Contacts of the helix formed by residues 1054 - 1066 (chain A) in PDB entry 1M8X
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 ARG1054 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023A LEU* 5.4 9.7 - - - +
1026A LEU* 5.4 5.4 - - - +
1053A GLY* 1.3 73.6 - - - -
1055A PRO* 1.3 75.7 - - + +
1056A GLU* 3.6 28.8 - - - +
1057A ASP* 3.0 45.4 + - - +
1058A LYS* 3.0 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1055 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1053A GLY 3.8 2.6 - - - +
1054A ARG* 1.3 87.1 - - + +
1056A GLU* 1.3 57.6 + - + +
1058A LYS* 3.2 15.8 + - + +
1059A SER* 2.9 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1056 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1054A ARG* 3.2 30.7 - - - +
1055A PRO* 1.3 80.6 - - + +
1057A ASP* 1.3 66.1 + - - +
1059A SER* 3.5 6.8 + - - -
1060A LYS* 3.2 45.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1057 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026A LEU* 3.6 27.0 - - - +
1030A HIS* 2.6 44.0 + - + +
1049A VAL* 3.9 18.6 - - + -
1053A GLY* 5.3 0.4 - - - -
1054A ARG* 3.0 45.7 + - - +
1056A GLU* 1.3 76.0 - - - +
1058A LYS* 1.3 65.0 + - - +
1060A LYS* 3.3 5.5 + - - +
1061A ILE* 3.2 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1058 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049A VAL 3.7 14.1 - - - +
1050A LEU* 3.2 42.1 + - + +
1051A GLU 4.6 6.9 + - - -
1052A HIS 5.1 0.8 - - - -
1053A GLY 2.9 26.6 + - - +
1054A ARG 3.0 13.5 + - - +
1055A PRO* 3.5 13.7 - - + +
1057A ASP* 1.3 76.8 - - - +
1059A SER* 1.3 58.8 + - - +
1061A ILE* 3.1 7.8 + - - +
1062A VAL* 2.9 33.7 + - + +
1088A HIS* 4.0 29.9 + - + +
1089A ALA* 6.0 0.2 - - - -
1093A GLU* 5.7 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1059 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055A PRO* 2.9 20.3 + - - +
1056A GLU* 3.8 8.2 - - - -
1057A ASP 3.3 0.2 - - - -
1058A LYS* 1.3 72.6 - - - +
1060A LYS* 1.3 60.9 + - - +
1062A VAL* 3.2 4.5 + - - +
1063A ALA* 2.9 30.3 + - - +
1090A SER* 5.8 0.3 - - - -
1093A GLU* 2.5 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1060 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027A GLU* 5.0 9.5 + - - -
1030A HIS* 3.8 42.9 + - + +
1033A THR* 5.9 0.2 - - - -
1056A GLU* 3.2 34.1 + - - +
1057A ASP* 3.6 10.9 + - - +
1058A LYS 3.2 0.4 - - - -
1059A SER* 1.3 79.2 - - - +
1061A ILE* 1.3 65.2 + - - +
1063A ALA* 3.3 12.3 + - - +
1064A GLU* 3.5 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1061 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030A HIS* 4.4 12.8 - - + +
1033A THR* 4.5 20.9 - - + +
1046A ILE* 3.4 47.3 - - + +
1049A VAL* 3.8 32.1 - - + -
1050A LEU* 4.1 22.4 - - + -
1057A ASP 3.2 9.8 + - - +
1058A LYS 3.1 6.6 + - - +
1060A LYS* 1.3 77.6 - - - +
1062A VAL* 1.3 63.5 + - - +
1064A GLU* 2.9 16.6 + - - +
1065A ILE* 3.3 13.4 + - + +
1081A VAL* 4.7 1.6 - - + -
1085A CYS* 4.3 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1062 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050A LEU* 4.5 6.3 - - + -
1058A LYS* 2.9 19.5 + - + +
1059A SER* 3.2 10.5 + - - +
1061A ILE* 1.3 76.5 - - - +
1063A ALA* 1.3 58.3 + - - +
1065A ILE* 3.0 4.7 + - - +
1066A ARG* 3.0 39.5 + - + +
1085A CYS* 4.1 23.8 - - + -
1089A ALA* 4.2 13.7 - - + -
1093A GLU* 4.1 38.4 - - + +
1097A LEU* 4.4 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1063 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059A SER 2.9 17.1 + - - +
1060A LYS* 3.7 8.1 - - - +
1061A ILE 3.2 0.6 - - - -
1062A VAL* 1.3 75.8 - - - +
1064A GLU* 1.3 62.0 + - - +
1066A ARG* 4.0 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1064 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030A HIS 5.2 4.7 - - - +
1033A THR* 3.8 32.3 - - + -
1034A GLU* 4.4 22.6 - - - +
1060A LYS 3.5 11.2 + - - +
1061A ILE 2.9 9.4 + - - +
1063A ALA* 1.3 78.4 - - - +
1065A ILE* 1.3 63.5 + - + +
1066A ARG 3.4 0.4 - - - +
1068A ASN* 2.9 24.3 + - - +
1072A LEU* 4.8 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1065 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037A VAL* 4.2 22.9 - - + -
1061A ILE* 3.5 13.2 - - + +
1062A VAL* 3.0 7.1 + - - +
1064A GLU* 1.3 81.5 - - + +
1066A ARG* 1.3 57.9 + - - +
1068A ASN* 2.9 23.2 + - - -
1069A VAL* 3.3 14.7 + - + +
1072A LEU* 3.6 26.2 - - + -
1078A ALA* 5.9 0.7 - - + +
1081A VAL* 4.2 11.2 - - + -
1082A VAL* 4.3 23.3 - - + -
1085A CYS* 3.4 27.1 - - + -
1097A LEU* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1066 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062A VAL* 3.0 25.2 + - + +
1063A ALA* 4.0 20.4 - - - +
1064A GLU 3.4 1.8 - - - +
1065A ILE* 1.3 77.6 - - - +
1067A GLY* 1.3 57.2 - - - +
1068A ASN* 3.3 11.8 + - - -
1093A GLU* 5.8 2.9 - - - +
1096A VAL* 3.3 39.0 - - + +
1097A LEU* 4.0 19.3 - - + -
1100A GLU* 3.8 7.1 + - - +
----------------------------------------------------------
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