Contacts of the helix formed by residues 1177 - 1184 (chain B) in PDB entry 1M7N
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 SER1177 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1175B TRP 3.9 0.2 + - - -
1176B MET* 1.3 74.6 - - - +
1178B PRO* 1.3 76.2 - - - +
1179B GLU* 3.1 26.5 + - - +
1180B SER* 2.8 27.1 + - - -
1181B LEU* 2.9 22.2 + - - +
1190B SER* 3.6 9.2 - - - -
1193B TRP* 3.8 18.8 - - - -
1194B SER* 5.2 1.0 + - - -
1253B ARG* 3.8 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177B SER* 1.3 86.5 - - - +
1179B GLU* 1.3 52.5 + - - +
1181B LEU* 3.2 7.7 + - + +
1182B LYS* 2.7 37.9 + - - +
1193B TRP* 3.5 30.5 - - + -
1222B VAL* 3.5 22.2 - - + +
1223B MET* 4.0 9.2 - - + +
1248B TYR* 3.4 47.8 - - + +
1253B ARG* 3.8 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177B SER* 3.1 16.5 + - - +
1178B PRO* 1.3 74.5 - - - +
1180B SER* 1.3 70.6 + - - +
1182B LYS* 3.0 1.7 + - - +
1183B ASP* 2.4 53.2 + - - +
1185B VAL* 4.4 18.2 - - + +
1187B THR* 4.6 4.9 + - + +
1189B TYR* 4.2 1.2 - - - +
1190B SER* 4.1 10.2 + - - -
1248B TYR 4.3 2.1 - - - +
1250B PRO* 3.3 27.7 - - + +
1253B ARG* 2.8 40.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1176B MET* 4.1 23.0 - - - +
1177B SER* 2.8 29.2 + - - -
1179B GLU* 1.3 77.8 - - - +
1181B LEU* 1.3 65.9 + - - +
1184B GLY* 2.8 23.2 + - - -
1185B VAL 2.7 30.1 + - - +
1186B PHE* 4.2 11.0 - - - -
1190B SER* 3.6 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1165B LYS* 4.3 20.6 + - - +
1173B VAL* 4.2 24.9 - - + +
1176B MET* 3.9 25.3 - - + +
1177B SER 2.9 13.9 + - - +
1178B PRO 3.3 6.7 - - - +
1180B SER* 1.3 78.4 - - - +
1182B LYS* 1.3 59.6 + - - +
1184B GLY 4.8 0.2 + - - -
1218B VAL* 5.1 0.4 - - + -
1219B LEU* 3.3 38.5 - - + +
1222B VAL* 3.6 40.6 - - + -
1223B MET* 4.0 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037A SER* 5.0 1.0 + - - -
1178B PRO 2.7 20.5 + - - +
1179B GLU* 3.9 2.2 - - - +
1181B LEU* 1.3 76.1 - - - +
1183B ASP* 1.3 72.7 + - - +
1184B GLY 3.7 0.4 - - - -
1223B MET* 3.7 26.5 + - + +
1224B GLU* 5.2 7.3 + - - -
1248B TYR* 5.2 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037A SER* 3.0 24.0 + - - +
1038A MET* 4.1 29.2 + - + +
1039A ARG* 3.1 9.0 + - - +
1179B GLU* 2.4 40.9 + - - +
1182B LYS* 1.3 85.5 - - - +
1184B GLY* 1.3 65.0 + - - +
1185B VAL* 3.0 13.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037A SER* 4.9 0.4 - - - -
1039A ARG* 2.6 43.6 + - - +
1176B MET* 6.3 0.2 - - - -
1180B SER 2.8 19.7 + - - -
1181B LEU 4.8 0.4 + - - -
1182B LYS 3.7 1.0 - - - -
1183B ASP* 1.3 77.2 - - - +
1185B VAL* 1.3 54.6 - - - +
1186B PHE* 4.4 9.0 - - - -
----------------------------------------------------------
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