Contacts of the helix formed by residues 206 - 226 (chain G) in PDB entry 6V3O
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 206 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204G ASP 5.0 4.5 - - - +
205G ILE* 1.3 79.4 - - - +
207G ASP* 1.3 62.2 + - - +
208G ASP* 3.8 5.2 + - - +
209G ASP* 3.1 35.1 + - - +
210G LYS* 3.0 28.0 + - - +
122H ARG* 6.1 5.4 - - - +
262H ARG* 4.8 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 207 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205G ILE 4.8 2.5 - - - +
206G THR* 1.3 74.7 - - - +
208G ASP* 1.3 64.4 + - - +
210G LYS* 3.2 10.4 + - - +
211G GLN* 2.8 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 208 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206G THR* 3.3 5.2 + - - +
207G ASP* 1.3 77.1 - - - +
209G ASP* 1.3 65.2 + - - +
211G GLN* 3.2 8.0 + - - +
212G GLU* 3.0 28.4 + - - +
142H ASP* 5.7 1.6 - - - +
144H GLU* 2.7 34.8 - - - +
262H ARG* 3.7 38.0 + - - +
265H THR* 3.6 14.2 - - + +
269H ASN* 3.4 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 209 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205G ILE* 3.4 28.0 - - + +
206G THR* 3.1 30.2 + - - +
208G ASP* 1.3 75.7 - - - +
210G LYS* 1.3 58.9 + - - +
212G GLU* 3.4 5.4 + - - +
213G LEU* 2.9 39.0 + - + +
262H ARG* 2.6 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 210 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200G LEU* 3.6 43.1 + - + +
202G ALA 4.9 1.6 + - - -
205G ILE* 3.4 39.8 - - + +
206G THR 3.0 10.5 + - - +
207G ASP* 3.5 12.8 - - - +
209G ASP* 1.3 73.9 - - - +
211G GLN* 1.3 61.2 + - - +
213G LEU* 3.2 3.3 + - - +
214G ASP* 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 211 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207G ASP* 2.8 20.2 + - - +
208G ASP* 3.2 9.9 + - - +
210G LYS* 1.3 73.5 - - - +
212G GLU* 1.3 57.4 + - - +
214G ASP* 3.6 6.2 - - + +
215G GLU* 3.1 47.4 + - + +
265H THR* 3.8 20.7 + - + +
268H LYS* 5.2 7.9 - - - +
269H ASN* 3.7 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 212 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208G ASP 3.0 14.7 + - - +
209G ASP* 3.9 5.1 - - - +
211G GLN* 1.3 75.9 - - - +
213G LEU* 1.3 63.5 + - + +
214G ASP 3.2 0.2 - - - -
215G GLU* 3.5 13.6 + - - +
216G ALA* 3.0 23.6 + - - +
219G ARG* 5.4 0.9 + - - -
258H LYS 5.3 1.9 - - - +
261H ARG* 3.5 23.3 - - + +
262H ARG* 3.1 50.5 + - - +
265H THR* 2.5 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G CYS* 4.1 18.2 - - + +
199G GLN* 3.2 59.7 - - + +
200G LEU* 3.8 19.9 - - + +
205G ILE* 4.7 11.2 - - + -
209G ASP* 2.9 29.2 + - + +
210G LYS* 3.8 4.3 - - - +
212G GLU* 1.3 76.5 - - - +
214G ASP* 1.3 57.0 + - - +
216G ALA* 3.3 6.9 + - + +
217G LEU* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 214 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G LEU* 5.6 1.1 - - - +
44G ARG* 2.8 46.3 + - - +
200G LEU* 4.3 16.7 - - + +
210G LYS 2.8 17.2 + - - +
211G GLN* 3.6 8.7 - - + +
212G GLU 3.2 0.2 - - - -
213G LEU* 1.3 73.6 - - - +
215G GLU* 1.3 65.5 + - - +
217G LEU* 3.1 9.1 + - - +
218G GLN* 2.9 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 215 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211G GLN* 3.1 37.6 + - + +
212G GLU* 3.9 14.3 - - - +
214G ASP* 1.3 75.2 - - + +
216G ALA* 1.3 58.1 + - - +
218G GLN* 3.5 13.5 + - - +
219G ARG* 2.9 44.1 + - - +
261H ARG* 4.9 2.3 + - - +
265H THR* 5.3 5.1 + - - +
268H LYS* 5.7 5.8 - - - +
275H ARG* 3.0 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G CYS* 4.3 13.7 - - - -
212G GLU 3.0 17.9 + - - +
213G LEU* 3.6 7.9 - - + +
214G ASP 3.2 0.2 - - - -
215G GLU* 1.3 76.7 - - - +
217G LEU* 1.3 58.5 + - - +
219G ARG* 3.3 22.2 + - - +
220G GLU* 2.9 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G LEU* 3.4 33.0 - - + -
41G LEU* 4.2 11.0 - - + -
44G ARG* 5.0 8.1 - - + -
193G ILE* 3.8 44.0 - - + +
196G CYS* 4.3 14.7 - - + -
197G LEU* 4.7 4.3 - - + +
200G LEU* 3.9 16.4 - - + -
213G LEU 2.9 16.7 + - - +
214G ASP* 3.1 8.0 + - - +
216G ALA* 1.3 72.6 - - - +
218G GLN* 1.3 66.2 + - - +
220G GLU* 3.1 5.2 + - - +
221G ILE* 3.0 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 218 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G ARG* 3.7 29.8 - - + +
48G ILE* 3.3 25.7 - - + +
214G ASP* 2.9 41.8 + - - +
215G GLU* 3.8 13.3 - - - +
217G LEU* 1.3 75.3 - - - +
219G ARG* 1.3 63.5 + - - +
221G ILE* 3.4 4.6 + - - -
222G GLN* 3.0 22.7 + - - +
430H ALA* 6.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 219 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212G GLU 5.5 0.4 + - - -
215G GLU* 2.9 35.9 + - - +
216G ALA* 3.4 27.6 - - - +
218G GLN* 1.3 77.3 - - - +
220G GLU* 1.3 61.7 + - + +
222G GLN* 3.4 5.3 + - - +
223G ALA* 3.0 27.7 + - - +
261H ARG* 3.3 27.7 - - - +
275H ARG* 3.8 13.3 - - - +
430H ALA* 3.1 40.2 + - + +
431H ILE* 3.8 11.0 - - + +
433H ASP* 3.6 12.7 + - - +
434H GLY* 3.4 24.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 220 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G LYS* 4.0 16.6 - - - +
192G ARG* 2.5 71.8 + - + +
193G ILE* 3.8 20.6 - - + +
196G CYS* 5.3 2.0 - - - -
216G ALA* 2.9 22.1 + - + +
217G LEU* 3.1 6.5 + - - +
219G ARG* 1.3 78.0 - - + +
221G ILE* 1.3 66.2 + - - +
223G ALA* 3.3 6.9 + - - +
224G ALA* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 221 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G LEU* 3.8 28.7 - - + +
44G ARG* 4.1 15.3 - - + -
45G PHE* 3.8 28.5 - - + -
48G ILE* 3.7 14.4 - - + -
108G LEU* 4.2 24.7 - - + -
193G ILE* 4.5 13.5 - - + -
217G LEU* 3.0 33.6 + - + +
218G GLN* 3.8 4.5 - - - +
220G GLU* 1.3 76.8 - - - +
222G GLN* 1.3 62.6 + - - +
224G ALA* 3.2 5.7 + - - +
225G PHE* 3.0 21.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 222 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ILE* 3.9 33.5 - - + +
51G ASP* 5.4 3.5 + - - +
52G LEU* 4.0 8.9 - - + +
218G GLN 3.0 16.7 + - - +
219G ARG 3.7 4.5 - - - +
221G ILE* 1.3 78.6 - - - +
223G ALA* 1.3 63.5 + - - +
225G PHE* 3.1 4.6 + - - +
226G ARG* 3.1 36.3 + - + +
427H GLY 3.6 15.8 + - - -
428H ASP* 3.4 29.5 + - - +
430H ALA* 3.2 28.2 - - - +
431H ILE* 4.0 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 223 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G LYS* 3.7 20.2 - - + -
192G ARG* 6.1 0.9 - - - +
219G ARG 3.0 17.9 + - - +
220G GLU* 3.7 10.8 - - - +
221G ILE 3.3 0.2 - - - -
222G GLN* 1.3 75.3 - - - +
224G ALA* 1.3 63.3 + - - +
226G ARG* 3.3 7.4 + - - +
227G THR* 3.1 24.8 + - - +
329H GLU 5.6 0.4 - - - +
332H MET* 4.7 4.8 - - - +
431H ILE* 4.1 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G HIS* 3.3 22.4 - - + +
186G LEU* 5.3 13.2 - - + +
189G LYS* 4.0 19.5 - - + +
190G ASN* 6.0 0.9 - - - +
193G ILE* 4.8 12.1 - - + -
220G GLU 3.0 14.0 + - - +
221G ILE* 3.6 8.7 - - - +
223G ALA* 1.3 76.9 - - - +
225G PHE* 1.3 62.1 + - - +
227G THR* 3.2 14.5 + - - -
228G ASP 4.3 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 225 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G PHE* 3.3 41.3 - + + -
48G ILE* 5.7 3.4 - - + -
49G LEU* 4.0 19.7 - - + -
52G LEU* 4.4 10.1 - - + -
53G HIS* 4.0 14.1 - - - -
97G LEU* 4.1 23.3 - - + -
100G SER* 4.5 9.9 - - - -
101G SER* 3.9 12.3 - - - -
104G HIS* 3.9 18.5 + + + +
221G ILE 3.0 14.1 + - - +
222G GLN* 3.1 10.9 + - - +
224G ALA* 1.3 78.0 - - - +
226G ARG* 1.3 84.0 + - + +
227G THR 3.4 0.9 + - - -
228G ASP* 3.8 16.6 - - - +
334H ARG* 4.9 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 226 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G LEU* 3.7 26.1 + - - +
53G HIS* 4.1 18.6 + - - -
222G GLN* 3.1 26.5 + - + +
223G ALA 3.3 0.9 + - - +
224G ALA 3.3 0.6 - - - -
225G PHE* 1.3 91.5 - - + +
227G THR* 1.3 62.3 + - - +
228G ASP 3.5 1.1 - - - -
332H MET* 3.4 29.1 - - + +
333H TRP* 4.2 10.8 + - - -
334H ARG* 2.9 50.0 + - - +
426H CYS* 3.0 29.7 + - - +
428H ASP* 2.9 28.1 + - - +
431H ILE* 4.7 2.7 - - + -
----------------------------------------------------------
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