Contacts of the helix formed by residues 217 - 225 (chain A) in PDB entry 3G0H
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 THR 217 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 4.7 0.9 - - - -
169A SER 3.6 9.9 - - - +
171A THR* 3.5 38.4 - - - +
172A TYR* 3.8 8.6 - - - +
175A ALA* 4.5 4.7 - - + -
197A ALA 3.1 8.4 + - - -
198A VAL* 3.9 10.2 - - + +
199A ARG 4.3 1.2 + - - -
216A GLY* 1.3 75.2 - - - -
218A PRO* 1.3 70.5 - - - +
219A GLY 3.2 1.6 + - - -
220A THR 3.4 2.1 + - - -
221A VAL* 3.1 22.0 + - - +
4E U 3.5 17.2 + - - -
5E U 2.8 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 4.8 4.2 - - + -
169A SER 3.3 14.8 - - - +
170A PRO* 4.7 0.2 - - + -
216A GLY 4.7 0.2 - - - +
217A THR* 1.3 86.3 - - - +
219A GLY* 1.3 61.3 + - - +
222A LEU* 3.1 24.1 + - - +
247A MET* 3.5 26.9 - - + -
253A HIS* 3.6 21.1 - - + -
256A GLN* 3.2 28.5 - - + +
257A SER* 4.6 3.1 - - - +
260A ILE* 3.4 17.5 - - + +
4E U 3.4 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A THR 3.2 1.0 + - - -
218A PRO* 1.3 72.7 - - - +
220A THR* 1.3 63.1 + - - +
222A LEU* 3.1 3.6 + - - +
223A ASP 3.0 18.2 + - - -
256A GLN* 3.7 15.5 - - - -
4E U 2.9 20.5 + - - -
5E U 3.1 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ALA* 3.3 32.1 - - - -
198A VAL 3.7 18.8 - - - +
199A ARG* 3.7 4.7 + - - +
201A ASN 5.5 2.2 - - - +
217A THR 3.4 0.6 + - - -
219A GLY* 1.3 70.2 - - - +
221A VAL* 1.3 67.9 + - - +
223A ASP* 3.1 7.0 + - - +
224A TRP* 2.9 49.8 + - + +
5E U 2.6 38.4 + - - +
6E U 5.8 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 4.0 26.2 - - + -
168A LEU* 3.7 17.9 - - + -
197A ALA* 3.5 26.7 - - + -
214A VAL* 4.7 0.2 - - + -
216A GLY* 3.7 10.1 - - - +
217A THR 3.1 16.7 + - - +
220A THR* 1.3 75.7 - - - +
222A LEU* 1.3 58.2 + - - +
224A TRP* 3.2 4.1 + - - +
225A CYS* 2.8 45.7 + - - -
231A ILE* 5.3 0.9 - - + -
260A ILE* 3.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A PRO 3.1 13.3 + - - +
219A GLY 3.1 11.4 + - - +
221A VAL* 1.3 77.3 - - - +
223A ASP* 1.3 57.5 + - - +
225A CYS* 3.5 2.2 + - - -
226A SER* 2.8 45.1 + - - +
256A GLN* 3.9 26.2 - - + +
259A ARG* 3.6 43.3 - - + +
260A ILE* 3.4 34.8 - - + +
263A MET* 4.4 6.3 - - - -
5E U 4.2 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A GLY 3.0 6.7 + - - +
220A THR* 3.6 8.1 - - + +
222A LEU* 1.3 76.4 - - - +
224A TRP* 1.3 62.0 + - - +
226A SER* 3.2 5.5 + - - -
227A LYS* 3.5 22.2 + - - +
228A LEU* 2.9 44.1 + - + +
5E U 2.7 54.7 + - - +
6E U 3.1 18.9 + - - +
7E U 4.3 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ALA* 4.3 6.7 - - + -
196A TYR 3.3 30.3 - - - -
197A ALA* 3.6 22.4 - - + -
201A ASN* 4.3 14.9 + - + -
202A LYS* 6.1 0.6 - - - +
203A LEU* 3.5 26.9 - - + -
209A ILE* 3.6 24.2 - - + -
214A VAL* 4.6 0.7 - - + -
220A THR* 2.9 30.8 + - + +
221A VAL* 3.2 8.9 + - - +
223A ASP* 1.3 75.7 - - + +
225A CYS* 1.3 59.1 + - - +
228A LEU* 3.5 24.4 - - + +
229A LYS* 3.4 5.5 + - - -
230A PHE* 2.8 48.7 + + + -
231A ILE* 3.1 36.5 + - + -
6E U 5.1 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 4.5 8.1 - - - -
221A VAL* 2.8 36.0 + - - +
222A LEU* 3.9 4.9 - - + +
224A TRP* 1.3 76.3 - - - +
226A SER* 1.3 59.2 + - - +
229A LYS* 5.0 5.6 - - - +
231A ILE* 3.6 32.4 - - - +
233A PRO* 4.0 26.6 - - + +
260A ILE* 5.1 5.6 - - + -
263A MET* 3.1 32.2 - - - +
----------------------------------------------------------
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