Contacts of the helix formed by residues 213 - 229 (chain C) in PDB entry 6PUO
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 213 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C GLY 3.7 1.8 - - - -
177C ALA 3.4 13.9 - - - -
178C LYS 3.4 16.8 - - - -
179C ASN* 4.1 14.2 - - - +
180C PHE* 4.4 6.1 - - - -
212C THR* 1.3 75.9 + - - +
214C VAL* 1.3 60.5 - - - -
216C LYS* 2.9 26.0 + - - +
217C GLN* 3.5 8.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C VAL* 4.2 21.8 - - + -
174C THR* 4.4 5.4 - - - +
175C GLY* 3.7 10.3 - - - +
176C GLY 3.3 34.9 + - - +
180C PHE* 3.6 21.5 - - + -
190C PHE* 6.0 0.7 - - + -
213C GLY* 1.3 70.1 - - - -
215C MET* 1.3 60.2 + - + +
217C GLN* 2.9 25.3 + - + +
218C VAL* 3.2 16.1 + - + +
330C LEU* 3.7 32.5 - - + -
331C GLU 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C GLY 5.8 1.3 - - - +
176C GLY 4.5 3.1 - - - +
177C ALA* 4.0 30.5 - - + -
207C THR* 3.5 13.7 - - - +
208C GLY* 3.2 39.5 - - - +
210C SER* 3.0 35.2 - - - +
212C THR* 3.5 17.9 - - + +
214C VAL* 1.3 77.5 - - + +
216C LYS* 1.3 62.1 + - - +
218C VAL* 3.6 17.8 - - - +
219C GLY 3.9 1.6 + - - -
278C ASP* 3.4 9.7 - - - +
281C HIS* 3.7 9.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ASN* 3.5 34.3 + - - +
191C ARG* 6.1 0.4 - - - +
210C SER 4.3 0.4 + - - -
211C HIS* 3.3 45.8 - - + +
212C THR 3.4 3.2 + - - -
213C GLY 2.9 12.2 + - - +
215C MET* 1.3 77.9 - - - +
217C GLN* 1.3 75.7 + - - +
219C GLY* 3.0 13.9 + - - -
220C GLU* 3.1 31.8 + - - +
278C ASP* 3.7 10.8 - - - +
280C ASN* 4.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ASN* 5.1 1.6 + - - -
180C PHE* 3.4 53.7 + - - -
181C ASN* 4.9 0.8 - - - +
182C MET* 3.4 26.3 - - - +
187C LYS* 4.3 11.9 - - - +
190C PHE* 5.3 12.1 - - + -
191C ARG* 4.5 11.3 + - - +
213C GLY 3.7 12.9 + - - +
214C VAL* 2.9 9.7 + - + +
216C LYS* 1.3 86.5 - - - +
218C VAL* 1.3 63.0 + - - +
220C GLU* 3.0 28.4 + - - +
221C ALA* 3.1 7.1 + - - +
330C LEU* 5.6 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C VAL* 4.8 15.0 - - + -
190C PHE* 5.2 9.3 - - + -
194C LEU* 3.8 27.8 - - + -
205C ILE* 4.6 19.5 - - + -
207C THR* 4.7 7.2 - - + +
214C VAL* 3.2 19.4 + - + +
215C MET* 3.6 15.5 - - - +
217C GLN* 1.3 76.9 - - - +
219C GLY* 1.3 64.4 + - - +
221C ALA* 3.0 17.8 + - - +
222C VAL* 3.1 19.9 + - + +
238C THR* 5.9 1.3 - - + -
281C HIS* 4.6 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C MET 3.9 3.7 + - - -
216C LYS 3.0 9.2 + - - -
218C VAL* 1.3 83.4 - - - +
220C GLU* 1.3 62.4 + - - +
222C VAL* 3.0 11.3 + - - +
223C ARG 2.9 18.4 + - - -
278C ASP* 4.8 2.9 - - - -
280C ASN* 3.1 31.9 + - - +
281C HIS* 5.2 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C ARG* 3.8 26.5 + - - +
211C HIS* 6.2 0.2 - - - -
216C LYS* 3.1 33.0 + - - +
217C GLN* 3.0 17.2 + - - +
219C GLY* 1.3 75.0 - - - +
221C ALA* 1.3 59.8 + - - +
223C ARG* 3.0 39.0 + - - +
224C ASP* 2.9 28.3 + - - +
280C ASN* 3.7 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C PHE* 5.8 0.9 - - + -
191C ARG* 3.7 43.5 - - + +
194C LEU* 5.1 10.3 - - + -
195C VAL* 4.7 12.0 - - + +
217C GLN 3.1 4.7 + - - +
218C VAL* 3.0 14.1 + - - +
220C GLU* 1.3 78.8 - - - +
222C VAL* 1.3 62.8 + - + +
224C ASP* 3.0 19.5 + - - +
225C PHE* 3.2 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C LEU* 6.4 0.2 - - + -
195C VAL* 5.6 0.2 - - - -
205C ILE* 5.7 3.8 - - + -
218C VAL* 3.1 19.5 + - + +
219C GLY* 3.0 13.8 + - - +
221C ALA* 1.3 75.5 - - + +
223C ARG* 1.3 63.5 + - - +
225C PHE* 3.0 14.4 + - - +
226C SER* 3.1 10.7 + - - -
236C LEU* 4.3 32.1 - - + +
238C THR* 4.1 25.4 - - + +
280C ASN* 4.2 17.7 - - + +
281C HIS* 6.3 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C ARG* 5.9 0.6 - - - +
219C GLY 2.9 11.6 + - - +
220C GLU* 3.0 36.4 + - - +
222C VAL* 1.3 77.8 - - - +
224C ASP* 1.3 70.3 + - - +
226C SER* 2.3 34.1 + - - +
227C LEU* 2.9 15.4 + - - +
280C ASN* 4.0 23.4 - - - +
505D GLU 4.2 16.6 + - - -
506D ASN* 5.0 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C ARG* 3.8 31.9 + - + +
195C VAL* 6.3 1.6 - - + -
220C GLU 2.9 16.8 + - - +
221C ALA* 3.0 10.2 + - - +
223C ARG* 1.3 92.8 + - - +
225C PHE* 1.3 56.7 + - - +
227C LEU* 3.0 25.2 + - + +
228C SER* 3.0 12.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 225 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C VAL* 3.6 25.0 - - + +
199C GLN* 3.8 31.2 - - + -
221C ALA 3.2 5.2 + - - +
222C VAL 3.0 11.0 + - - +
224C ASP* 1.3 76.1 - - - +
226C SER* 1.3 54.2 + - - +
228C SER* 2.9 14.9 + - - +
229C SER* 2.6 39.2 + - - -
230C SER* 4.8 11.4 - - - -
231C TYR 4.4 14.1 - - - -
232C LYS 4.3 13.5 - - - -
233C GLU* 4.5 16.4 - - - -
236C LEU* 3.6 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 226 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C VAL* 3.1 8.8 + - - -
223C ARG* 2.3 40.7 + - - +
225C PHE* 1.3 75.1 - - - +
227C LEU* 1.3 63.1 + - - +
229C SER* 4.0 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C ARG* 2.9 11.1 + - - +
224C ASP* 3.0 19.0 + - - +
226C SER* 1.3 79.3 + - - +
228C SER* 1.3 61.4 + - - +
229C SER* 5.1 0.2 - - - -
505D GLU* 5.9 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ASP 3.0 9.8 + - - -
225C PHE* 2.9 18.8 + - - -
227C LEU* 1.3 81.0 - - - +
229C SER* 1.3 70.6 + - - +
230C SER* 3.4 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C PHE* 2.6 30.5 + - - -
226C SER* 4.0 14.6 - - - -
228C SER* 1.3 74.8 - - - +
230C SER* 1.3 65.9 + - - +
231C TYR* 3.6 2.9 - - - -
233C GLU* 4.8 17.6 - - - +
1134D GLN* 3.7 10.2 + - - +
----------------------------------------------------------
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