Contacts of the helix formed by residues 1177 - 1184 (chain A) in PDB entry 3ETA
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 ALA1177 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1175A TRP 3.9 0.2 + - - -
1176A MET* 1.3 76.1 - - - +
1178A PRO* 1.3 74.4 - - + +
1179A GLU* 3.4 27.4 - - - +
1180A SER* 3.1 6.9 + - - +
1181A LEU* 3.0 19.8 + - - +
1190A SER* 3.7 15.8 + - - -
1193A TRP* 3.5 28.5 - - + +
1222A VAL* 4.4 0.2 - - - -
1253A ARG* 3.7 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177A ALA* 1.3 87.1 - - + +
1179A GLU* 1.3 63.5 + - - +
1181A LEU* 3.4 6.9 + - + +
1182A LYS* 3.0 29.1 + - - +
1193A TRP* 3.5 31.2 - - + -
1222A VAL* 3.7 23.1 - - + +
1223A MET* 3.8 8.8 - - - +
1248A PHE* 3.6 44.2 - - + +
1253A ARG* 3.9 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177A ALA* 3.4 11.8 - - - +
1178A PRO* 1.3 76.4 - - - +
1180A SER* 1.3 60.4 + - - +
1182A LYS* 4.4 2.7 - - - +
1183A ASP* 2.8 49.5 + - - +
1184A GLY 3.7 0.2 + - - -
1185A VAL* 4.2 10.1 + - + +
1187A THR* 4.8 4.4 + - + +
1190A SER* 4.0 8.7 + - - -
1248A PHE 4.0 3.8 - - - +
1250A PRO* 3.7 22.8 - - + +
1253A ARG* 2.8 45.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1165A LYS* 5.1 1.0 + - - -
1176A MET* 3.6 23.3 - - - +
1177A ALA* 3.1 15.3 + - - +
1179A GLU* 1.3 78.8 - - - +
1181A LEU* 1.3 61.1 + - - +
1184A GLY* 3.0 24.4 + - - -
1185A VAL 2.6 27.5 + - - +
1186A PHE* 3.9 11.6 - - - -
1190A SER* 3.4 25.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1165A LYS* 2.5 34.3 + - + +
1173A VAL* 4.0 18.2 - - + +
1176A MET* 3.9 32.3 - - + +
1177A ALA 3.0 13.7 + - - +
1178A PRO* 3.7 7.2 - - + +
1180A SER* 1.3 79.0 - - - +
1182A LYS* 1.3 58.0 + - - +
1184A GLY 4.9 0.2 + - - -
1218A VAL 4.7 0.4 - - - +
1219A LEU* 3.8 40.6 - - + +
1222A VAL* 3.7 37.5 - - + -
1223A MET* 3.8 17.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
1165A LYS* 5.0 1.2 + - - -
1178A PRO 3.0 16.9 + - - +
1179A GLU* 4.1 3.6 - - - +
1180A SER 3.3 0.2 - - - -
1181A LEU* 1.3 81.5 - - - +
1183A ASP* 1.3 78.3 + - - +
1184A GLY 4.0 0.2 + - - -
1223A MET* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179A GLU* 2.8 31.1 + - - +
1182A LYS* 1.3 95.6 + - - +
1184A GLY* 1.3 60.0 + - - +
1185A VAL* 3.2 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1176A MET* 5.9 0.2 - - - -
1180A SER 3.0 21.0 + - - -
1181A LEU 4.7 0.2 - - - -
1182A LYS 3.6 1.2 - - - -
1183A ASP* 1.3 77.2 - - - +
1185A VAL* 1.3 58.2 - - - +
1186A PHE* 3.3 24.6 - - - -
----------------------------------------------------------
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