Contacts of the helix formed by residues 203 - 215 (chain C) in PDB entry 1C2O
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 203 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120C GLY* 4.4 11.2 - - - -
121C GLY* 5.2 0.8 - - - -
122C GLY* 4.5 9.0 + - - -
202C GLU* 1.3 92.6 + - - +
204C ALA* 1.4 66.3 + - - -
206C ALA* 3.0 5.2 + - - +
207C ALA* 3.0 16.6 + - - +
228C GLN 3.1 6.1 + - - -
229C SER 3.8 13.4 + - - -
230C GLY* 3.8 4.2 - - - -
236C TRP* 4.0 13.3 - - - -
295C PHE* 5.1 3.5 - - - -
297C PHE* 6.0 1.6 - - - -
338C PHE* 5.4 0.7 - - - -
447C HIS* 2.8 25.1 + - - -
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Residues in contact with ALA 204 (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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119C TYR 4.6 0.4 - - - -
120C GLY* 3.9 3.3 - - - -
121C GLY 4.4 2.9 - - - +
122C GLY 4.2 4.3 - - - +
123C PHE* 3.5 54.5 - - + +
151C TYR* 4.8 1.8 - - - +
203C SER* 1.4 82.3 + - - +
205C GLY* 1.3 49.1 + - - +
207C ALA* 3.2 7.5 - - - +
208C SER* 2.6 41.7 + - - -
236C TRP* 3.8 9.1 - - + -
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Residues in contact with GLY 205 (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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118C ILE* 3.2 33.4 - - - +
119C TYR 3.4 7.9 - - - -
120C GLY* 3.5 8.3 - - - -
201C GLY* 4.0 4.3 - - - -
202C GLU 2.6 13.7 + - - -
204C ALA* 1.3 71.6 - - - +
206C ALA* 1.3 49.5 + - - -
208C SER* 2.9 5.2 + - - -
209C VAL* 2.7 37.6 + - - +
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Residues in contact with ALA 206 (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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201C GLY 3.1 25.2 - - - +
202C GLU 2.7 8.9 + - - -
203C SER 3.1 10.3 - - - +
205C GLY* 1.3 70.1 - - - +
207C ALA* 1.4 51.5 + - - +
209C VAL* 2.9 7.9 + - - +
210C GLY* 2.7 32.9 + - - -
227C LEU* 3.8 10.1 - - - +
228C GLN 3.4 20.2 - - - +
230C GLY 3.3 21.3 - - - +
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Residues in contact with ALA 207 (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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123C PHE* 4.0 6.3 - - + -
203C SER 3.0 8.1 + - - +
204C ALA* 3.2 20.2 - - - +
206C ALA* 1.4 76.4 - - - +
208C SER* 1.3 57.8 + - - +
210C GLY* 3.3 3.3 + - - -
211C MET* 3.0 31.8 + - + +
230C GLY 4.1 0.6 - - - -
231C THR* 3.4 30.3 - - - +
232C PRO* 3.7 3.1 - - - +
236C TRP* 4.0 3.1 - - + -
237C ALA* 3.9 18.8 - - + -
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Residues in contact with SER 208 (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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118C ILE* 4.2 3.4 - - - -
123C PHE* 3.5 16.1 - - - -
151C TYR* 4.8 0.7 + - - -
173C LEU* 3.8 8.9 - - - +
176C GLN* 3.2 36.6 + - - -
204C ALA 2.6 23.9 + - - -
205C GLY* 2.9 14.7 - - - -
207C ALA* 1.3 70.1 - - - +
209C VAL* 1.4 56.4 + - - +
210C GLY 2.9 0.9 - - - -
211C MET* 2.5 28.9 + - - +
212C HIS* 2.8 16.7 + - - -
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Residues in contact with VAL 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ILE* 4.4 8.0 - - + +
199C LEU* 4.0 27.4 - - + +
200C PHE 4.1 1.6 - - - +
201C GLY 3.7 16.8 - - - +
205C GLY 2.7 21.0 + - - +
206C ALA* 3.3 7.2 - - - +
208C SER* 1.4 71.4 - - - +
210C GLY* 1.4 65.5 + - - +
212C HIS* 2.9 21.0 + - - +
213C ILE* 3.1 13.1 + - + +
225C ALA* 3.7 24.9 - - + -
226C VAL 3.6 26.2 - - - +
227C LEU* 4.1 6.7 - - + -
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Residues in contact with GLY 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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206C ALA 2.7 14.1 + - - -
207C ALA 3.3 6.3 + - - -
208C SER 2.9 0.2 - - - -
209C VAL* 1.4 78.8 - - - +
211C MET* 1.3 55.2 + - - +
213C ILE* 3.1 10.9 + - - +
214C LEU* 2.9 37.3 + - - +
227C LEU* 4.0 9.8 - - - +
232C PRO* 3.9 18.8 - - - -
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Residues in contact with MET 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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123C PHE* 3.8 7.9 - - + -
173C LEU* 4.0 19.3 - - + -
207C ALA* 3.0 32.9 + - + +
208C SER* 2.5 15.5 + - - +
210C GLY* 1.3 70.2 - - - +
212C HIS* 1.4 66.7 + - + +
214C LEU* 3.5 5.0 - - + +
215C SER* 2.7 28.8 + - - -
232C PRO* 3.8 19.5 - - + +
237C ALA* 3.8 11.4 - - + +
238C THR* 4.1 4.7 - - + -
301C PRO* 3.7 40.2 - - + -
307C PHE* 4.0 2.4 - - + -
308C LEU* 3.5 32.7 - - + +
312C PRO* 5.5 0.9 - - + -
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Residues in contact with HIS 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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118C ILE* 4.1 13.8 - - + +
173C LEU* 3.7 14.3 + - + +
176C GLN* 3.1 41.3 + - + -
177C ARG* 3.9 5.1 + - - +
180C LEU* 4.1 17.7 - - + +
199C LEU* 3.9 17.1 - - + +
208C SER 2.8 17.6 + - - -
209C VAL 2.9 6.9 + - - +
211C MET* 1.4 77.6 - - + +
213C ILE* 1.3 57.8 + - - +
215C SER 2.9 29.1 + - - +
218C SER* 2.7 38.7 - - - -
219C ARG* 4.1 2.6 - - - -
222C PHE* 4.1 4.3 - - + -
307C PHE* 3.7 15.8 - + - -
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Residues in contact with ILE 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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209C VAL 3.1 16.0 + - - +
210C GLY* 3.4 12.1 - - - +
212C HIS* 1.3 76.9 - - - +
214C LEU* 1.3 65.0 + - + +
215C SER 3.4 0.5 + - - -
216C LEU* 5.3 1.9 - - - +
219C ARG* 3.2 35.4 + - - +
222C PHE* 3.8 23.5 - - + -
225C ALA* 3.9 20.6 - - + -
227C LEU* 4.6 12.3 - - + -
321C PHE* 4.1 20.1 - - + -
324C LEU* 3.6 25.4 - - + -
326C VAL* 4.4 7.4 - - + -
414C LEU* 6.4 0.2 - - + -
418C LEU* 5.3 7.9 - - + -
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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
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210C GLY* 2.9 23.3 + - - +
211C MET* 3.1 8.2 + - + +
213C ILE* 1.3 80.8 - - + +
215C SER* 1.3 59.3 + - - +
216C LEU* 3.9 5.0 + - - +
232C PRO* 3.3 32.1 - - + -
307C PHE 4.8 1.7 - - - +
308C LEU* 4.4 7.8 - - + -
309C SER* 4.9 3.1 + - - -
312C PRO* 4.5 8.3 - - + -
315C LEU* 3.4 55.0 - - + +
316C ILE* 4.1 14.8 - - + +
321C PHE* 4.0 27.1 - - + -
414C LEU* 5.5 0.9 - - + -
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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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177C ARG* 3.0 26.6 + - - -
211C MET 2.7 16.8 + - - -
212C HIS 2.9 18.2 + - - +
214C LEU* 1.3 78.6 - - - +
216C LEU* 1.3 73.4 + - - +
217C PRO* 4.5 2.4 - - - +
218C SER* 3.1 4.7 + - - -
219C ARG* 3.5 5.6 - - - +
307C PHE* 2.6 40.1 + - - -
308C LEU* 5.1 0.4 - - - -
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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