Contacts of the helix formed by residues 189 - 193 (chain C) in PDB entry 2JET
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 ASP 189 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B THR* 3.2 11.1 - - - +
158C ALA* 3.1 33.6 - - + +
159C ALA 4.7 5.8 - - - +
160C LEU* 3.9 17.1 - - + +
184C GLY* 3.6 6.4 - - - -
185C ALA* 3.0 42.7 + - - +
186C SER* 3.5 19.3 + - - -
187C GLY 5.0 0.4 - - - -
188C VAL* 1.3 77.0 - - - +
190C SER* 1.3 77.2 + - - +
191C CYS 3.3 5.5 + - - +
192C MET* 3.6 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 190 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B THR* 4.2 1.8 + - - +
160C LEU* 3.6 13.9 - - - -
183C ALA 4.1 10.3 - - - -
184C GLY* 5.1 1.4 - - - -
186C SER* 5.2 2.6 + - - -
189C ASP* 1.3 85.9 + - - +
191C CYS* 1.3 64.1 + - - +
192C MET 3.2 4.0 + - - -
193C GLY* 3.5 11.5 + - - -
213C VAL* 5.5 1.0 - - - +
216C GLY 5.3 0.5 + - - -
217C SER* 3.3 29.5 + - - -
224C THR 5.0 4.9 + - - -
226C GLY* 4.4 7.8 + - - -
228C TYR* 3.2 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 191 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B GLY* 3.5 18.6 - - - +
144B THR* 5.5 0.2 - - - +
188C VAL* 5.0 0.2 - - - -
189C ASP 3.3 6.4 - - - +
190C SER* 1.3 78.8 + - - +
192C MET* 1.3 68.1 + - - +
193C GLY 3.3 4.0 + - - +
217C SER* 4.2 15.5 - - - +
218C GLY 4.5 3.4 - - - -
219C VAL* 3.5 10.1 - - - +
220C CYS* 2.0 70.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 192 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLY* 4.3 7.2 - - - -
138B THR 4.7 6.3 - - - +
140B GLY 3.1 15.0 - - - +
142B GLY* 2.8 27.8 + - - +
152C PRO* 5.6 4.7 - - + -
156C GLN* 3.4 50.0 - - + +
157C GLN 4.1 6.5 - - - +
158C ALA* 3.8 16.8 - - + -
188C VAL* 3.7 28.9 - - + -
189C ASP 3.6 17.7 - - - +
190C SER 3.2 0.6 - - - -
191C CYS* 1.3 85.0 - - - +
193C GLY* 1.3 54.7 + - - +
220C CYS* 5.1 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 193 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B THR* 3.9 16.0 + - - -
139B THR 3.5 16.4 - - - -
142B GLY* 4.0 3.4 - - - -
144B THR* 4.3 10.4 - - - +
190C SER 3.5 10.4 + - - +
191C CYS 3.3 9.3 - - - +
192C MET* 1.3 81.2 - - - +
194C ASP* 1.3 66.8 + - - -
213C VAL* 4.4 10.8 - - - +
217C SER* 4.9 1.2 - - - +
----------------------------------------------------------
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