Contacts of the helix formed by residues 781 - 796 (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 SER 781 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619M GLN* 3.7 29.9 - - - +
779M LEU 3.2 7.3 + - - -
780M GLY* 1.3 71.8 - - - +
782M GLY* 1.3 57.6 - - - +
783M HIS* 3.1 5.8 - - - +
784M LEU* 2.9 30.5 + - - +
785M LEU* 2.8 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 782 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739M TYR* 6.4 0.2 - - - -
776M LEU* 3.7 31.5 - - - +
780M GLY 3.1 11.1 + - - +
781M SER* 1.3 74.3 - - - +
783M HIS* 1.3 58.2 + - - +
785M LEU* 3.7 15.7 - - - -
786M ALA* 2.6 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 783 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469M SER* 2.8 27.5 + - - -
471M ASP* 5.1 11.3 + - + +
598M ALA* 2.6 45.5 + - + -
599M THR* 4.0 4.3 - - + -
739M TYR* 3.2 33.9 + + + -
776M LEU* 4.1 6.2 - - - +
779M LEU* 4.9 20.2 - - + +
781M SER* 4.5 5.8 - - - +
782M GLY* 1.3 72.2 - - - +
784M LEU* 1.3 76.8 + - + +
786M ALA* 4.1 0.3 - - - +
787M GLU* 3.0 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 784 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467M LEU* 6.1 3.1 - - + -
469M SER* 3.6 7.2 - - - +
598M ALA 5.5 0.2 - - - +
606M TYR* 5.0 11.7 + - - +
617M SER* 3.5 28.3 - - - +
619M GLN* 3.3 26.2 - - - +
781M SER* 2.9 26.4 + - - +
783M HIS* 1.3 96.6 - - + +
785M LEU* 1.3 59.2 + - + +
787M GLU* 3.1 12.0 + - - +
788M ARG* 2.8 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 785 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776M LEU* 6.0 1.6 - - + -
780M GLY 4.5 4.0 - - - +
781M SER* 2.8 40.5 + - - +
782M GLY* 3.7 10.1 - - - +
784M LEU* 1.3 76.0 - - + +
786M ALA* 1.3 61.8 + - + +
788M ARG* 3.1 11.6 + - + +
789M ASP* 2.9 46.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 786 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735M LEU* 4.1 15.2 - - + +
739M TYR* 5.9 5.6 - - + -
772M ALA* 4.5 18.8 - - + +
776M LEU* 5.3 5.8 - - + -
782M GLY* 2.6 24.6 + - - +
783M HIS* 4.1 1.1 - - - +
785M LEU* 1.3 78.7 - - + +
787M GLU* 1.3 60.1 + - - +
789M ASP* 3.5 9.1 + - - +
790M MET* 2.9 30.2 + - - +
793M ARG* 4.8 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 787 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598M ALA 3.1 24.6 - - - +
599M THR* 3.5 7.4 - - - +
600M PRO* 3.5 22.1 - - + +
603M ARG* 3.6 2.0 + - - -
606M TYR* 4.6 6.5 + - + -
735M LEU* 5.1 5.6 - - + +
736M ALA* 5.6 0.3 - - - +
739M TYR* 2.4 34.2 + - + +
783M HIS* 3.0 32.2 + - - +
784M LEU* 3.4 7.0 - - - +
786M ALA* 1.3 76.1 - - - +
788M ARG* 1.3 57.5 + - - +
790M MET* 4.2 5.4 - - - -
791M GLU* 2.9 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 788 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ARG* 3.8 31.7 - - - +
603M ARG* 3.3 25.7 + - - +
606M TYR* 3.8 20.0 + - - -
610M VAL* 4.4 28.1 - - - +
615M LEU* 5.5 4.9 - - - +
784M LEU* 2.8 22.2 + - + +
785M LEU* 3.1 16.1 + - + +
787M GLU* 1.3 77.3 - - - +
789M ASP* 1.3 61.2 + - - +
792M ILE* 2.9 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 789 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772M ALA* 5.2 9.7 - - + +
785M LEU* 2.9 29.6 + - - +
786M ALA* 3.9 6.8 - - - +
788M ARG* 1.3 77.8 - - - +
790M MET* 1.3 59.7 + - - +
792M ILE* 3.3 13.4 + - - +
793M ARG* 2.3 52.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 790 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602M PRO* 4.5 7.0 - - + -
734M GLY* 6.6 0.2 - - - -
735M LEU* 3.7 39.3 - - + +
769M ARG* 4.7 13.0 - - + -
786M ALA 2.9 19.5 + - - +
787M GLU* 3.7 6.7 - - - +
788M ARG 3.3 0.4 - - - -
789M ASP* 1.3 76.1 - - - +
791M GLU* 1.3 82.3 + - + +
793M ARG* 3.1 19.2 + - - +
794M GLY* 2.8 27.2 + - - -
13N G 3.7 24.7 - - - +
14N C 5.6 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 791 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600M PRO* 3.4 25.1 - - - +
601M ILE 2.8 20.7 - - - +
602M PRO* 3.4 7.8 - - + +
603M ARG* 2.5 54.0 + - + +
606M TYR* 3.1 20.7 - - - +
787M GLU* 2.9 17.4 + - - +
790M MET* 1.3 94.6 - - + +
792M ILE* 1.3 63.0 + - - +
794M GLY* 3.8 3.4 - - - +
795M VAL* 3.0 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 792 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TYR* 3.7 56.2 + - + +
35D ARG* 4.5 14.4 - - + +
603M ARG* 3.5 14.3 - - - +
788M ARG* 2.9 34.8 + - + +
789M ASP* 3.3 14.4 - - - +
791M GLU* 1.3 76.0 - - - +
793M ARG* 1.3 70.2 + - - +
796M GLY* 3.4 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 793 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735M LEU* 5.9 1.2 - - - +
765M ALA* 5.8 2.0 - - + -
768M LYS* 3.1 60.0 + - - +
769M ARG* 4.8 11.9 - - - +
772M ALA* 4.9 12.3 - - - +
786M ALA 4.8 0.8 + - - -
789M ASP* 2.3 58.1 + - - +
790M MET* 3.3 17.0 - - - +
792M ILE* 1.3 86.0 - - - +
794M GLY* 1.3 63.0 + - - +
796M GLY 3.3 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 794 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602M PRO* 5.1 4.5 - - - -
790M MET* 2.8 21.5 + - - -
791M GLU* 3.1 7.6 + - - -
793M ARG* 1.3 80.3 - - - +
795M VAL* 1.3 65.1 + - - +
796M GLY 4.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 795 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602M PRO 3.3 24.7 - - - +
603M ARG* 3.3 29.4 - - + +
604M THR* 3.9 12.8 - - + +
791M GLU 3.0 10.4 + - - +
794M GLY* 1.3 73.3 - - - +
796M GLY* 1.3 68.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 796 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716C LYS* 6.5 1.3 - - - -
34D TYR* 5.1 9.2 - - - -
791M GLU 4.4 0.2 + - - -
792M ILE 3.4 17.6 + - - -
793M ARG* 3.3 18.3 - - - +
794M GLY 4.0 1.6 - - - +
795M VAL* 1.3 86.6 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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