Contacts of the helix formed by residues 1180 - 1191 (chain A) in PDB entry 2DGZ
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 THR1180 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1164A ARG* 5.2 0.2 - - - +
1176A ALA* 3.6 14.7 + - - +
1179A ALA* 1.3 75.7 - - - +
1181A ASN* 1.3 70.2 + - - +
1182A LYS* 3.5 25.3 + - + +
1183A ILE* 2.7 33.0 + - + +
1184A LEU* 3.2 9.6 + - - +
1203A GLY* 6.0 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1157A TYR* 2.5 26.2 + - - +
1164A ARG* 4.4 14.3 - - - +
1179A ALA 3.9 0.8 + - - -
1180A THR* 1.3 77.0 + - - +
1182A LYS* 1.3 57.7 + - - +
1184A LEU* 3.2 11.5 + - - +
1185A VAL* 2.8 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1180A THR* 3.0 17.8 + - + +
1181A ASN* 1.3 79.9 - - - +
1183A ILE* 1.3 58.1 + - - +
1185A VAL* 3.7 6.4 + - - +
1186A ASP* 2.4 57.4 + - - +
1202A ASP* 3.8 41.7 - - - +
1203A GLY* 5.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1178A LEU 5.0 2.0 - - - +
1179A ALA* 4.2 18.2 - - + -
1180A THR* 2.7 39.7 + - + +
1182A LYS* 1.3 69.6 - - + +
1184A LEU* 1.3 65.8 + - + +
1186A ASP* 3.1 5.1 + - - +
1187A MET* 3.0 40.9 + - + +
1198A VAL* 6.1 0.7 - - + -
1201A ILE* 4.3 9.9 - - + -
1202A ASP 3.6 21.3 - - - +
1203A GLY* 4.0 21.3 - - - +
1204A VAL* 4.1 10.8 - - + +
1208A LYS* 5.3 5.4 - - + -
1212A LEU* 4.9 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1157A TYR* 3.6 19.5 - - + +
1160A LEU* 3.9 24.5 - - + +
1161A VAL* 4.1 20.9 - - + -
1164A ARG* 3.9 38.6 - - + +
1179A ALA* 4.2 10.1 - - + +
1180A THR 3.9 4.7 - - - +
1181A ASN* 3.2 15.2 + - - +
1183A ILE* 1.3 78.4 - - - +
1185A VAL* 1.3 64.7 + - - +
1187A MET* 3.2 8.4 + - - +
1188A ALA* 2.9 23.6 + - - +
1215A LEU* 3.8 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1157A TYR* 4.1 17.2 - - + -
1181A ASN* 2.8 37.8 + - + +
1182A LYS* 3.8 7.4 - - - +
1184A LEU* 1.3 72.7 - - - +
1186A ASP* 1.3 65.8 + - - +
1188A ALA* 3.0 10.1 + - - +
1189A LYS* 3.0 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182A LYS* 2.4 51.5 + - - +
1183A ILE 3.1 7.9 + - - +
1185A VAL* 1.3 77.8 - - - +
1187A MET* 1.3 58.8 + - - +
1189A LYS* 2.8 30.0 + - - +
1190A MET* 2.8 39.0 + - + +
1201A ILE* 3.6 22.4 - - + -
1202A ASP* 4.0 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1160A LEU* 4.2 8.3 - - + -
1183A ILE* 3.0 31.5 + - + +
1184A LEU* 3.5 9.4 - - - +
1186A ASP* 1.3 76.0 - - - +
1188A ALA* 1.3 54.4 + - - +
1191A ARG* 2.7 33.1 + - - -
1192A PRO* 3.1 22.4 - - + +
1198A VAL* 4.2 14.8 - - + -
1201A ILE* 4.3 11.9 - - + -
1212A LEU* 4.7 4.3 - - - +
1215A LEU* 3.9 25.6 - - + -
1216A TRP* 3.5 44.9 - - + +
1219A ILE* 3.8 15.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1153A GLN* 3.3 29.6 - - + +
1156A LEU* 4.1 6.5 - - + +
1157A TYR* 4.1 27.1 - - + +
1160A LEU* 4.0 16.1 - - + +
1184A LEU 2.9 12.8 + - - +
1185A VAL* 3.0 10.3 + - - +
1187A MET* 1.3 76.9 - - - +
1189A LYS* 1.3 61.6 + - + +
1191A ARG* 3.8 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1142A GLN* 5.6 6.3 - - - +
1145A ILE* 4.9 12.7 - - + +
1153A GLN* 3.8 22.4 - - + +
1185A VAL* 3.0 37.0 + - + +
1186A ASP* 2.8 14.3 + - - +
1188A ALA* 1.3 77.6 - - + +
1190A MET* 1.3 65.7 + - + +
1191A ARG* 3.0 27.4 + - - -
1232A LEU* 4.0 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1186A ASP* 2.8 35.6 + - + +
1189A LYS* 1.3 74.1 - - + +
1191A ARG* 1.3 72.6 + - - +
1192A PRO* 3.4 4.6 - - + -
1200A ARG 5.5 1.1 - - - +
1201A ILE* 3.3 26.7 - - + -
1202A ASP 5.1 1.1 - - - +
1230A THR* 4.0 0.7 - - - -
1231A ASP* 3.3 15.1 + - - -
1232A LEU* 3.5 18.5 + - - +
1233A PHE* 3.1 51.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1149A GLU* 4.7 15.0 + - - +
1152A THR* 3.6 31.8 - - - +
1153A GLN* 4.3 17.1 - - - +
1156A LEU* 3.2 32.1 - - + -
1187A MET 2.7 14.2 + - - -
1188A ALA 3.8 10.2 + - - +
1189A LYS 3.0 17.5 + - - -
1190A MET* 1.3 78.1 - - - +
1192A PRO* 1.3 68.4 - - - +
1193A THR* 3.4 0.9 + - - +
1219A ILE* 3.7 13.9 - - + -
1222A PHE* 5.3 1.6 - - + -
1223A CYS* 6.0 0.4 - - + -
1228A VAL* 4.1 10.2 - - - +
1229A GLN* 3.7 14.2 + - - +
1230A THR* 3.2 30.5 - - + +
1231A ASP 3.3 1.4 + - - -
1232A LEU* 2.9 32.3 - - - +
----------------------------------------------------------
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