Contacts of the helix formed by residues 213 - 228 (chain C) in PDB entry 3N6J
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 GLU 213 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212C PHE* 1.3 86.2 - - - +
214C GLY* 1.3 67.9 + - - +
215C SER* 3.1 11.7 - - - +
216C LYS* 2.8 40.0 + - + +
217C GLU* 3.6 1.7 + - - +
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Residues in contact with GLY 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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212C PHE 3.3 4.7 + - - -
213C GLU* 1.3 69.5 - - - +
215C SER* 1.3 56.7 + - - +
217C GLU* 3.1 8.8 + - - +
218C ILE* 3.0 28.8 + - - +
241C TRP* 3.4 32.2 - - - +
245C GLU* 4.6 5.1 + - - -
249C LEU* 3.5 17.5 - - - -
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Residues in contact with SER 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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213C GLU* 2.9 11.1 + - - +
214C GLY* 1.3 69.2 - - - +
216C LYS* 1.3 74.1 + - - +
218C ILE* 3.1 7.1 + - - +
219C ASP* 3.0 32.3 + - - +
249C LEU* 3.6 22.9 - - - +
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Residues in contact with LYS 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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154C TYR* 4.5 1.6 - - - +
186C THR* 4.4 1.7 + - - -
212C PHE* 3.9 27.3 - - + -
213C GLU* 2.8 37.6 + - + +
215C SER* 1.3 85.5 + - - +
217C GLU* 1.3 62.3 + - - +
218C ILE 3.4 0.2 + - - -
219C ASP* 3.4 12.8 + - - +
220C THR* 3.3 23.0 + - - -
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Residues in contact with GLU 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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154C TYR* 3.5 25.3 - - + +
207C LEU* 4.1 8.8 - - + +
209C GLY* 3.3 9.2 - - - -
210C GLY* 2.9 22.6 + - - -
211C VAL* 2.5 16.8 + - - +
212C PHE* 2.5 49.3 + - + +
213C GLU 3.6 0.4 + - - +
214C GLY 3.1 7.9 + - - +
216C LYS* 1.3 75.7 - - - +
218C ILE* 1.3 63.5 + - - +
220C THR* 3.7 2.8 - - - -
221C VAL* 3.2 26.7 + - - +
235C LEU* 4.5 10.7 - - + +
237C PRO* 4.6 0.2 - - - +
241C TRP* 4.4 14.2 + - + -
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Residues in contact with ILE 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 GLY 3.0 21.4 + - - +
215C SER* 3.1 11.6 + - - +
217C GLU* 1.3 76.0 - - - +
219C ASP* 1.3 55.8 + - - +
221C VAL* 3.0 6.7 + - + +
222C ILE* 2.7 47.8 + - + +
235C LEU* 3.9 12.6 - - + -
241C TRP* 3.7 24.0 - - + -
249C LEU* 4.1 26.2 - - + +
250C CYS* 4.9 3.6 - - - -
253C LEU* 3.7 35.2 - - + -
257C LEU* 4.9 3.4 - - + -
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Residues in contact with ASP 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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186C THR* 4.4 7.0 - - - +
215C SER* 3.0 17.7 + - - +
216C LYS* 3.5 14.6 - - - +
218C ILE* 1.3 75.6 - - - +
220C THR* 1.3 57.5 + - - +
222C ILE* 3.2 20.9 - - - +
223C GLU* 2.9 33.2 + - + +
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Residues in contact with THR 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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154C TYR* 3.2 22.7 + - - +
186C THR* 2.5 44.8 + - + +
189C VAL* 4.1 25.8 - - + -
207C LEU* 3.8 20.4 - - + -
216C LYS 3.3 4.7 + - - -
217C GLU 3.7 5.8 - - - -
218C ILE 3.2 0.2 - - - -
219C ASP* 1.3 76.1 - - - +
221C VAL* 1.3 60.1 + - - +
223C GLU* 3.1 4.3 + - - +
224C LEU* 2.9 33.4 + - + +
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Residues in contact with VAL 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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207C LEU* 4.3 13.0 - - + -
217C GLU 3.2 13.0 + - - +
218C ILE* 3.0 11.7 + - + +
220C THR* 1.3 78.1 - - - +
222C ILE* 1.3 60.7 + - - +
224C LEU* 3.8 8.5 - - + +
225C LYS* 3.3 13.9 + - - +
233C ILE* 3.9 21.0 - - + +
235C LEU* 3.8 31.9 - - + -
253C LEU* 5.5 2.9 - - + -
256C VAL* 3.3 26.0 - - + +
257C LEU* 3.9 23.8 - - + -
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Residues in contact with ILE 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 ILE* 2.7 35.5 + - + +
219C ASP* 3.2 20.6 - - - +
220C THR 3.1 0.2 - - - -
221C VAL* 1.3 77.1 - - - +
223C GLU* 1.3 64.0 + - - +
224C LEU 3.4 0.2 + - - -
225C LYS* 3.4 4.7 + - - +
226C LYS* 3.1 50.8 + - + +
253C LEU* 4.3 20.6 - - + -
256C VAL* 4.0 12.2 - - + +
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Residues in contact with GLU 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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186C THR* 3.8 22.7 - - + -
190C ILE* 4.1 12.2 - - + +
219C ASP* 2.9 20.2 + - + +
220C THR 3.1 5.6 + - - +
222C ILE* 1.3 76.4 - - - +
224C LEU* 1.3 61.1 + - - +
226C LYS* 3.7 26.0 - - - +
227C HIS* 2.8 53.0 + - - +
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Residues in contact with LEU 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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152C LEU* 4.1 20.6 - - + -
189C VAL* 4.4 10.3 - - + +
190C ILE* 4.4 14.1 - - + -
193C ALA* 4.2 25.1 - - + -
205C PHE* 5.4 1.1 - - + -
207C LEU* 4.6 9.0 - - + +
220C THR* 2.9 32.8 + - + +
221C VAL* 3.8 18.8 - - + +
222C ILE 3.2 0.4 - - - -
223C GLU* 1.3 74.1 - - - +
225C LYS* 1.3 59.0 + - - +
228C PHE* 2.9 44.6 + - + +
233C ILE* 3.6 28.5 - - + +
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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 VAL 3.3 4.6 + - - +
222C ILE 3.4 2.7 + - - +
224C LEU* 1.3 74.8 - - - +
226C LYS* 1.3 68.6 + - - +
228C PHE 3.2 10.0 + - - -
229C PRO* 3.2 44.8 + - + +
231C ALA 2.9 29.3 + - - -
232C ARG* 5.3 2.2 - - - +
233C ILE* 3.9 9.8 - - + +
255C ASP 4.0 13.9 + - - +
256C VAL* 3.6 50.8 + - + +
258C THR* 5.5 2.4 + - - -
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Residues in contact with LYS 226 (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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222C ILE* 3.1 33.8 + - + +
223C GLU* 3.6 29.6 - - - +
225C LYS* 1.3 78.7 - - + +
227C HIS* 1.3 64.6 + - + +
229C PRO* 4.2 7.4 - - - +
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Residues in contact with HIS 227 (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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187C GLN* 6.2 0.2 + - - -
190C ILE* 3.9 30.6 - - + +
223C GLU* 2.8 51.0 + - - +
226C LYS* 1.3 77.7 - - + +
228C PHE* 1.3 90.2 + + + +
229C PRO* 3.6 7.1 - - - +
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Residues in contact with PHE 228 (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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190C ILE* 3.8 21.1 - - + -
193C ALA* 3.7 24.0 - - + -
194C ALA* 3.8 31.4 - - + -
197C LYS* 4.1 26.9 - - - +
205C PHE* 4.7 9.0 - + + -
224C LEU* 2.9 30.8 + - + +
225C LYS* 3.3 4.7 - - - +
227C HIS* 1.3 97.1 - + + +
229C PRO* 1.4 61.7 - - - +
230C ASP 3.5 2.0 - - - -
231C ALA* 3.2 40.5 + - + +
233C ILE* 3.7 2.8 - - + +
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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