Contacts of the helix formed by residues 884 - 893 (chain M) in PDB entry 6D6Q
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 ASP 884 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567M TYR* 4.2 15.3 - - - -
883M ALA* 1.3 74.3 - - - +
885M GLU* 1.3 65.5 + - - +
886M LEU* 3.7 12.6 + - - +
887M LEU* 4.0 11.7 + - + +
888M LEU* 3.2 26.3 + - - +
912M PHE* 5.3 5.4 - - + +
958M TYR* 2.3 40.1 + - - -
962M PHE* 3.8 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 885 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567M TYR* 2.9 34.9 - - + +
568M ASN* 2.7 35.7 + - - +
571M LEU* 4.5 4.4 - - + +
877M ALA* 3.8 22.9 - - + +
880M ILE* 3.7 26.9 - - + -
883M ALA 2.8 14.8 - - - +
884M ASP* 1.3 73.4 + - - +
886M LEU* 1.3 70.3 + - + +
887M LEU 3.2 1.8 - - - -
888M LEU* 3.2 8.8 + - - +
889M THR* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 886 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567M TYR* 3.1 52.3 - - + +
571M LEU* 5.1 2.9 - - + -
857M VAL* 4.5 15.9 - - + -
858M LEU* 3.9 14.8 - - + -
861M LEU* 4.6 4.5 - - + -
863M PHE* 3.6 40.2 - - + -
884M ASP* 3.6 5.3 + - - +
885M GLU* 1.3 82.8 - - + +
887M LEU* 1.3 56.5 + - - +
889M THR* 2.7 21.9 + - - -
890M GLU* 3.0 20.3 + - - +
942M ILE* 4.9 17.3 - - + -
958M TYR* 5.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 887 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884M ASP* 4.0 17.9 + - + +
885M GLU 3.2 0.4 - - - -
886M LEU* 1.3 77.4 - - - +
888M LEU* 1.3 60.3 + - - +
890M GLU* 3.4 6.5 + - - +
891M MET* 2.9 62.1 + - + +
912M PHE* 3.6 17.9 - - + -
935M MET* 4.4 9.9 - - + +
938M CYS* 4.8 5.4 - - + -
939M ALA* 3.7 39.0 - - + +
942M ILE* 4.9 7.2 - - + -
958M TYR* 4.5 9.0 - - + +
962M PHE* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 888 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880M ILE* 3.8 39.9 - - + -
883M ALA* 4.2 7.0 - - + -
884M ASP 3.2 20.4 + - - +
885M GLU 3.2 5.8 + - - +
887M LEU* 1.3 79.1 - - - +
889M THR* 1.3 57.0 + - - +
891M MET* 3.2 10.0 + - - +
892M MET* 2.9 32.3 + - - +
897M PHE* 5.1 2.2 - - + -
909M LEU* 3.7 17.3 - - + -
912M PHE* 3.4 32.3 - - + -
1003M LEU* 4.2 11.9 - - + -
1007M MET* 4.1 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 889 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863M PHE* 2.8 26.7 - - + -
873M LYS* 4.3 2.7 - - - +
876M VAL* 4.1 16.2 - - + +
877M ALA* 3.8 34.1 - - + +
880M ILE* 4.8 6.1 - - + -
885M GLU 2.9 11.5 + - - +
886M LEU 2.7 20.3 + - - -
888M LEU* 1.3 74.9 - - - +
890M GLU* 1.3 57.1 + - - +
892M MET* 3.3 10.9 + - - +
893M PHE* 2.9 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 890 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H ASN* 4.1 7.8 + - - +
861M LEU* 3.3 19.9 - - - +
863M PHE* 3.4 13.4 - - + -
873M LYS* 2.9 31.4 + - - -
886M LEU 3.0 21.8 + - - +
887M LEU* 3.7 7.0 - - - +
889M THR* 1.3 73.7 - - - +
891M MET* 1.3 65.2 + - - +
893M PHE* 4.5 2.8 - - - +
894M ASN* 2.5 40.6 + - - +
938M CYS* 4.9 5.8 - - + -
941M ARG* 3.4 23.0 + - - +
942M ILE* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 891 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887M LEU* 2.9 45.1 + - + +
888M LEU* 3.4 10.8 - - - +
890M GLU* 1.3 76.1 - - - +
892M MET* 1.3 65.0 + - - +
895M GLY 3.3 4.2 + - - -
896M LEU* 3.2 59.5 + - + +
897M PHE* 3.9 23.1 - - + -
908M LEU* 3.6 26.0 - - + -
912M PHE* 3.7 20.9 - - + -
935M MET* 4.4 11.7 - - + -
938M CYS* 4.9 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 892 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H MET* 3.7 17.4 - - + +
876M VAL* 4.0 22.4 - - + -
880M ILE* 4.9 2.7 - - + -
888M LEU 2.9 16.5 + - - +
889M THR* 3.4 9.4 - - - +
890M GLU 3.2 0.2 - - - -
891M MET* 1.3 75.6 - - - +
893M PHE* 1.3 68.5 + - + +
895M GLY* 2.8 27.7 + - - -
896M LEU 5.3 0.4 - - - +
897M PHE* 4.8 10.5 - - + +
898M ASN* 4.3 1.3 + - - +
1007M MET* 3.3 40.4 - - + +
1010M ALA* 3.7 25.8 - - + -
1011M ALA 4.6 3.6 - - - +
1014M ILE* 5.1 7.2 - - - -
1019M LEU* 4.8 19.1 - - + -
1023M PHE* 5.0 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 893 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H MET* 4.9 7.2 - - + -
63H VAL* 4.9 7.6 - - + -
64H ASN* 3.3 20.8 - - + +
65H LYS* 2.8 34.8 + - - +
66H LEU* 4.5 21.8 - - + +
872M MET* 4.5 10.1 - - + -
873M LYS* 3.4 49.4 - - + -
876M VAL* 3.9 14.6 - - + -
889M THR* 2.9 22.2 + - - +
890M GLU* 3.5 4.3 - - - +
892M MET* 1.3 81.2 - - + +
894M ASN* 1.3 56.9 + - - +
1014M ILE* 3.8 42.2 - - + -
----------------------------------------------------------
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