Contacts of the helix formed by residues 209 - 225 (chain C) in PDB entry 3OX4
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 209 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C SER* 3.9 29.2 - - - +
6C PHE* 5.7 0.7 - - - -
207C ALA 3.6 10.5 - - - +
208C ALA* 1.3 78.6 - - - +
210C PRO* 1.3 76.2 - - - +
211C ILE* 3.1 17.8 + - - +
212C THR* 2.9 22.1 + - + +
213C ASP* 3.0 27.4 + - - -
256C ASN 5.8 1.6 - - - +
245D TYR* 4.2 10.1 - - - +
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Residues in contact with PRO 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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209C THR* 1.3 89.0 - - - +
211C ILE* 1.3 60.4 + - - +
213C ASP* 3.6 5.7 + - - +
214C ALA* 3.3 19.4 + - - +
218D LYS* 3.5 21.1 - - - +
222D MET* 3.5 40.6 - - + -
245D TYR* 4.1 30.1 - - + -
249D LEU* 4.7 2.5 - - + -
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Residues in contact with ILE 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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6C PHE* 3.6 32.8 - - + -
209C THR* 3.1 6.8 + - - +
210C PRO* 1.3 75.4 - - - +
212C THR* 1.3 64.6 + - - +
214C ALA* 3.4 3.5 + - - +
215C CYS* 3.3 24.1 + - - -
14D MET* 3.6 40.8 - - + -
245D TYR* 4.0 15.5 - - + -
248D PHE* 3.7 18.2 - - + -
249D LEU* 4.0 24.7 - - + -
252D MET* 3.9 20.2 - - + -
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Residues in contact with THR 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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6C PHE* 4.6 5.6 - - + -
202C ALA 4.7 2.8 + - - -
208C ALA* 3.5 10.4 - - - +
209C THR* 2.9 38.1 + - + +
211C ILE* 1.3 75.3 - - - +
213C ASP* 1.3 59.4 + - - +
215C CYS* 3.3 2.6 + - - -
216C ALA* 2.8 33.6 + - - +
252C MET 4.0 3.1 - - - +
253C ALA* 3.4 37.1 - - - +
256C ASN* 3.8 22.0 - - + -
257C ALA* 3.7 11.2 - - + +
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Residues in contact with ASP 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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203C TYR* 3.6 23.9 + - + +
208C ALA* 3.5 13.1 - - - +
209C THR 3.0 28.9 + - - +
210C PRO* 3.6 9.3 - - + +
212C THR* 1.3 78.1 + - - +
214C ALA* 1.3 64.1 + - - +
216C ALA* 3.8 1.2 - - - +
217C LEU* 3.0 31.2 + - + +
299C ARG* 3.0 32.0 + - - -
218D LYS* 4.6 11.2 + - - +
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Residues in contact with ALA 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 PRO 3.3 7.3 + - - +
211C ILE 3.8 4.7 - - - +
212C THR 3.4 0.2 - - - -
213C ASP* 1.3 79.6 - - - +
215C CYS* 1.3 58.6 + - - +
217C LEU* 3.6 6.3 + - - +
218C LYS* 3.1 30.5 + - - +
214D ALA* 4.2 15.2 - - + +
215D CYS* 5.2 0.9 - - - +
218D LYS* 3.7 39.7 - - + +
249D LEU* 4.7 6.5 - - + -
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Residues in contact with CYS 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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211C ILE* 3.3 26.5 + - - +
212C THR* 3.8 4.5 - - - +
214C ALA* 1.3 78.5 - - - +
216C ALA* 1.3 60.0 + - - +
218C LYS* 3.4 1.4 + - - +
219C ALA* 2.9 30.1 + - - +
249C LEU* 3.4 35.9 - - + +
252C MET* 3.8 40.2 - - + -
253C ALA* 4.2 4.0 - - + +
214D ALA* 5.4 0.9 - - - -
215D CYS* 5.0 7.9 - - - -
252D MET* 4.9 2.2 - - - -
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Residues in contact with ALA 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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199C ALA* 3.4 38.0 - - - +
202C ALA* 4.4 0.2 - - + -
203C TYR* 4.2 17.7 - - + +
212C THR 2.8 21.8 + - - +
213C ASP 3.8 3.1 - - - +
215C CYS* 1.3 73.0 - - - +
217C LEU* 1.3 64.5 + - - +
219C ALA* 3.4 1.7 + - - -
220C ALA* 3.0 20.6 + - - +
253C ALA* 3.9 15.4 - - + +
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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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203C TYR* 3.2 57.2 - - + +
213C ASP* 3.0 17.0 + - + +
214C ALA* 4.0 6.1 - - - +
216C ALA* 1.3 75.3 - - - +
218C LYS* 1.3 65.9 + - - +
220C ALA* 3.3 2.1 + - - -
221C SER* 3.0 24.0 + - - -
302C ASP* 4.5 7.4 - - + +
303C VAL* 4.1 22.0 - - + -
306C ALA* 3.5 21.0 - - + +
218D LYS* 6.2 1.3 - - - +
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Residues in contact with LYS 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 ALA 3.1 18.6 + - - +
215C CYS* 3.7 4.5 - - - +
217C LEU* 1.3 75.8 - - - +
219C ALA* 1.3 62.5 + - - +
221C SER* 3.1 12.0 + - - -
222C MET* 3.0 45.8 + - + +
249C LEU* 3.5 22.2 - - + -
210D PRO* 3.3 26.3 - - - +
213D ASP* 4.8 9.7 + - - +
214D ALA* 3.6 25.9 - - + +
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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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199C ALA* 4.1 3.6 - - + -
215C CYS 2.9 19.0 + - - +
216C ALA 3.5 6.1 - - - +
218C LYS* 1.3 77.3 - - - +
220C ALA* 1.3 62.1 + - - +
222C MET 3.3 1.2 + - - -
223C ILE* 3.0 32.0 + - + +
246C ALA* 3.5 30.3 - - - +
249C LEU* 4.0 4.5 - - + +
250C ALA* 3.6 22.0 - - + +
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Residues in contact with ALA 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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196C LEU* 4.0 24.5 - - + -
199C ALA* 4.2 4.9 - - + +
216C ALA 3.0 16.7 + - - +
217C LEU* 3.3 5.6 + - - +
219C ALA* 1.3 76.1 - - - +
221C SER* 1.3 56.4 + - - +
223C ILE* 4.1 1.1 - - - +
224C ALA* 3.2 27.9 + - - +
303C VAL* 3.9 29.4 - - + +
306C ALA* 4.6 1.1 - - + -
307C MET* 3.6 12.4 - - + +
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Residues in contact with SER 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 13.1 + - - -
218C LYS* 3.1 19.1 + - - +
220C ALA* 1.3 76.7 - - - +
222C MET* 1.3 63.3 + - - +
224C ALA* 3.6 1.7 + - - +
225C LYS* 3.1 51.0 + - - +
306C ALA* 3.2 26.8 + - - -
307C MET* 4.6 0.2 - - - +
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Residues in contact with MET 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 LYS* 3.0 24.9 + - + +
221C SER* 1.3 78.3 - - - +
223C ILE* 1.3 59.8 + - - +
225C LYS* 3.3 2.4 + - - -
226C ASN* 2.8 44.0 + - - +
242C ALA* 3.5 31.2 - - + +
243C MET* 4.5 0.6 - - - +
245C TYR* 3.9 5.2 - - + -
246C ALA* 3.7 20.9 - - + -
249C LEU* 3.8 22.4 - - - -
210D PRO* 3.5 40.2 - - + -
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Residues in contact with ILE 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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192C GLY 3.9 4.9 - - - +
195C ALA* 3.9 16.4 - - + +
196C LEU* 3.5 51.8 - - + +
199C ALA* 5.4 0.2 - - + -
219C ALA* 3.0 27.4 + - + +
220C ALA* 4.1 4.5 - - - +
222C MET* 1.3 73.5 - - - +
224C ALA* 1.3 63.2 + - - +
225C LYS 3.1 2.0 - - - -
227C LEU* 3.0 51.0 + - + +
228C LYS 4.8 0.2 + - - -
243C MET* 4.0 15.7 - - + -
246C ALA* 3.9 15.7 - - + +
330C LEU* 4.6 3.8 - - + +
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Residues in contact with ALA 224 (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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220C ALA 3.2 16.7 + - - +
221C SER 4.0 3.4 - - - +
222C MET 3.4 0.4 - - - -
223C ILE* 1.3 80.6 - - - +
225C LYS* 1.3 60.2 + - + +
226C ASN 3.9 0.2 + - - -
227C LEU 5.3 0.2 + - - -
228C LYS* 5.9 1.9 + - - +
307C MET* 3.3 48.9 - - + +
330C LEU* 5.2 10.1 - - - +
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Residues in contact with LYS 225 (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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221C SER* 3.1 34.9 + - - +
222C MET* 3.3 2.3 + - - -
223C ILE 3.1 0.4 - - - -
224C ALA* 1.3 83.4 - - + +
226C ASN* 1.3 76.4 + - - +
228C LYS* 6.6 0.2 - - - -
229C THR* 4.8 5.5 + - - -
306C ALA 5.0 4.0 - - - -
307C MET 5.5 2.0 - - - +
308C GLY* 5.8 7.0 - - - +
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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
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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