Contacts of the helix formed by residues 866 - 874 (chain A) in PDB entry 1MWH
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 PRO 866 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASN* 3.1 22.7 - - - +
27A PHE* 3.8 0.9 - - + -
28A GLU* 3.8 6.1 - - - +
864A GLN 3.5 2.2 - - - +
865A TYR* 1.3 87.6 - - - +
867A MET* 1.3 64.4 + - - +
868A TRP* 3.0 3.6 - - + +
869A SER* 2.9 29.3 + - - +
870A PHE* 3.7 3.8 - - - -
941A LYS* 3.9 19.1 - - + +
945A GLY* 3.8 11.0 - - - +
948A MET* 3.5 34.1 - - + -
1042A ARG* 3.7 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 867 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN* 3.7 22.2 - - + +
23A SER* 3.6 14.8 - - - +
24A ASN* 2.8 40.6 + - - +
27A PHE* 3.3 36.7 - - + -
843A TRP* 3.4 29.0 - - + -
866A PRO* 1.3 71.2 - - - +
868A TRP* 1.3 93.3 + - + +
870A PHE* 3.1 13.5 + - - +
871A VAL* 3.4 2.3 + - - -
877A LEU* 3.5 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 868 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN 5.1 4.7 - - - -
23A SER* 5.5 1.1 - - - -
24A ASN* 4.1 10.3 - - - +
866A PRO* 3.0 1.0 + - + -
867A MET* 1.3 109.3 - - + +
869A SER* 1.3 61.3 + - - +
870A PHE 3.2 0.2 - - - -
871A VAL* 3.3 12.5 + - + +
872A TYR* 3.2 21.0 + - - +
877A LEU* 3.8 20.2 - - + -
880A ALA* 4.7 6.3 - - + -
881A PHE* 4.1 25.4 - + - -
899A MET* 5.0 6.1 - - + +
902A TRP* 3.6 33.0 - + - -
940A LEU* 3.0 36.0 + - + +
941A LYS 3.5 8.7 - - - +
942A LEU* 3.5 45.6 - - + +
945A GLY* 4.4 6.4 - - - -
946A TYR* 4.7 1.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 869 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865A TYR* 3.5 31.4 - - - -
866A PRO* 2.9 14.8 + - - +
868A TRP* 1.3 79.6 - - - +
870A PHE* 1.3 59.0 + - - +
872A TYR* 3.4 4.3 + - - +
873A TRP* 3.1 37.9 + - - -
945A GLY* 2.7 35.5 + - - -
948A MET* 4.0 0.3 - - - +
949A ALA* 3.7 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 870 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 3.8 25.8 - + - -
818A LEU* 4.0 21.1 - - + -
821A ILE* 6.1 0.2 - - + -
822A MET* 4.2 5.8 - - + +
843A TRP* 4.2 3.4 - + + -
846A CYS* 3.0 51.6 - - + -
850A SER* 3.9 13.0 - - - -
865A TYR* 4.2 8.7 - - + -
866A PRO 3.7 15.5 - - - -
867A MET 3.1 9.1 + - - +
869A SER* 1.3 77.4 - - - +
871A VAL* 1.3 62.7 + - - +
873A TRP* 3.3 33.5 + + - +
874A GLY 3.1 6.1 + - - -
875A LEU* 2.8 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 871 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A TRP* 3.9 6.3 - - + -
867A MET 3.4 13.4 + - - +
868A TRP* 3.3 18.6 + - + +
869A SER 3.3 0.4 - - - -
870A PHE* 1.3 76.0 - - - +
872A TYR* 1.3 65.4 + - - +
874A GLY* 2.9 15.9 + - - -
875A LEU 3.2 17.9 - - - +
877A LEU* 3.6 32.3 - - + -
892A MET* 3.6 12.6 - - + +
893A PRO 5.0 1.2 - - - +
898A GLY 6.1 0.3 - - - -
899A MET* 4.1 5.1 - - - +
902A TRP* 3.4 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 872 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A TRP 3.2 9.6 + - - +
869A SER* 3.5 8.7 - - - +
871A VAL* 1.3 81.8 - - - +
873A TRP* 1.3 67.5 + + - +
874A GLY 3.2 1.0 + - - -
894A THR* 3.5 0.7 + - - -
895A GLY* 2.8 58.6 + - - +
896A ASP* 3.9 6.4 + - - -
899A MET* 3.9 16.1 - - + -
946A TYR* 3.7 40.6 - + - -
949A ALA* 3.5 27.4 - - + -
950A GLN* 3.3 36.7 + - + +
953A ARG* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 873 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A LEU* 3.6 31.9 - - + -
819A ASP* 5.3 2.0 - - - -
822A MET* 3.9 25.4 - - + -
826A PHE* 3.3 18.9 - - - -
865A TYR* 3.6 22.0 - + - -
869A SER* 3.1 19.2 + - - +
870A PHE* 3.6 46.2 - + - +
871A VAL 3.2 0.4 - - - -
872A TYR* 1.3 87.6 - + - +
874A GLY* 1.3 57.2 + - - +
875A LEU 3.8 0.2 - - - -
894A THR* 2.9 14.0 + - - -
949A ALA* 3.0 38.0 + - + +
953A ARG* 3.1 39.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 874 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822A MET* 4.3 6.5 - - - -
825A PHE* 3.8 9.3 - - - -
826A PHE* 4.4 7.7 - - - -
871A VAL 2.9 8.4 + - - -
872A TYR 3.1 2.1 - - - -
873A TRP* 1.3 79.8 - - - +
875A LEU* 1.3 59.9 + - - +
876A PRO* 3.2 13.0 - - - +
890A TRP 4.8 3.1 - - - +
892A MET* 3.4 20.9 - - - +
893A PRO 4.4 6.3 - - - -
894A THR* 4.0 7.2 - - - -
----------------------------------------------------------
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