Contacts of the helix formed by residues 213 - 233 (chain C) in PDB entry 5FN3
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 213 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C LEU* 4.7 4.0 - - - +
203C LEU* 3.7 15.4 + - - +
204C THR* 4.5 3.3 - - - -
206C LEU 3.5 9.4 - - - -
207C ASN* 4.3 11.0 + - - -
209C TRP 3.5 10.8 - - - -
210C TYR* 3.4 8.3 + - - -
211C GLU 3.0 5.7 + - - -
212C ALA* 1.3 80.7 - - - +
214C LEU* 1.3 68.4 + - - +
215C LEU 3.3 1.6 - - - -
216C PRO* 3.2 11.4 - - - +
217C ILE* 2.9 44.8 + - - +
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Residues in contact with LEU 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C THR* 3.5 36.3 - - + +
162C PHE* 3.6 37.7 - - + -
163C LEU* 3.7 22.0 - - + +
210C TYR* 3.3 21.9 + - + +
213C SER* 1.3 83.5 + - - +
215C LEU* 1.3 68.8 + - + +
217C ILE* 3.2 8.1 + - + +
218C TYR* 2.9 39.3 + - + +
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Residues in contact with LEU 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C TYR 3.9 7.2 + - - +
211C GLU* 4.5 12.3 - - + +
214C LEU* 1.3 90.9 - - + +
216C PRO* 1.3 67.2 - - + +
218C TYR* 3.2 9.3 + - + +
219C ALA* 2.9 28.5 + - - +
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Residues in contact with PRO 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C LEU* 4.0 20.6 - - + -
211C GLU* 3.0 28.0 - - - +
212C ALA* 4.3 3.4 - - - -
213C SER* 3.2 17.7 - - - +
215C LEU* 1.3 94.7 - - + +
217C ILE* 1.3 57.7 + - - +
219C ALA* 3.2 8.9 + - + +
220C VAL* 2.9 35.8 + - + +
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Residues in contact with ILE 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C LEU* 3.3 31.9 - - + +
166C ALA* 3.8 24.5 - - + -
167C ILE* 5.4 4.0 - - + +
170C LEU* 4.4 9.5 - - + +
200C THR* 3.9 10.3 - - + +
203C LEU* 3.4 36.6 - - + -
204C THR* 3.7 13.9 - - + -
213C SER* 2.9 27.7 + - - +
214C LEU* 3.2 6.7 + - + +
216C PRO* 1.3 76.5 - - - +
218C TYR* 1.3 52.4 + - + +
220C VAL* 3.2 6.2 + - - +
221C THR* 2.7 36.6 + - - +
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Residues in contact with TYR 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A ILE* 5.3 6.8 - - - +
162C PHE* 3.1 61.5 + + + -
165C ALA* 4.4 8.7 - - - +
166C ALA* 4.1 16.2 - - + -
169C LEU* 5.3 9.9 - - + +
214C LEU* 2.9 28.5 + - + +
215C LEU* 3.4 13.2 - - + +
217C ILE* 1.3 75.9 - - - +
219C ALA* 1.3 57.3 + - - +
221C THR* 3.2 10.5 + - - -
222C VAL* 2.9 41.5 + - + +
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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
----------------------------------------------------------
215C LEU 2.9 13.0 + - - +
216C PRO* 3.4 12.3 - - + +
218C TYR* 1.3 75.0 - - - +
220C VAL* 1.3 59.7 + - + +
222C VAL* 3.2 11.4 + - - +
223C SER* 2.9 29.0 + - - -
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Residues in contact with VAL 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C LEU* 4.2 13.0 - - + -
196C SER* 4.6 9.9 - - - +
199C LEU* 5.0 13.7 - - + -
200C THR* 4.6 9.2 - - + -
203C LEU* 4.4 14.4 - - + -
216C PRO* 2.9 21.7 + - + +
217C ILE* 3.5 8.5 - - - +
219C ALA* 1.3 76.2 - - + +
221C THR* 1.3 56.6 + - - +
223C SER* 3.2 9.0 + - - -
224C MET* 2.9 47.0 + - + +
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Residues in contact with THR 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C ALA* 3.6 31.7 - - - +
169C LEU* 3.6 18.2 - - + -
170C LEU* 3.6 34.4 - - - +
173C PHE* 3.6 7.8 - - + -
217C ILE 2.7 23.3 + - - -
218C TYR* 3.3 12.0 + - - -
220C VAL* 1.3 75.4 - - - +
222C VAL* 1.3 55.8 + - - +
224C MET* 3.2 2.9 + - - +
225C GLY* 2.7 31.4 + - - -
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Residues in contact with VAL 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C PHE* 5.7 0.7 - - - -
218C TYR* 2.9 28.3 + - + +
219C ALA* 3.3 11.7 - - - +
221C THR* 1.3 77.3 - - - +
223C SER* 1.3 58.3 + - - +
225C GLY* 3.2 3.0 + - - -
226C LEU* 2.9 36.3 + - + +
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Residues in contact with SER 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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219C ALA 2.9 13.2 + - - -
220C VAL* 3.3 12.3 - - - -
222C VAL* 1.3 77.7 - - - +
224C MET* 1.3 64.5 + - - +
226C LEU* 3.2 9.8 + - - +
227C TRP* 2.9 27.9 + - - +
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Residues in contact with MET 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C LEU* 3.5 28.9 - - + -
173C PHE* 3.9 13.4 - - + +
174C TRP* 3.6 24.0 - - + +
177C VAL* 4.4 3.6 - - + +
192C LEU* 5.4 3.1 - - + -
193C VAL* 4.9 5.6 - - - -
196C SER* 3.4 32.8 - - - +
220C VAL* 2.9 26.0 + - + +
221C THR 3.5 4.5 - - - +
223C SER* 1.3 83.3 - - - +
225C GLY* 1.3 57.0 + - - +
227C TRP* 3.2 28.0 + - + +
228C ALA* 2.9 28.8 + - - +
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Residues in contact with GLY 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C PHE* 3.2 39.1 - - - -
221C THR 2.7 14.5 + - - -
222C VAL* 3.2 4.2 + - - -
224C MET* 1.3 73.1 - - - +
226C LEU* 1.3 55.9 + - - +
228C ALA* 3.2 4.3 + - - +
229C PHE* 2.9 29.9 + - - +
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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
----------------------------------------------------------
222C VAL* 2.9 19.5 + - + +
223C SER* 3.2 12.1 + - - +
225C GLY* 1.3 75.7 - - - +
227C TRP* 1.3 56.8 + - - +
229C PHE* 3.2 14.1 + - + +
230C ILE* 2.9 44.1 + - + +
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Residues in contact with TRP 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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177C VAL* 4.1 26.7 - - + -
186C ARG* 6.1 3.8 - - - -
188C TRP* 4.8 15.9 - + - -
189C ALA* 4.3 20.9 - - + -
192C LEU* 3.6 46.9 - - + -
193C VAL* 4.5 8.3 - - + -
223C SER 2.9 12.8 + - - +
224C MET* 3.2 25.1 + - + +
226C LEU* 1.3 76.7 - - - +
228C ALA* 1.3 56.7 + - - +
230C ILE* 3.2 27.0 + - + +
231C THR* 2.9 40.7 + - + +
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Residues in contact with ALA 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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173C PHE* 3.6 22.9 - - + +
176C VAL* 3.7 26.1 - - + +
177C VAL* 3.6 10.7 - - + +
224C MET 2.9 12.7 + - - +
225C GLY 3.3 9.2 - - - +
227C TRP* 1.3 74.5 - - - +
229C PHE* 1.3 58.4 + - - +
231C THR* 2.4 23.1 + - - -
232C ALA* 2.9 18.2 + - - +
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Residues in contact with PHE 229 (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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697A LEU* 4.7 28.5 - - + -
698A PHE* 5.0 10.8 - + - -
225C GLY 2.9 13.3 + - - +
226C LEU* 3.2 19.5 + - + +
228C ALA* 1.3 75.1 - - - +
230C ILE* 1.3 64.2 + - + +
232C ALA* 3.2 6.0 + - - +
233C GLY* 2.9 28.2 + - - -
234C GLY 3.1 25.1 - - - -
235C SER* 4.1 11.4 - - - -
238C SER* 4.2 13.9 - - - -
239C ILE* 4.6 15.9 - - + -
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Residues in contact with ILE 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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226C LEU* 2.9 31.0 + - + +
227C TRP* 3.3 30.1 - - + +
229C PHE* 1.3 84.3 - - + +
231C THR* 1.3 67.0 + - + +
233C GLY 3.0 19.8 - - - +
234C GLY 4.7 3.6 - - - +
235C SER* 6.5 1.1 - - - -
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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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115C ARG* 5.2 2.4 + - - -
176C VAL* 3.9 9.1 + - - +
177C VAL* 4.2 14.2 - - + +
180C ASP* 3.2 43.8 - - + +
184C ARG* 4.9 8.0 + - - +
186C ARG* 5.9 3.8 - - - +
227C TRP* 2.9 24.0 + - + +
228C ALA* 2.4 29.5 + - - -
230C ILE* 1.3 82.0 - - + +
232C ALA* 1.3 59.7 + - - +
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Residues in contact with ALA 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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698A PHE* 3.5 39.6 - - + +
115C ARG* 4.0 30.4 + - - +
176C VAL* 5.1 8.3 - - + +
228C ALA 2.9 12.8 + - - +
229C PHE* 3.2 10.1 + - - +
231C THR* 1.3 80.0 + - - +
233C GLY* 1.3 58.1 + - - +
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Residues in contact with GLY 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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697A LEU 3.3 15.3 - - - -
698A PHE* 3.7 11.7 - - - -
229C PHE* 2.9 14.7 + - - -
230C ILE* 3.0 15.8 - - - +
232C ALA* 1.3 75.4 - - - +
234C GLY* 1.3 67.8 + - - +
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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
------------------------------------------------------------
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