Contacts of the helix formed by residues 215 - 234 (chain C) in PDB entry 4O46
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 SER 215 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170C PRO* 4.6 16.4 - - - -
211C LEU* 4.2 11.7 - - - -
212C ASN* 3.0 14.3 + - - -
214C ASP* 1.4 77.1 - - - +
216C TYR* 1.4 65.0 + - - +
217C LYS 3.4 2.7 - - - -
218C ASP* 3.4 11.2 + - - +
219C SER* 3.2 24.6 + - - -
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Residues in contact with TYR 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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208C LEU* 5.6 4.7 - - + -
211C LEU* 4.0 30.7 - - + +
212C ASN 2.8 23.3 + - - +
213C GLU* 4.3 8.7 + - - +
214C ASP 3.9 0.4 - - - -
215C SER* 1.4 71.6 - - - +
217C LYS* 1.4 64.0 + - + +
219C SER* 3.9 0.5 - - - -
220C THR* 2.8 63.4 + - + +
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Residues in contact with LYS 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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213C GLU 5.1 7.3 + - - +
214C ASP 5.5 1.3 - - - +
215C SER 3.4 0.6 - - - -
216C TYR* 1.4 86.3 - - + +
218C ASP* 1.4 60.0 + - - +
220C THR* 3.1 7.2 + - - -
221C LEU* 3.1 31.6 + - - +
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Residues in contact with ASP 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C PRO* 4.1 18.2 - - + +
214C ASP 3.8 18.0 - - - +
215C SER* 3.4 9.3 + - - +
216C TYR 3.4 0.4 - - - -
217C LYS* 1.4 78.3 - - - +
219C SER* 1.3 61.9 + - - +
221C LEU* 3.6 8.9 + - - +
222C ILE* 3.4 29.4 + - + +
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Residues in contact with SER 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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168C THR 2.6 28.4 + - - -
170C PRO* 3.4 13.6 - - - +
173C LEU* 3.7 14.6 - - - +
211C LEU* 3.3 26.9 - - - +
215C SER 3.2 11.7 + - - -
218C ASP* 1.3 73.5 - - - +
220C THR* 1.4 59.4 + - - +
222C ILE* 3.2 6.0 + - - -
223C MET* 3.0 32.8 + - - +
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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
----------------------------------------------------------
211C LEU* 4.4 8.3 - - + -
216C TYR* 2.8 60.3 + - + +
217C LYS* 3.1 13.7 + - - -
219C SER* 1.4 72.2 - - - +
221C LEU* 1.3 58.4 + - - +
223C MET* 3.6 14.7 - - - +
224C GLN* 2.9 30.1 + - - +
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Residues in contact with LEU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C LYS 3.1 19.5 + - - +
218C ASP* 3.7 11.0 - - - +
219C SER 3.3 0.4 - - - -
220C THR* 1.3 76.2 + - - +
222C ILE* 1.4 62.0 + - + +
224C GLN* 3.6 7.8 - - + +
225C LEU* 3.4 30.7 + - + +
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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
----------------------------------------------------------
170C PRO* 3.4 37.0 - - + +
173C LEU* 3.6 35.2 - - + +
174C GLY* 3.8 7.2 - - - +
177C LEU* 3.9 23.3 - - + -
218C ASP* 3.4 18.6 + - + +
219C SER* 3.2 5.5 + - - +
221C LEU* 1.4 75.8 - - + +
223C MET* 1.3 61.0 + - - +
224C GLN 3.2 0.2 - - - -
225C LEU* 3.0 12.5 + - + +
226C LEU* 2.8 29.2 + - + +
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Residues in contact with MET 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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168C THR* 5.5 0.7 - - - -
173C LEU* 4.0 21.1 - - + -
201C PHE* 3.3 32.1 - - + +
204C ALA* 3.9 31.9 - - + +
205C ILE* 3.6 31.9 - - + +
208C LEU* 6.0 2.2 - - + -
211C LEU* 4.9 7.4 - - - -
219C SER* 3.0 28.9 + - - +
220C THR* 3.6 18.2 - - + +
222C ILE* 1.3 75.1 - - - +
224C GLN* 1.4 59.8 + - - +
226C LEU* 3.4 9.3 + - + +
227C ARG* 3.1 17.5 + - - +
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Residues in contact with GLN 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C PHE* 5.5 0.2 - - - -
220C THR 2.9 16.4 + - - +
221C LEU* 3.6 10.3 - - + +
223C MET* 1.4 75.9 - - - +
225C LEU* 1.4 52.7 + - + +
227C ARG* 3.2 7.5 + - - +
228C ASP* 2.8 44.5 + - - +
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Residues in contact with LEU 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C LEU* 3.8 31.6 - - + -
221C LEU* 3.4 22.0 + - + +
222C ILE* 3.0 12.7 + - + +
224C GLN* 1.4 76.2 - - + +
226C LEU* 1.4 59.8 + - - +
228C ASP* 3.7 14.5 - - + +
229C ASN* 2.9 39.1 + - - +
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Residues in contact with LEU 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C LEU* 3.9 32.1 - - + +
176C ALA 4.3 2.5 - - - -
177C LEU* 3.9 36.1 - - + +
180C SER* 4.5 0.7 - - - +
197C ALA* 3.8 37.9 - - + +
200C ALA* 4.4 11.0 - - + -
201C PHE* 4.4 13.2 - - + +
222C ILE* 2.8 23.3 + - + +
223C MET* 3.5 12.6 - - - +
224C GLN 3.3 0.2 - - - -
225C LEU* 1.4 76.1 - - - +
227C ARG* 1.4 56.1 + - - +
229C ASN* 3.8 3.6 + - - +
230C LEU* 3.2 32.5 + - - +
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Residues in contact with ARG 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C PHE* 4.1 21.5 - - + -
223C MET 3.1 13.1 + - - +
224C GLN* 3.2 9.1 + - - +
226C LEU* 1.4 74.6 - - - +
228C ASP* 1.4 54.3 - - - +
230C LEU* 3.2 8.8 + - - +
231C THR* 2.7 43.5 + - - +
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Residues in contact with ASP 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C GLN* 2.8 28.6 + - - +
225C LEU* 3.7 18.8 - - + +
227C ARG* 1.4 76.8 - - - +
229C ASN* 1.4 59.1 + - - +
231C THR* 3.4 7.6 + - - -
232C LEU* 3.1 28.6 + - - +
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Residues in contact with ASN 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C LEU* 3.5 25.7 - - - +
180C SER* 4.9 0.8 + - - -
181C VAL* 3.6 23.8 - - - +
197C ALA* 5.8 0.7 - - + -
225C LEU* 2.9 20.1 + - - +
226C LEU* 4.0 4.7 - - + +
228C ASP* 1.4 76.7 - - - +
230C LEU* 1.4 53.1 + - - +
232C LEU* 3.3 11.0 + - - +
233C TRP* 2.8 65.7 + - + +
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Residues in contact with LEU 230 (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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194C CYS* 4.0 30.1 - - + +
197C ALA* 3.7 15.7 - - + +
198C LYS* 3.5 35.7 - - + +
201C PHE* 5.1 6.3 - - + -
226C LEU 3.2 20.7 + - - +
227C ARG* 3.2 8.0 + - - +
229C ASN* 1.4 74.2 - - - +
231C THR* 1.4 54.3 + - - +
233C TRP* 3.4 5.5 + - + +
234C THR* 2.7 54.5 + - + +
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Residues in contact with THR 231 (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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227C ARG* 2.7 30.4 + - - +
228C ASP* 3.6 8.8 + - - -
230C LEU* 1.4 71.5 - - - +
232C LEU* 1.3 57.9 + - - +
234C THR* 3.6 6.4 + - - -
235C SER* 3.1 28.5 + - - -
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Residues in contact with LEU 232 (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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184C TYR* 5.3 2.8 + - + -
228C ASP 3.1 13.2 + - - +
229C ASN* 3.4 12.1 - - - +
231C THR* 1.3 76.1 - - - +
233C TRP* 1.3 81.8 + - + +
235C SER* 3.4 19.8 + - - +
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Residues in contact with TRP 233 (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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180C SER* 3.6 34.1 - - - -
181C VAL* 3.9 10.8 - - + -
184C TYR* 3.4 64.1 + + + -
185C GLU* 6.0 1.7 - - + +
190C PRO* 6.0 0.9 - - - +
193C ALA* 3.6 27.8 - - + -
194C CYS* 3.7 32.6 - - - -
197C ALA* 4.2 8.3 - - + -
229C ASN* 2.8 52.3 + - + +
230C LEU* 3.9 4.7 - - - +
232C LEU* 1.3 90.5 - - + +
234C THR* 1.3 59.0 + - - +
235C SER 3.3 1.9 + - - -
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Residues in contact with THR 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C CYS* 4.2 18.8 - - + -
230C LEU* 2.7 37.8 + - + +
231C THR* 3.6 8.0 + - - -
233C TRP* 1.3 76.9 - - - +
235C SER* 1.4 61.8 + - - +
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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
------------------------------------------------------------
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