Contacts of the helix formed by residues 220 - 244 (chain H) in PDB entry 2R9R
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 ASP 220 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207H GLN* 3.4 13.2 + - - -
212H TYR* 3.6 5.4 - - - -
213H GLN* 2.8 56.3 + - + +
218H PHE* 3.5 0.7 - - - +
219H THR* 1.3 78.4 - - - +
221H PRO* 1.3 70.4 - - - +
222H PHE* 2.7 41.8 + - - +
223H PHE* 3.1 16.0 + - + +
224H ILE* 3.1 15.6 + - - +
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Residues in contact with PRO 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219H THR 3.2 11.7 - - - +
220H ASP* 1.3 89.7 - - - +
222H PHE* 1.3 60.6 + - + +
224H ILE* 3.3 14.7 + - + +
225H VAL* 3.0 38.1 + - + +
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Residues in contact with PHE 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179H SER* 3.8 28.5 + - - -
182H LEU* 4.0 15.9 - - + -
183H GLU* 3.6 31.7 - - + +
188H PHE* 3.7 48.2 - + + -
211H GLY 4.8 4.3 - - - -
212H TYR* 3.9 15.9 - - + +
220H ASP* 2.7 26.8 + - - +
221H PRO* 1.3 76.2 - - + +
223H PHE* 1.3 56.9 + - - +
225H VAL* 3.6 4.8 + - + +
226H GLU* 3.0 30.7 + - - +
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Residues in contact with PHE 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212H TYR* 3.6 34.6 - + + +
213H GLN 3.2 24.5 - - - +
214H GLN* 4.1 16.6 - - + -
215H SER 3.4 29.2 - - - -
218H PHE* 3.5 35.0 - + - -
220H ASP* 3.1 14.2 + - + +
222H PHE* 1.3 77.0 - - - +
224H ILE* 1.3 58.1 + - - +
226H GLU* 4.5 1.3 - - + -
227H THR* 2.6 48.9 + - - -
266H TYR* 3.4 29.4 - + - -
270H ILE* 5.9 2.2 - - + -
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Residues in contact with ILE 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H PHE* 3.3 39.9 - - + +
219H THR 4.8 1.8 - - - +
220H ASP 3.1 15.3 + - - +
221H PRO* 3.4 17.3 - - + +
223H PHE* 1.3 74.9 - - - +
225H VAL* 1.3 62.4 + - + +
227H THR* 3.2 5.5 + - - -
228H LEU* 2.8 55.7 + - + +
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Residues in contact with VAL 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175H ILE* 4.0 22.4 - - + -
179H SER* 3.6 33.9 - - - +
221H PRO* 3.0 20.0 + - + +
222H PHE* 4.0 2.9 - - + +
224H ILE* 1.3 78.3 - - + +
226H GLU* 1.3 56.4 + - - +
228H LEU* 3.7 10.1 - - + +
229H CYS* 2.9 40.1 + - - -
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Residues in contact with GLU 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176H SER* 5.1 0.7 - - - -
179H SER* 4.9 3.9 + - - +
183H GLU* 5.0 0.9 - - - +
212H TYR* 3.7 26.0 + - + -
222H PHE 3.0 20.3 + - - +
223H PHE* 4.1 3.4 - - - +
225H VAL* 1.3 76.4 - - - +
227H THR* 1.3 57.5 + - - +
229H CYS* 3.4 3.4 + - - +
230H ILE* 2.8 50.8 + - - +
266H TYR* 3.8 20.0 + - + +
296H ARG* 3.0 27.8 + - - +
299H ARG* 2.8 42.7 + - - -
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Residues in contact with THR 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H PHE* 3.9 20.7 - - + -
223H PHE* 2.6 35.7 + - - -
224H ILE* 3.6 4.0 - - - -
226H GLU* 1.3 74.2 - - - +
228H LEU* 1.3 63.9 + - + +
230H ILE* 3.2 2.6 + - - +
231H ILE* 2.8 50.4 + - + +
266H TYR* 2.8 32.2 + - + +
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Residues in contact with LEU 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224H ILE* 2.8 45.6 + - + +
225H VAL* 3.7 9.0 - - + +
227H THR* 1.3 75.2 - - + +
229H CYS* 1.3 66.2 + - - +
231H ILE* 3.0 21.7 + - + +
232H TRP* 3.2 13.3 + - - +
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Residues in contact with CYS 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172H VAL* 3.9 24.5 - - + -
175H ILE* 4.1 7.4 - - - -
176H SER* 3.8 39.7 - - - -
225H VAL* 2.9 34.5 + - - +
226H GLU* 3.7 5.8 - - - +
228H LEU* 1.3 77.9 - - - +
230H ILE* 1.3 62.9 + - + +
232H TRP* 3.3 3.8 + - - +
233H PHE* 3.0 34.9 + - + -
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Residues in contact with ILE 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226H GLU* 2.8 54.5 + - - +
227H THR 3.8 3.1 - - - +
229H CYS* 1.3 80.8 - - + +
231H ILE* 1.3 58.8 + - + +
233H PHE* 3.8 16.1 - - + +
234H SER* 2.6 47.6 + - - +
262H ALA 4.6 11.9 - - - +
263H ILE* 4.6 4.5 - - + -
266H TYR* 3.5 49.6 - - + -
267H TYR* 3.8 10.5 - - + +
299H ARG* 4.3 7.6 - - - +
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Residues in contact with ILE 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227H THR* 2.8 41.4 + - + +
228H LEU* 3.0 13.9 + - + +
230H ILE* 1.3 80.0 - - + +
232H TRP* 1.3 56.9 + - - +
234H SER* 3.6 5.7 - - - -
235H PHE* 2.9 28.0 + - + +
266H TYR* 6.2 2.0 - - + -
267H TYR* 5.3 7.2 - - - +
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Residues in contact with TRP 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153H PHE* 5.3 1.8 - + - -
165H ILE* 3.9 22.9 - - + -
168H VAL* 3.7 31.6 - - + -
169H SER* 3.5 25.0 + - - +
172H VAL* 4.1 23.6 - - + -
228H LEU 3.2 8.0 + - - +
229H CYS 3.6 6.1 - - - +
231H ILE* 1.3 79.3 - - - +
233H PHE* 1.3 72.4 + + - +
235H PHE* 3.1 28.0 + + + +
236H GLU* 2.9 54.7 + - + +
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Residues in contact with PHE 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169H SER 5.0 0.2 - - - -
172H VAL* 3.6 21.8 - - + -
173H ILE* 3.9 29.8 - - + -
176H SER* 3.6 32.8 - - - -
229H CYS* 3.0 22.1 + - + +
230H ILE* 4.0 10.8 - - + +
231H ILE 3.4 0.2 - - - -
232H TRP* 1.3 85.2 - + - +
234H SER* 1.3 61.2 - - - +
236H GLU* 3.6 2.9 + - - +
237H PHE* 3.2 24.6 + - - +
259H ASP 4.9 0.5 - - - +
262H ALA* 4.0 20.4 - - + -
263H ILE* 3.5 19.3 - - + +
299H ARG* 4.6 15.7 - - + -
302H LYS* 3.3 32.4 + - + +
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Residues in contact with SER 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230H ILE* 2.6 26.0 + - - +
231H ILE* 3.6 6.5 - - - -
233H PHE* 1.3 73.6 - - - +
235H PHE* 1.3 65.9 + - - +
237H PHE* 3.6 2.2 + - - +
238H LEU* 3.1 37.8 + - - +
263H ILE* 3.9 14.6 - - - +
267H TYR* 2.7 36.6 + - - -
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Residues in contact with PHE 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153H PHE* 3.6 29.4 - + - -
231H ILE* 2.9 16.4 + - + +
232H TRP* 3.1 36.3 + + - +
234H SER* 1.3 73.8 - - - +
236H GLU* 1.3 62.2 + - + +
238H LEU* 3.2 8.4 + - + +
239H VAL* 2.8 51.1 + - + +
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Residues in contact with GLU 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153H PHE* 4.2 17.3 - - + -
165H ILE* 5.3 0.3 - - - +
169H SER* 2.7 26.0 + - - -
173H ILE* 5.8 1.0 - - - +
232H TRP* 2.9 44.8 + - + +
233H PHE* 3.9 4.2 - - - +
234H SER 3.5 0.2 - - - -
235H PHE* 1.3 76.9 - - + +
237H PHE* 1.3 57.1 + - - +
239H VAL* 3.7 5.0 - - - +
240H ARG* 2.8 69.7 + - - +
259H ASP* 5.0 0.4 - - - +
302H LYS* 2.9 31.4 + - - +
305H ARG* 5.4 0.6 - - - -
306H HIS* 5.1 1.7 + - - -
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Residues in contact with PHE 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233H PHE 3.2 16.4 + - - +
234H SER* 3.8 4.0 - - - +
236H GLU* 1.3 77.8 - - - +
238H LEU* 1.3 76.6 + - + +
240H ARG* 3.9 6.0 - - - +
241H PHE* 3.0 33.0 + + + +
250H PHE* 3.5 31.3 - + - -
251H PHE* 4.5 8.3 - + - -
256H ASN 5.0 0.2 - - - -
259H ASP* 4.6 22.3 + - + +
260H ILE* 3.5 36.1 - - + -
263H ILE* 4.1 23.1 - - + -
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Residues in contact with LEU 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234H SER* 3.1 29.7 + - - +
235H PHE* 3.6 6.7 - - + +
237H PHE* 1.3 92.2 - - + +
239H VAL* 1.3 67.1 + - + +
241H PHE* 3.0 14.8 + - + -
242H PHE* 3.1 45.2 + - + -
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Residues in contact with VAL 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H VAL* 3.5 16.8 - - + -
153H PHE* 3.4 39.5 - - + -
235H PHE* 2.8 62.1 + - + +
236H GLU 3.7 3.6 - - - +
238H LEU* 1.3 73.1 - - + +
240H ARG* 1.3 56.8 + - - +
242H PHE* 3.7 3.5 + - - +
243H ALA* 3.1 27.4 + - - +
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Residues in contact with ARG 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150H TRP* 3.4 21.5 - - + -
153H PHE* 3.1 42.0 + - + +
154H GLU* 5.1 2.1 - - - +
236H GLU* 2.8 63.6 + - - +
237H PHE* 3.9 5.8 - - - +
239H VAL* 1.3 77.5 - - - +
241H PHE* 1.3 59.2 + - - +
244H CYS* 3.1 32.1 + - - +
250H PHE* 4.1 11.6 - - + -
256H ASN* 4.4 8.1 - - - -
259H ASP* 4.3 11.5 + - - -
305H ARG* 3.2 53.8 - - - +
306H HIS* 5.4 2.4 - - - -
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Residues in contact with PHE 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237H PHE* 3.0 25.9 + + + +
238H LEU* 3.0 10.1 + - + +
240H ARG* 1.3 77.5 - - - +
242H PHE* 1.3 84.6 + + - +
244H CYS* 4.0 0.9 - - - -
247H LYS* 2.7 57.2 + - + +
250H PHE* 3.6 42.3 - + + -
251H PHE* 4.4 17.5 - + - -
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Residues in contact with PHE 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146H GLN* 3.5 17.5 + - - +
238H LEU* 3.1 47.4 + - + +
239H VAL* 4.6 2.7 - - - +
241H PHE* 1.3 105.9 - + - +
243H ALA* 1.3 58.6 + - - +
247H LYS* 3.2 19.8 + - - +
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Residues in contact with ALA 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146H GLN* 4.0 19.4 - - - +
149H VAL* 3.9 26.2 - - + -
150H TRP* 3.1 39.2 - - + +
153H PHE* 6.3 0.4 - - + -
239H VAL* 3.1 20.0 + - + +
242H PHE* 1.3 77.4 - - - +
244H CYS* 1.3 61.7 + - - +
245H PRO* 3.9 1.4 - - - +
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Residues in contact with CYS 244 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146H GLN* 3.9 6.5 - - - +
150H TRP* 3.5 20.4 - - + -
240H ARG 3.1 14.6 + - - +
241H PHE 3.5 10.3 - - - -
243H ALA* 1.3 78.8 - - - +
245H PRO* 1.3 72.4 - - + +
246H SER 3.1 25.8 - - - +
247H LYS* 3.4 32.7 + - - -
250H PHE* 4.3 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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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