Contacts of the helix formed by residues 225 - 243 (chain X) in PDB entry 2PMO
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 GLY 225 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163X HIS* 4.9 0.4 - - - -
169X CYS* 3.3 26.3 - - - -
197X MET* 3.6 17.3 - - - -
200X LYS 2.9 13.7 + - - -
201X LYS* 4.0 0.2 - - - +
202X ILE* 4.1 13.2 - - - -
223X TYR 3.4 3.4 + - - -
224X ASN* 1.3 69.4 - - - +
226X ALA* 1.3 65.8 + - - +
228X VAL* 3.2 9.0 + - - +
229X ASP* 3.3 8.7 + - - +
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Residues in contact with ALA 226 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163X HIS* 3.9 32.9 + - + -
197X MET* 4.0 9.1 - - + -
200X LYS* 6.0 4.3 - - + -
224X ASN* 3.1 11.8 - - - +
225X GLY* 1.3 73.2 - - - +
227X LYS* 1.3 61.6 + - + +
229X ASP* 3.0 21.7 + - - +
230X ILE* 3.0 20.9 + - + +
312X SER* 5.4 4.3 - - - +
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Residues in contact with LYS 227 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215X GLU* 5.2 0.4 - - - +
224X ASN* 3.3 28.4 - - + +
226X ALA* 1.3 74.6 - - + +
228X VAL* 1.3 60.2 + - - +
230X ILE* 3.5 8.8 - - + +
231X TRP 2.9 23.6 + - - -
306X PRO* 2.8 35.8 + - + +
307X ALA* 3.7 16.8 + - - +
309X ARG* 3.0 48.7 + - + +
310X ILE 4.3 8.7 - - - +
311X THR* 4.2 22.6 - - - +
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Residues in contact with VAL 228 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169X CYS* 4.7 4.5 - - - -
171X ARG* 5.0 12.8 - - + +
202X ILE* 4.1 20.6 - - + -
213X PRO* 3.8 27.3 - - + +
215X GLU* 3.7 18.4 - - - +
216X PHE* 4.1 16.6 - - + -
223X TYR* 4.4 4.0 - - + -
224X ASN 3.4 15.5 + - - +
225X GLY 3.2 9.4 + - - +
226X ALA 3.2 0.6 - - - -
227X LYS* 1.3 74.7 - - - +
229X ASP* 1.3 66.1 + - - +
231X TRP* 3.4 4.9 + - - +
232X SER* 3.1 25.7 + - - +
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Residues in contact with ASP 229 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159X PHE* 3.6 20.9 - - + -
162X ILE* 3.8 1.0 - - - +
163X HIS* 2.8 31.7 - - + +
169X CYS* 3.7 6.8 - - - -
170X HIS* 2.9 32.3 + - - +
171X ARG* 3.0 25.7 + - - -
172X ASP 4.4 0.2 + - - -
173X VAL* 3.6 9.2 - - - +
225X GLY 3.3 1.6 + - - +
226X ALA 3.0 9.7 + - - +
228X VAL* 1.3 80.4 - - - +
230X ILE* 1.3 55.8 + - - +
232X SER* 3.2 8.1 + - - -
233X LEU 2.9 24.3 + - - -
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Residues in contact with ILE 230 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156X LEU* 5.0 4.7 - - + -
159X PHE* 3.8 26.7 - - + -
163X HIS* 5.0 1.8 - - - +
226X ALA* 3.0 23.3 + - + +
227X LYS* 3.5 13.0 - - + +
228X VAL 3.3 0.2 - - - -
229X ASP* 1.3 72.8 - - - +
231X TRP* 1.3 66.1 + - - +
233X LEU* 3.1 3.1 + - - +
234X GLY 2.9 17.5 + - - -
301X PHE* 3.3 25.8 - - + -
309X ARG* 4.1 12.6 - - + -
310X ILE* 3.4 24.7 - - + +
311X THR 4.2 0.4 - - - +
312X SER* 3.8 35.0 - - - +
315X ALA* 6.2 0.2 - - + -
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Residues in contact with TRP 231 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210X GLU 4.7 1.0 + - - -
211X PHE 3.1 26.2 + - - -
212X MET 3.4 12.9 + - - -
213X PRO* 3.7 17.0 - - + -
214X PRO* 3.7 29.4 - - + -
227X LYS 2.9 16.9 + - - +
228X VAL 3.4 4.7 + - - +
230X ILE* 1.3 74.9 - - - +
232X SER* 1.3 59.0 + - - +
234X GLY* 2.8 19.2 + - - -
235X ILE* 3.0 36.1 + - + +
247X PHE* 3.9 23.1 - + - -
260X ILE* 3.9 13.7 - - + -
265X ILE* 5.8 0.7 - - + -
301X PHE 4.1 3.1 - - - -
302X LEU* 3.4 41.8 - - + +
303X ARG 4.1 5.2 - - - -
304X LYS* 4.7 4.5 - - + -
309X ARG* 3.5 36.3 - - - +
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Residues in contact with SER 232 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171X ARG* 5.8 0.9 - - - -
172X ASP* 5.4 2.6 + - - -
173X VAL* 3.6 29.9 + - - -
211X PHE* 2.8 27.9 + - - +
228X VAL* 3.1 16.1 + - - +
229X ASP* 3.2 10.5 + - - -
231X TRP* 1.3 82.9 - - - +
233X LEU* 1.3 60.9 - - - +
235X ILE* 3.1 8.9 + - - +
236X CYS* 3.0 26.3 + - - -
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Residues in contact with LEU 233 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151X ILE* 6.4 0.4 - - + -
152X ILE* 3.8 29.2 - - + +
155X VAL* 3.7 26.9 - - + -
156X LEU* 3.3 33.9 - - + -
159X PHE* 3.9 15.5 - - + -
173X VAL* 4.3 7.3 - - + +
178X ILE* 4.5 5.8 - - + -
229X ASP 2.9 13.2 + - - +
230X ILE 3.1 8.9 + - - +
232X SER* 1.3 75.6 - - - +
234X GLY* 1.3 57.5 + - - +
236X CYS* 3.1 16.4 + - + +
237X LEU* 2.8 28.1 + - - +
240X MET* 5.5 0.4 - - + -
301X PHE* 3.7 12.8 - - + -
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Residues in contact with GLY 234 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230X ILE 2.9 6.7 + - - -
231X TRP 2.8 10.3 + - - -
233X LEU* 1.3 76.3 - - - +
235X ILE* 1.3 53.7 + - - -
237X LEU* 3.1 2.2 + - - -
238X TYR* 2.8 25.5 + - - +
298X LEU* 3.1 12.6 - - - +
301X PHE* 3.6 29.5 - - - -
302X LEU* 3.7 11.4 - - - -
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Residues in contact with ILE 235 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210X GLU 3.9 18.4 - - - +
211X PHE* 3.4 29.8 - - + -
231X TRP* 3.0 45.9 + - + +
232X SER* 3.1 6.9 + - - +
234X GLY* 1.3 71.5 - - - +
236X CYS* 1.3 55.8 + - - +
238X TYR* 3.1 6.2 + - - +
239X VAL* 2.7 37.7 + - + +
245X VAL* 4.5 2.0 - - + -
246X PRO* 3.7 36.8 - - + -
247X PHE* 5.0 3.4 - - + -
302X LEU* 3.7 14.6 - - + +
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Residues in contact with CYS 236 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173X VAL* 3.7 13.2 - - - -
174X LYS* 3.6 21.1 - - - -
175X PRO* 3.6 31.7 - - + +
178X ILE* 3.9 9.6 - - + -
211X PHE* 4.0 1.6 - - - -
232X SER 3.0 18.8 + - - -
233X LEU* 3.1 17.9 + - + +
235X ILE* 1.3 76.7 - - - +
237X LEU* 1.3 56.4 + - - +
239X VAL* 3.4 9.0 + - - +
240X MET* 2.8 38.6 + - + +
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Residues in contact with LEU 237 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148X ILE* 3.3 26.0 - - + -
152X ILE* 3.7 17.7 - - + -
233X LEU 2.8 12.7 + - - +
234X GLY* 3.4 10.5 - - - +
236X CYS* 1.3 74.1 - - - +
238X TYR* 1.3 53.5 - - - +
240X MET* 3.0 9.9 + - + +
241X PHE* 2.7 63.6 + - + -
297X PHE* 4.4 18.4 - - + -
298X LEU* 3.6 36.1 - - + +
301X PHE* 5.2 4.3 - - + -
320X TRP* 4.3 2.7 - - + -
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Residues in contact with TYR 238 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234X GLY 2.8 13.8 + - - +
235X ILE* 3.1 10.3 + - - +
237X LEU* 1.3 73.9 - - - +
239X VAL* 1.3 57.6 + - - +
241X PHE* 3.0 4.5 + - - +
242X TYR* 2.9 44.9 + + - -
244X VAL* 3.4 26.0 - - + +
245X VAL 4.2 1.1 - - - -
246X PRO* 3.3 39.5 + - + +
265X ILE* 3.8 14.5 - - + +
266X GLU* 2.7 22.1 + - - +
267X TYR* 3.6 37.7 - + - -
273X HIS* 3.5 17.8 + - - -
298X LEU* 3.7 15.1 - - + +
302X LEU* 4.3 6.1 - - + -
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Residues in contact with VAL 239 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126X LEU* 4.0 8.5 - - + -
132X PHE* 3.5 51.1 - - + -
175X PRO* 3.9 14.6 - - + -
211X PHE* 4.7 1.8 - - + -
235X ILE* 2.7 27.4 + - + +
236X CYS* 3.5 7.4 - - - +
238X TYR* 1.3 74.0 - - - +
240X MET* 1.3 55.1 + - - +
243X ASN* 2.7 35.3 + - - +
244X VAL 3.3 21.5 - - - +
245X VAL* 4.0 13.7 - - + -
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Residues in contact with MET 240 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125X ILE* 4.4 11.0 - - + -
126X LEU* 4.0 22.0 - - + -
142X PHE* 4.8 3.1 - - - +
143X ILE* 4.2 15.6 + - + +
148X ILE* 3.9 31.9 - - + +
151X ILE* 4.1 34.5 - - + -
152X ILE* 3.7 26.5 - - + -
175X PRO* 6.3 0.7 - - + -
178X ILE* 5.9 1.3 - - + -
233X LEU* 5.5 0.7 - - + -
236X CYS* 2.8 28.3 + - + +
237X LEU* 3.0 22.9 + - + +
239X VAL* 1.3 76.7 - - + +
241X PHE* 1.3 65.2 + - - +
243X ASN* 3.9 7.6 - - - +
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Residues in contact with PHE 241 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142X PHE* 3.6 5.4 - - - -
145X ILE* 3.6 19.3 - - + -
148X ILE* 4.0 9.9 - - + -
237X LEU* 2.7 44.4 + - + +
238X TYR* 3.3 9.2 - - - +
240X MET* 1.3 76.3 - - - +
242X TYR* 1.3 77.3 + + + +
270X ASP* 2.8 29.0 - - - +
290X LEU* 3.5 19.3 - - + -
294X ASP* 3.7 34.5 - - + -
295X ILE* 4.5 2.2 - - + -
298X LEU* 3.5 24.2 - - + -
320X TRP* 3.8 24.5 - + - -
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Residues in contact with TYR 242 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142X PHE* 3.8 5.7 - - - -
238X TYR* 2.9 48.8 + + - +
241X PHE* 1.3 90.9 - + + +
243X ASN* 1.3 69.7 + - - +
244X VAL* 3.1 22.1 + - + +
267X TYR* 3.5 21.8 - + - +
268X PRO* 3.1 52.2 + - + -
269X LEU 4.0 1.3 - - - -
270X ASP* 3.5 40.4 - - - +
273X HIS* 4.3 9.2 - + + +
274X PHE* 4.5 8.5 - - - +
290X LEU* 3.9 19.1 - - + +
295X ILE* 4.5 1.0 - - - +
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Residues in contact with ASN 243 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126X LEU* 3.8 24.1 - - - +
131X TYR* 4.6 0.2 - - - +
132X PHE* 3.6 46.3 + - - +
133X PHE* 4.6 3.0 - - - +
140X THR* 5.7 1.6 - - - +
141X CYS 3.2 25.9 + - - +
142X PHE* 3.8 24.5 - - + +
143X ILE* 5.1 1.9 + - - +
239X VAL 2.7 29.9 + - - +
240X MET 3.9 8.5 - - - +
241X PHE 3.5 0.8 - - - -
242X TYR* 1.3 73.0 - - - +
244X VAL* 1.3 58.7 + - - +
274X PHE* 4.5 15.9 - - + -
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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