Contacts of the helix formed by residues 211 - 222 (chain G) in PDB entry 6O81
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 GLY 211 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G HIS* 3.3 23.0 + - - -
153G THR* 5.9 0.3 - - - +
180G ASP* 5.0 1.6 - - - -
183G VAL* 5.2 1.9 - - - +
209G LYS* 3.1 1.8 + - - +
210G ILE* 1.3 82.2 - - - +
212G THR* 1.3 61.9 + - - +
213G ASN 3.7 0.4 - - - -
214G GLN* 3.9 13.3 + - - +
215G MET* 3.8 15.4 - - - +
181H ALA* 3.7 24.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 212 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G HIS* 3.3 18.4 + - - -
195G VAL* 3.8 19.7 - - + -
206G ILE* 4.0 11.7 - - + -
208G ASN* 3.2 22.9 + - + +
209G LYS 3.1 16.6 + - - -
210G ILE 3.3 0.4 - - - -
211G GLY* 1.3 77.5 - - - +
213G ASN* 1.3 62.2 + - - +
215G MET* 3.0 25.8 + - - +
216G ALA 3.0 9.9 + - - -
226G PHE* 3.8 15.8 - - + -
274G ASP* 4.0 2.2 - - - -
276G THR* 3.8 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 213 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210G ILE 5.2 0.2 - - - +
212G THR* 1.3 75.1 - - - +
214G GLN* 1.3 59.3 + - - +
216G ALA* 3.0 5.9 + - - +
217G VAL* 2.8 31.0 + - - +
243G GLN* 3.3 24.1 + - - +
274G ASP* 3.0 21.5 + - + +
275G TYR 3.2 18.2 - - - +
276G THR* 3.3 24.9 + - - +
277G ALA 4.5 0.5 + - - -
280G LEU* 3.9 15.2 - - - +
184H GLY 3.8 17.6 + - - -
185H TYR* 5.5 0.2 - - - +
222H GLN* 5.3 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 214 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180G ASP* 4.3 9.1 + - - -
183G VAL* 4.7 3.8 - - - +
210G ILE 4.7 2.0 + - - +
211G GLY 3.9 17.5 + - - +
213G ASN* 1.3 79.6 - - - +
215G MET* 1.3 60.4 + - + +
217G VAL* 3.0 15.1 + - - +
218G CYS* 2.8 31.4 + - - -
181H ALA* 3.4 43.4 + - - +
183H VAL* 3.3 23.8 - - - +
184H GLY* 4.3 10.9 - - - +
214H GLN* 3.2 27.8 + - + +
218H CYS* 4.0 18.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 215 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G LEU* 3.7 22.0 - - + -
128G HIS* 3.8 27.4 - - + +
153G THR* 3.8 16.6 - - - +
183G VAL* 3.8 29.8 - - + -
187G MET* 3.8 18.4 - - + +
193G VAL* 3.7 17.0 - - + -
195G VAL* 3.7 16.8 - - + -
211G GLY 3.8 8.1 - - - +
212G THR* 3.0 13.1 + - - +
214G GLN* 1.3 81.1 - - - +
216G ALA* 1.3 50.4 + - - +
218G CYS* 3.0 7.2 + - - +
219G ALA* 2.6 31.4 + - - +
226G PHE* 4.3 4.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
212G THR 3.0 7.4 + - - +
213G ASN 3.0 12.4 + - - +
215G MET* 1.3 73.0 - - - +
217G VAL* 1.3 60.2 + - - +
219G ALA* 3.0 23.5 + - - +
220G LYS* 3.0 13.9 + - - +
226G PHE* 3.9 21.5 - - + -
276G THR* 3.7 28.5 - - + -
280G LEU* 3.9 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 217 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213G ASN* 2.8 26.6 + - - +
214G GLN* 3.2 16.6 - - - +
216G ALA* 1.3 75.6 - - - +
218G CYS* 1.3 57.1 + - - +
220G LYS* 3.0 18.9 + - + +
221G ALA* 3.1 12.5 + - + +
280G LEU* 4.1 17.5 - - + -
184H GLY* 6.1 0.9 - - - -
217H VAL* 3.7 29.5 - - + +
218H CYS* 4.4 12.6 - - - -
221H ALA* 3.9 27.1 - - + -
222H GLN* 5.9 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 218 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183G VAL* 4.3 5.4 - - - +
184G GLY* 3.9 25.8 - - - -
187G MET* 3.3 37.1 - - + +
214G GLN 2.8 19.1 + - - -
215G MET* 3.2 9.9 - - - +
217G VAL* 1.3 76.0 - - - +
219G ALA* 1.3 59.2 + - - +
221G ALA* 4.8 0.9 - - - +
222G GLN* 3.3 19.9 + - + +
214H GLN* 3.9 23.1 - - - -
217H VAL* 4.4 16.2 - - - -
218H CYS* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187G MET* 4.6 2.2 - - + -
193G VAL* 4.5 7.6 - - + -
215G MET 2.6 15.9 + - - +
216G ALA* 3.0 17.6 + - - +
218G CYS* 1.3 75.2 - - - +
220G LYS* 1.3 59.3 + - - +
223G ASN* 3.5 3.3 + - - -
224G LYS* 3.0 49.4 + - - +
226G PHE* 3.8 23.3 - - + -
280G LEU 4.7 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 220 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C GLU* 5.4 14.5 + - - +
216G ALA 3.0 3.6 + - - +
217G VAL* 3.0 10.5 + - + +
219G ALA* 1.3 80.1 + - - +
221G ALA* 1.3 65.0 + - - +
222G GLN 3.2 1.3 - - - -
223G ASN* 3.4 13.0 + - - +
279G SER* 3.2 28.5 + - - -
280G LEU* 3.8 36.9 + - + +
281G ILE 6.2 0.4 - - - -
282G THR* 5.8 1.6 + - - -
221H ALA* 6.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 221 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431F ASN* 4.5 3.6 - - - +
217G VAL* 3.1 7.7 + - + +
218G CYS 5.1 0.4 - - - +
220G LYS* 1.3 77.1 - - - +
222G GLN* 1.3 63.9 + - + +
223G ASN* 3.5 1.1 + - - +
217H VAL* 3.7 32.5 - - + -
220H LYS* 6.3 3.4 - - + -
221H ALA* 6.4 0.9 - - + -
280H LEU* 6.3 3.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
431F ASN* 2.6 33.5 + - - +
184G GLY* 3.7 22.2 + - - -
187G MET* 3.2 19.4 - - + +
188G GLU* 3.1 39.0 + - - +
218G CYS* 3.3 21.4 + - - +
220G LYS 3.2 0.4 - - - -
221G ALA* 1.3 81.3 - - + +
223G ASN* 1.3 64.3 + - - +
224G LYS* 2.9 21.5 + - - +
213H ASN* 5.2 4.8 - - - +
217H VAL* 5.9 5.6 - - + +
243H GLN* 5.5 2.2 - - - +
----------------------------------------------------------
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