M ALA* 1.3 56.8 + - - +
768M LYS* 3.1 30.1 + - - +
769M ARG* 2.9 27.6 + - - +
793M ARG* 5.8 2.5 - - + -
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Residues in contact with ALA 766 (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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731M ASP* 4.1 14.8 - - - +
763M THR* 2.6 33.8 + - + +
765M ALA* 1.3 72.8 - - - +
767M GLU* 1.3 57.0 + - - +
769M ARG* 3.3 33.4 - - - +
770M LEU* 2.9 34.9 + - - +
14N C 5.1 3.6 - - - -
15N T 5.1 0.2 - - - +
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Residues in contact with GLU 767 (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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731M ASP* 5.4 0.7 - - - +
758M HIS* 5.2 3.6 - - - +
760M PRO 3.4 12.5 - - - +
761M ARG* 3.3 41.6 + - - +
763M THR* 2.9 45.6 + - - +
764M GLU* 3.4 12.6 - - - +
765M ALA 3.2 0.4 - - - -
766M ALA* 1.3 76.3 - - - +
768M LYS* 1.3 58.3 + - - +
770M LEU* 3.2 15.7 + - - +
771M ALA* 3.0 24.5 + - - +
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Residues in contact with LYS 768 (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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545D ARG* 5.6 8.1 - - - +
549D ASN* 6.4 0.2 - - - +
764M GLU* 2.9 13.6 + - - +
765M ALA* 3.1 35.1 + - - +
767M GLU* 1.3 76.3 - - - +
769M ARG* 1.3 57.6 + - - +
771M ALA* 3.4 10.8 - - + +
772M ALA* 2.9 30.1 + - - +
793M ARG* 3.1 51.9 + - - +
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Residues in contact with ARG 769 (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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730M ALA 3.1 19.2 + - - -
731M ASP* 2.9 26.2 + - - +
733M LEU 3.3 17.0 + - - -
734M GLY* 5.5 0.2 - - - -
735M LEU* 3.6 31.9 - - + +
738M LEU* 5.9 0.8 - - - +
765M ALA 2.9 19.1 + - - +
766M ALA* 3.3 17.6 + - - +
767M GLU 3.1 0.2 - - - -
768M LYS* 1.3 78.3 - - - +
770M LEU* 1.3 64.6 + - - +
772M ALA* 3.3 6.8 + - - +
773M ILE* 2.9 32.1 + - - +
790M MET* 4.7 15.3 - - + -
793M ARG* 4.8 13.5 - - - +
13N G 3.6 0.2 + - - -
14N C 2.4 45.4 + - - -
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Residues in contact with LEU 770 (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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632M LEU* 4.3 10.5 - - + +
730M ALA* 3.4 30.1 - - + +
731M ASP* 4.0 9.4 - - + +
738M LEU* 5.4 0.9 - - + -
756M LEU* 6.2 4.9 - - + -
758M HIS* 3.7 43.1 - - + +
766M ALA 2.9 22.2 + - - +
767M GLU* 3.2 11.6 + - - +
769M ARG* 1.3 81.3 - - - +
771M ALA* 1.3 59.7 + - - +
773M ILE* 3.4 23.8 - - + +
774M ALA* 2.9 31.2 + - - +
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Residues in contact with ALA 771 (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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549D ASN* 6.1 6.5 - - + -
553D ARG* 5.6 9.6 - - + +
556D LYS* 5.9 0.9 - - - -
632M LEU* 4.5 13.8 - - + +
767M GLU 3.0 14.3 + - - +
768M LYS* 3.4 15.5 - - + +
769M ARG 3.2 0.2 - - - -
770M LEU* 1.3 76.8 - - - +
772M ALA* 1.3 58.1 + - - +
774M ALA* 3.2 1.9 + - - +
775M ASP* 3.0 30.9 + - - +
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Residues in contact with ALA 772 (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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735M LEU* 5.5 1.8 - - - +
768M LYS 2.9 17.6 + - - +
769M ARG* 3.5 5.2 - - - +
771M ALA* 1.3 71.9 - - - +
773M ILE* 1.3 57.6 + - - +
775M ASP* 2.8 29.4 - - - +
776M LEU* 4.8 2.4 - - - +
786M ALA* 4.5 18.0 - - + +
789M ASP* 5.2 9.4 - - + +
793M ARG* 4.9 14.4 - - - +
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Residues in contact with ILE 773 (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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735M LEU* 3.7 39.0 - - + -
738M LEU* 3.9 36.3 - - + -
739M TYR* 6.4 1.3 - - + -
742M ARG* 2.9 30.7 + - - +
756M LEU* 5.4 7.6 - - + -
769M ARG* 2.9 21.5 + - - +
770M LEU* 3.4 31.4 - - + +
771M ALA 3.1 0.4 - - - -
772M ALA* 1.3 78.8 - - - +
774M ALA* 1.3 65.4 + - + +
775M ASP* 3.2 1.7 + - - +
776M LEU* 3.2 12.4 + - - +
786M ALA* 6.2 0.2 - - - -
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Residues in contact with ALA 774 (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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556D LYS* 4.6 10.4 - - - +
630M THR* 3.7 27.7 + - - +
632M LEU* 4.1 33.7 - - + -
742M ARG* 4.2 6.3 - - - +
756M LEU* 5.5 6.5 - - + -
770M LEU 2.9 15.7 + - - +
771M ALA 4.2 1.1 - - - +
773M ILE* 1.3 78.6 - - + +
775M ASP* 1.3 63.1 + - - +
776M LEU 3.2 5.0 + - - +
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Residues in contact with ASP 775 (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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556D LYS* 4.7 18.0 - - + +
771M ALA 3.0 17.5 + - - +
772M ALA* 2.8 33.7 - - - +
774M ALA* 1.3 76.3 - - - +
776M LEU* 1.3 80.4 + - - +
777M SER* 3.4 2.9 + - - -
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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