Contacts of the helix formed by residues 203 - 223 (chain C) in PDB entry 3GXM
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 203 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198C LYS 3.2 3.6 - - - +
199C GLY* 3.0 13.5 - - - -
200C GLN* 2.4 64.3 + - - +
202C GLY* 1.3 75.6 - - - +
204C ILE* 1.3 70.9 + - + +
205C TYR* 3.0 20.1 + - + +
206C HIS* 3.0 16.9 + - - +
207C GLN* 3.1 27.4 + - - +
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Residues in contact with ILE 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C PHE* 4.3 25.6 - - + -
203C ASP* 1.3 83.6 - - + +
205C TYR* 1.3 71.3 + - + +
207C GLN* 3.7 5.9 + - + +
208C THR* 2.9 33.9 + - - +
211C ARG* 5.1 0.4 + - - +
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Residues in contact with TYR 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C PHE* 3.4 35.2 - + - -
184C TRP 4.4 3.4 - - - -
185C LEU* 3.9 25.1 - - + +
197C LEU* 4.6 3.8 - - + +
198C LYS* 3.0 74.7 + - + +
199C GLY* 4.6 2.7 - - - -
203C ASP* 3.0 11.6 + - + +
204C ILE* 1.3 85.2 - - + +
206C HIS* 1.3 60.9 + - - +
208C THR* 3.2 2.9 + - - -
209C TRP* 2.8 29.7 + - - +
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Residues in contact with HIS 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C LEU* 3.8 26.0 - - + +
198C LYS 3.4 19.5 + - - -
199C GLY 4.0 4.0 - - - -
200C GLN 3.3 16.9 + - - -
201C PRO* 3.5 22.7 - - + -
202C GLY 4.0 2.9 - - - +
203C ASP* 3.0 27.2 + - - +
205C TYR* 1.3 72.5 - - - +
207C GLN* 1.3 60.2 + - - +
209C TRP* 3.4 5.9 + - - -
210C ALA* 3.0 30.5 + - - +
255C HIS* 2.9 30.8 + + - -
259C PHE* 3.7 16.0 - + + -
263C ASP* 3.1 24.2 - - + +
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Residues in contact with GLN 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C GLY* 3.8 9.6 + - - +
203C ASP 3.1 21.7 + - - +
204C ILE* 3.9 6.5 - - - +
205C TYR 3.3 0.2 - - - -
206C HIS* 1.3 77.5 - - - +
208C THR* 1.3 56.1 + - - +
210C ALA* 3.7 2.8 + - - +
211C ARG* 3.2 46.4 + - - +
262C ARG 4.0 5.7 + - - -
263C ASP* 2.3 45.4 + - - +
266C PRO* 6.1 0.6 - - - +
267C THR* 4.1 13.9 + - - +
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Residues in contact with THR 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ASP 4.2 0.7 - - - +
142C PHE* 2.6 46.5 + - - +
144C LEU* 3.6 27.1 - - + +
184C TRP* 4.5 1.8 - - + -
185C LEU* 4.3 18.8 - - + -
204C ILE* 2.9 22.8 + - - +
205C TYR 3.2 4.5 + - - -
207C GLN* 1.3 72.5 - - - +
209C TRP* 1.3 67.1 + - - +
211C ARG* 3.2 12.0 + - - +
212C TYR* 2.9 21.7 + - + +
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Residues in contact with TRP 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C PRO* 3.6 29.6 - - + -
180C THR 3.6 19.3 - - - -
181C SER* 3.5 23.8 - - - -
185C LEU* 4.3 7.1 - - + +
197C LEU* 3.6 31.2 - - + -
205C TYR 2.8 17.5 + - - +
206C HIS 3.4 4.9 + - - +
208C THR* 1.3 76.7 - - - +
210C ALA* 1.3 57.2 + - - +
212C TYR* 2.9 67.1 - + + +
213C PHE* 3.4 23.5 - + - -
232C ALA 4.6 2.2 + - - -
233C GLU* 4.7 1.7 + - - -
249C LEU* 3.5 25.0 - - + +
251C PHE* 4.2 6.0 - + - -
259C PHE* 3.4 25.6 - + + -
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Residues in contact with ALA 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C HIS 3.0 17.5 + - - +
207C GLN 3.9 3.6 - - - +
209C TRP* 1.3 76.6 - - - +
211C ARG* 1.3 60.9 + - - +
213C PHE* 3.1 27.5 + - - +
214C VAL* 3.6 4.0 + - - +
259C PHE* 4.0 5.7 - - + -
263C ASP* 3.9 18.4 - - + -
264C LEU* 3.9 10.4 - - - +
267C THR* 3.5 32.2 - - - +
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Residues in contact with ARG 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C PHE* 2.9 28.7 + - - +
143C GLN* 3.5 40.1 + - - +
144C LEU* 4.0 9.5 - - + +
204C ILE* 6.4 0.2 - - - +
207C GLN* 3.2 36.3 + - - +
208C THR* 3.2 20.7 + - - +
210C ALA* 1.3 72.5 - - - +
212C TYR* 1.3 54.7 + - - +
213C PHE 3.3 0.2 - - - -
214C VAL* 3.0 8.6 + - + +
215C LYS* 2.8 48.6 + - + +
267C THR* 4.0 13.3 - - + +
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Residues in contact with TYR 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C MET* 4.2 20.1 + - + -
124C ALA* 4.0 5.2 - - - +
134C THR* 3.6 9.2 - - - -
135C TYR* 3.0 46.0 + + - -
136C ALA* 4.1 12.1 - - + -
144C LEU* 3.7 13.2 - - + +
147C PHE* 3.9 17.4 - + - -
180C THR 4.5 2.8 + - - -
182C PRO* 3.4 29.2 - - + -
185C LEU* 5.7 0.9 - - + -
208C THR* 2.9 12.0 + - + +
209C TRP* 2.9 50.5 - + + +
211C ARG* 1.3 77.1 - - - +
213C PHE* 1.3 51.9 + + - +
215C LYS* 3.3 4.0 + - - +
216C PHE* 2.7 36.8 + - + +
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Residues in contact with PHE 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C MET* 4.0 19.3 - - + -
178C PRO* 3.5 20.4 - - + -
209C TRP* 3.4 40.6 - + - -
210C ALA* 3.1 9.2 + - - +
212C TYR* 1.3 78.7 - - + +
214C VAL* 1.3 60.3 + - + +
216C PHE* 3.6 1.9 + - - +
217C LEU* 3.2 34.1 + - + +
230C VAL* 4.0 23.3 - - + -
231C THR 3.4 20.9 - - - -
232C ALA 3.2 23.8 - - - -
259C PHE* 4.1 9.0 - + - -
264C LEU* 3.8 28.7 - - + -
268C LEU* 5.1 6.7 - - + -
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Residues in contact with VAL 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C ALA 4.1 3.1 - - - +
211C ARG* 3.0 13.3 + - + +
213C PHE* 1.3 76.6 - - - +
215C LYS* 1.3 55.8 + - - +
217C LEU* 3.4 5.9 + - - +
218C ASP* 2.7 57.0 + - - +
267C THR* 4.0 28.9 - - + +
268C LEU* 4.5 11.7 - - + -
271C SER* 3.9 34.1 - - - +
272C THR* 5.5 1.1 - - + +
273C HIS* 4.1 5.6 - - + -
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Residues in contact with LYS 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C GLN 4.2 10.5 - - - -
144C LEU* 3.9 37.0 - - + +
147C PHE* 3.7 26.8 - - + -
211C ARG* 2.8 36.5 + - - +
212C TYR 3.7 3.8 - - - +
214C VAL* 1.3 73.0 - - - +
216C PHE* 1.3 62.9 + - - +
218C ASP* 3.3 19.7 + - + +
219C ALA* 2.9 25.8 + - - +
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Residues in contact with PHE 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C VAL* 4.7 5.2 - - + -
122C PRO 4.8 0.7 - - - -
123C MET* 3.6 38.1 - - + -
135C TYR* 3.4 35.0 - + + -
147C PHE* 3.5 14.6 - - + -
149C LEU* 4.5 2.0 - - + -
176C ALA* 3.7 15.9 - - + -
212C TYR* 2.7 21.2 + - + +
213C PHE 3.8 1.6 - - - +
214C VAL 3.3 0.2 - - - -
215C LYS* 1.3 73.0 - - - +
217C LEU* 1.3 70.1 + - + +
219C ALA* 3.3 3.5 + - - +
220C TYR* 3.1 60.0 + + - +
227C PHE* 3.6 34.5 - + - -
230C VAL* 5.6 0.7 - - + -
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Residues in contact with LEU 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C PHE* 3.2 18.9 + - + +
214C VAL* 3.7 0.9 - - - +
216C PHE* 1.3 85.7 - - + +
218C ASP* 1.3 60.9 + - - +
220C TYR* 3.8 4.8 - - - +
221C ALA* 3.0 29.3 + - - +
225C LEU 4.7 1.4 - - - +
227C PHE* 3.7 40.1 - - + +
230C VAL* 4.2 15.7 - - + -
268C LEU* 3.9 20.9 - - + -
273C HIS* 3.6 42.5 + - + +
276C VAL* 4.4 12.8 - - + -
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Residues in contact with ASP 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C VAL* 2.7 35.6 + - - +
215C LYS* 3.3 29.7 + - + +
217C LEU* 1.3 71.1 - - - +
219C ALA* 1.3 63.2 + - - +
221C ALA* 3.1 13.5 + - - +
222C GLU* 3.2 24.9 + - - +
272C THR* 4.6 4.2 + - - +
273C HIS* 2.9 25.6 + - - -
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Residues in contact with ALA 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C PHE* 4.2 8.3 - - + -
148C SER* 6.3 0.2 - - - -
149C LEU* 3.7 29.8 - - + +
215C LYS 2.9 17.2 + - - +
216C PHE 3.6 4.5 - - - +
218C ASP* 1.3 76.1 - - - +
220C TYR* 1.3 63.2 + - - +
222C GLU* 3.4 22.1 + - - +
223C HIS* 3.1 23.1 + - - -
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Residues in contact with TYR 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C VAL* 3.6 20.6 - - + +
149C LEU* 3.9 18.8 - - + -
153C ASP* 2.4 31.9 + - - +
157C LYS* 3.7 8.3 - - - +
158C ILE* 3.6 23.4 - - + +
161C ILE* 4.5 5.2 - - + -
174C LEU* 5.5 0.4 - - + -
216C PHE* 3.1 42.9 + + - +
217C LEU 4.1 4.0 - - - +
219C ALA* 1.3 76.9 - - - +
221C ALA* 1.3 56.2 + - - +
223C HIS* 3.2 14.5 + - - +
224C LYS 3.5 0.2 + - - -
225C LEU* 2.9 50.7 + - + +
227C PHE* 3.5 38.8 - + + -
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Residues in contact with ALA 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C LEU 3.0 15.4 + - - +
218C ASP* 3.1 11.1 + - - +
220C TYR* 1.3 72.9 - - - +
222C GLU* 1.3 60.1 + - - +
223C HIS 3.0 1.8 - - - -
224C LYS* 2.9 23.4 + - - +
225C LEU 3.3 12.3 + - - +
226C GLN* 4.6 9.6 - - + +
273C HIS* 4.3 15.3 - - + -
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Residues in contact with GLU 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C ASP* 3.2 23.0 + - - +
219C ALA* 3.4 15.1 + - - +
221C ALA* 1.3 75.1 - - - +
223C HIS* 1.3 64.4 + - + +
224C LYS* 3.2 10.4 + - - +
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Residues in contact with HIS 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C LEU* 3.9 8.3 - - + +
154C THR* 3.7 33.3 - - + +
158C ILE* 3.7 40.8 - - + +
162C HIS* 2.8 33.5 + - - +
219C ALA 3.1 22.8 + - - -
220C TYR 3.2 9.5 + - - +
221C ALA 3.0 1.0 - - - -
222C GLU* 1.3 84.2 + - + +
224C LYS* 1.3 63.6 + - - +
225C LEU* 3.3 3.0 + - + +
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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
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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) + - + + + + + -
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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