Contacts of the helix formed by residues 1180 - 1187 (chain B) in PDB entry 2ZM3
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 SER1180 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1178B TRP 3.9 0.6 + - - -
1179B MET* 1.3 76.2 - - - +
1181B PRO* 1.3 76.3 - - - +
1182B GLU* 2.9 29.9 + - - -
1183B SER* 3.0 21.8 + - - -
1184B LEU* 3.1 19.6 + - - +
1193B SER* 3.7 9.9 + - - -
1196B TRP* 3.6 29.8 - - - -
1197B SER* 5.2 0.2 + - - -
1256B ARG* 3.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179B MET 3.8 0.2 - - - -
1180B SER* 1.3 87.5 - - - +
1182B GLU* 1.3 58.3 + - - +
1184B LEU* 3.5 6.7 + - + +
1185B LYS* 3.1 30.4 + - - +
1196B TRP* 3.4 37.5 - - + -
1225B VAL* 3.5 26.2 - - + +
1226B MET* 4.2 7.7 - - - +
1251B TYR* 3.7 37.7 - - + +
1256B ARG* 3.9 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1180B SER* 2.9 18.7 + - - +
1181B PRO* 1.3 75.7 - - - +
1183B SER* 1.3 59.2 + - - +
1185B LYS* 4.5 5.4 - - - -
1186B ASP* 3.0 35.1 + - - +
1187B GLY 3.7 2.3 + - - -
1188B VAL* 3.9 23.9 + - + +
1190B THR* 4.7 2.5 + - + +
1192B TYR* 4.4 0.9 - - - +
1193B SER* 3.9 11.4 + - - -
1251B TYR 4.4 1.7 - - - +
1253B PRO* 3.5 28.4 - - + +
1256B ARG* 2.7 43.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179B MET* 3.6 24.7 - - - +
1180B SER* 3.0 26.7 + - - -
1182B GLU* 1.3 74.9 - - - +
1184B LEU* 1.3 62.8 + - - +
1187B GLY* 2.8 26.7 + - - -
1188B VAL 2.8 25.4 + - - +
1189B PHE* 3.5 20.5 - - - -
1193B SER* 3.7 5.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1176B VAL* 3.8 20.4 - - + +
1179B MET* 3.6 47.3 - - + +
1180B SER 3.1 11.7 + - - +
1181B PRO* 3.8 6.5 - - + +
1183B SER* 1.3 77.3 - - - +
1185B LYS* 1.3 61.7 + - - +
1187B GLY 4.9 0.2 + - - -
1221B VAL 5.6 0.2 - - - -
1222B LEU* 3.4 44.6 - - + +
1225B VAL* 3.8 26.2 - - + -
1226B MET* 4.0 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181B PRO 3.1 17.9 + - - +
1182B GLU* 4.0 3.4 - - - +
1184B LEU* 1.3 80.3 - - - +
1186B ASP* 1.3 93.9 + - - +
1187B GLY 3.8 0.2 - - - -
1226B MET* 3.8 22.0 - - + -
1251B TYR* 5.2 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1167B ARG* 3.4 33.7 + - - +
1168B LYS 5.2 0.9 - - - +
1182B GLU* 3.0 15.1 + - - +
1185B LYS* 1.3 119.1 + - - +
1187B GLY* 1.3 64.8 + - - +
1188B VAL* 3.3 6.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1167B ARG* 3.3 2.6 - - - -
1168B LYS* 2.8 39.2 + - - -
1183B SER 2.8 20.1 + - - -
1184B LEU 4.7 0.6 + - - -
1185B LYS 3.8 0.2 - - - -
1186B ASP* 1.3 78.4 - - - +
1188B VAL* 1.3 59.0 + - - +
1189B PHE* 3.4 15.8 - - - -
----------------------------------------------------------
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