Contacts of the helix formed by residues 891 - 902 (chain A) in PDB entry 3MP1
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 GLU 891 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780A LYS* 5.8 2.1 + - - -
782A GLU* 5.6 2.3 - - - +
888A ASN* 3.5 25.0 + - - +
889A LEU 3.4 2.2 - - - -
890A GLN* 1.3 87.0 - - + +
892A PRO* 1.3 72.1 - - - +
893A TYR 3.0 1.4 + - - -
894A PHE* 3.1 27.9 + - + +
895A THR* 4.2 3.4 + - - -
1082A ARG* 4.5 10.1 + - - -
1085A VAL* 6.1 0.4 - - - -
1B GLC 3.6 17.7 - - - +
2B GLC 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 892 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A GLN 3.8 0.6 - - - +
891A GLU* 1.3 86.0 - - - +
893A TYR* 1.3 62.5 + - - +
895A THR* 3.0 9.9 + - - +
896A TRP* 3.0 25.1 + - - +
899A ILE* 5.6 0.3 - - - +
1078A TRP* 3.7 25.6 - - + +
1081A VAL* 3.7 28.9 - - + +
1082A ARG* 3.5 40.8 - - + +
1085A VAL* 4.6 8.9 - - + -
2B GLC 3.5 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 893 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849A GLU* 4.3 14.4 + - - -
850A ALA* 4.4 0.5 - - - -
851A LEU* 3.5 44.3 + - + +
892A PRO* 1.3 77.7 - - - +
894A PHE* 1.3 69.8 + + + +
896A TRP* 3.7 4.6 + - + +
897A PRO* 3.5 14.9 - - - +
968A TRP* 4.1 20.2 - + - -
996A PHE* 3.7 36.1 + - + -
998A GLY* 5.0 2.7 + - - -
1068A MET* 4.8 7.4 - - + -
1078A TRP* 4.1 17.0 - + - -
1B GLC 4.0 28.4 + - - -
2B GLC 3.0 45.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 894 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A LEU* 3.9 22.8 - - + +
867A TRP* 6.1 0.2 - - - -
887A PHE* 3.7 16.2 - + + -
888A ASN* 3.3 49.8 - - + +
891A GLU* 3.1 15.6 + - + +
892A PRO 3.1 0.8 - - - -
893A TYR* 1.3 86.2 - + - +
895A THR* 1.3 57.7 + - - +
896A TRP 3.4 0.2 - - - -
897A PRO* 3.3 13.3 - - - +
948A TYR* 3.8 25.8 - + - -
964A ILE* 3.2 37.3 - - + +
965A ASN* 3.9 16.2 - - - -
968A TRP* 4.8 2.5 - + - -
1B GLC 3.8 27.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 895 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A PHE* 4.3 10.6 - - + -
888A ASN 4.5 1.9 + - - -
889A LEU* 4.5 5.7 - - - +
891A GLU 4.2 7.1 + - - -
892A PRO* 3.0 6.9 + - - +
894A PHE* 1.3 76.6 - - - +
896A TRP* 1.3 66.2 + - - +
897A PRO* 3.3 2.0 - - - -
898A LEU* 3.2 18.0 + - + +
899A ILE* 3.2 30.2 + - + +
930A LEU* 4.9 0.7 - - + -
933A LEU* 3.1 43.9 - - + +
1085A VAL* 3.9 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 896 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A PRO 3.0 13.6 + - - +
893A TYR* 3.8 9.0 - - - +
895A THR* 1.3 78.1 - - - +
897A PRO* 1.3 70.0 - - + +
899A ILE* 3.0 30.0 + - + +
900A ALA* 2.9 34.7 + - + +
904A GLY* 4.3 3.4 - - - -
905A TYR* 3.4 46.7 - - - -
906A ALA 3.8 2.7 - - - -
921A VAL* 4.3 8.5 - - + -
994A LYS* 3.8 14.7 + - - +
996A PHE* 3.4 52.2 - + + +
1077A PHE* 3.8 25.1 - + - -
1078A TRP* 5.0 4.9 - + + -
1081A VAL* 4.4 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 897 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A LEU* 4.1 14.4 - - + -
867A TRP* 5.9 3.4 - - + -
893A TYR 3.5 6.3 - - - +
894A PHE 3.3 14.8 - - - +
895A THR 3.3 5.2 - - - -
896A TRP* 1.3 93.8 - - + +
898A LEU* 1.3 55.7 + - - +
900A ALA* 3.6 0.3 + - - -
901A ALA 3.1 21.0 + - - -
964A ILE* 5.6 3.1 - - + -
985A LEU* 4.1 10.1 - - + -
993A SER* 3.5 22.5 - - - +
994A LYS 3.1 23.8 + - - +
995A PRO* 3.6 27.4 - - + -
996A PHE 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 898 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867A TRP* 4.1 39.0 - - + -
895A THR* 3.2 13.4 + - + +
896A TRP 3.1 0.4 - - - -
897A PRO* 1.3 77.5 - - - +
899A ILE* 1.3 62.9 + - + +
900A ALA 3.0 5.5 + - - -
901A ALA* 3.3 13.5 + - - +
902A ASP 4.2 2.8 + - - -
929A GLY* 3.7 35.6 - - - +
932A PHE* 4.7 3.6 - - + -
933A LEU* 3.9 32.3 - - + +
988A PHE* 3.8 34.9 - - + -
993A SER* 4.4 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 899 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A PRO 5.6 0.4 - - - +
895A THR* 3.5 34.3 - - + +
896A TRP* 3.0 39.3 + - + +
898A LEU* 1.3 76.6 - - + +
900A ALA* 1.3 57.4 + - - +
904A GLY* 3.2 17.4 + - - -
921A VAL* 5.8 1.1 - - + -
925A GLY 3.9 3.3 - - - +
926A ALA* 3.5 30.7 - - + +
929A GLY* 4.5 8.5 - - - -
930A LEU* 4.4 25.4 - - + +
1081A VAL* 4.8 4.3 - - + -
1085A VAL* 4.3 17.7 - - + -
1099A LEU* 5.9 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 900 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896A TRP* 2.9 27.9 + - + +
897A PRO 4.0 0.2 - - - +
899A ILE* 1.3 79.1 - - - +
901A ALA* 1.3 66.3 + - - +
902A ASP 3.2 2.7 - - - -
903A GLY* 3.0 12.5 + - - -
904A GLY 3.2 21.0 - - - +
994A LYS* 3.4 43.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 901 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897A PRO 3.1 13.8 + - - +
898A LEU* 3.3 12.7 + - - +
900A ALA* 1.3 77.8 - - - +
902A ASP* 1.3 58.9 + - - +
903A GLY 3.5 0.3 + - - -
988A PHE* 3.9 23.8 - - + +
991A GLN* 3.4 23.4 - - - +
992A PRO 3.1 26.9 - - - +
993A SER* 3.9 4.7 - - - +
994A LYS* 4.1 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 902 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A LEU 4.2 3.6 + - - +
900A ALA 3.2 0.6 - - - -
901A ALA* 1.3 77.2 - - - +
903A GLY* 1.3 55.8 + - - +
925A GLY* 3.3 26.5 + - - +
928A ALA* 4.1 12.0 - - - +
988A PHE* 3.9 20.2 - - + -
989A LYS* 3.5 40.5 - - - +
991A GLN* 4.1 11.2 - - - +
----------------------------------------------------------
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