Contacts of the helix formed by residues 230 - 248 (chain D) in PDB entry 2C47
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 230 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162D ILE* 3.7 15.2 - - - +
195D TYR* 5.8 1.1 - - - -
203D HIS* 4.2 12.6 - - - -
228D GLU 3.7 0.6 + - - -
229D GLN* 1.3 75.8 - - - +
231D ARG* 1.3 68.9 + - - +
232D ARG* 3.2 23.7 + - - +
233D ASP* 2.8 23.6 + - - +
234D ASP* 3.7 4.3 + - - -
299D PHE* 2.7 42.4 + - - -
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Residues in contact with ARG 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D HIS* 3.5 38.7 - - + +
162D ILE* 3.6 8.8 - - + +
195D TYR* 3.3 42.7 + - + -
196D ILE* 5.7 0.4 - - - +
203D HIS* 4.0 14.8 + - - -
230D SER* 1.3 76.5 - - - +
232D ARG* 1.3 65.3 + - - +
233D ASP 3.0 1.4 + - - -
234D ASP 3.1 9.4 + - - -
235D LEU* 3.5 7.3 + - - +
299D PHE 5.7 0.4 + - - -
300D PHE 3.1 27.3 + - - -
301D GLU 4.0 5.8 + - - +
302D LYS* 3.3 45.7 - - - +
303D PRO* 4.0 13.5 - - + -
305D TYR* 3.6 16.0 + - - -
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Residues in contact with ARG 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D TYR* 4.6 10.1 - - - -
222D ASN* 4.6 17.5 - - - +
227D LYS* 5.2 2.4 - - - +
228D GLU 4.8 3.4 + - - -
230D SER* 3.3 15.8 + - - +
231D ARG* 1.3 78.1 - - - +
233D ASP* 1.3 77.4 + - - +
235D LEU* 3.2 6.7 + - - +
236D GLU* 3.0 29.6 + - - +
294D VAL* 4.1 9.1 - - - +
295D ARG 5.7 0.2 + - - -
297D LEU* 2.7 67.6 + - + -
298D ASP* 3.1 10.8 - - - +
299D PHE* 2.9 42.1 - - - +
301D GLU 5.2 3.1 + - - +
303D PRO* 4.7 1.8 - - - +
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Residues in contact with ASP 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D SER* 2.5 37.8 + - - +
222D ASN* 3.8 15.9 - - - +
223D THR* 3.3 11.4 + - - +
228D GLU 4.3 2.0 - - - +
229D GLN* 3.5 17.7 - - + +
230D SER 2.8 33.1 + - - +
232D ARG* 1.3 92.6 + - - +
234D ASP* 1.3 65.6 + - - +
236D GLU* 4.0 3.0 - - - +
237D ALA* 3.1 25.1 + - - +
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Residues in contact with ASP 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D MET* 3.8 13.0 - - + -
157D HIS* 2.6 31.1 + - + +
162D ILE* 3.6 7.5 - - - +
163D TYR* 3.0 28.4 + - - +
164D ARG* 2.9 29.7 + - - +
166D VAL* 3.8 11.3 - - - +
229D GLN* 5.5 0.3 - - - +
230D SER 3.7 2.4 + - - -
231D ARG 3.1 9.1 + - - +
233D ASP* 1.3 80.6 - - - +
235D LEU* 1.3 58.0 + - - +
237D ALA* 3.5 3.7 + - - +
238D LEU* 3.1 30.7 + - - +
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Residues in contact with LEU 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D ILE* 5.1 7.6 - - + -
153D MET* 3.9 29.6 - - + -
157D HIS* 4.5 4.7 - - + -
231D ARG 3.5 9.4 + - - +
232D ARG* 3.2 7.5 + - - +
234D ASP* 1.3 75.0 - - - +
236D GLU* 1.3 63.3 + - - +
238D LEU* 3.4 7.9 + - + -
239D GLY 3.0 12.0 + - - -
290D TYR* 2.8 33.5 + - - +
294D VAL* 3.8 12.6 - - + -
297D LEU* 4.8 2.0 - - + -
303D PRO* 3.5 37.7 - - + -
305D TYR* 4.3 13.0 - - + -
308D LEU* 3.8 20.0 - - + -
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Residues in contact with GLU 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D SER* 3.1 23.7 - - - -
221D ILE* 2.8 25.6 + - - +
222D ASN* 5.0 2.6 + - - +
232D ARG* 3.0 18.1 + - - +
233D ASP* 4.0 2.0 - - - +
234D ASP 3.4 0.2 - - - -
235D LEU* 1.3 76.3 - - - +
237D ALA* 1.3 59.0 + - - +
239D GLY* 3.1 2.9 + - - -
240D HIS* 3.0 37.9 + - + +
291D LEU* 4.1 3.8 - - + +
294D VAL* 3.8 22.6 - - + +
295D ARG* 2.9 49.9 + - - +
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Residues in contact with ALA 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D VAL* 3.7 26.5 - - + +
218D TYR* 3.1 29.1 - - + +
219D MET* 4.6 5.2 - - - -
220D SER 4.8 1.0 - - - +
233D ASP 3.1 17.3 + - - +
234D ASP* 3.6 4.9 - - - +
236D GLU* 1.3 74.9 - - - +
238D LEU* 1.3 63.8 + - - +
240D HIS* 3.3 4.0 + - - +
241D MET* 3.0 22.3 + - - +
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Residues in contact with LEU 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D LEU* 3.8 37.9 - - + +
150D ILE* 4.4 2.5 - - + +
153D MET* 4.1 22.7 - - + -
166D VAL* 3.8 19.2 - - + +
171D PHE* 4.1 13.0 - - + -
234D ASP 3.1 18.2 + - - +
235D LEU* 3.5 18.8 - - + +
237D ALA* 1.3 75.8 - - - +
239D GLY* 1.3 52.2 + - - +
241D MET* 3.1 22.1 + - + +
242D PHE* 2.8 52.0 + - + -
290D TYR* 3.8 4.7 - - - +
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Residues in contact with GLY 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D LEU 3.0 10.7 + - - -
236D GLU 3.1 5.1 + - - -
238D LEU* 1.3 77.3 - - - +
240D HIS* 1.3 60.4 + - - +
242D PHE* 3.3 9.8 + - - +
243D MET* 3.2 26.4 + - - +
287D MET* 5.3 1.1 - - - +
290D TYR* 3.5 26.2 - - - -
291D LEU* 4.1 12.0 - - - +
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Residues in contact with HIS 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D ARG 4.8 0.2 + - - -
218D TYR* 3.0 31.4 + - - +
219D MET 3.5 18.0 + - - -
220D SER 4.8 0.9 - - - -
221D ILE* 4.8 2.9 - - + -
236D GLU* 3.0 38.2 + - + +
237D ALA* 3.6 6.3 - - - +
238D LEU 3.3 0.2 - - - -
239D GLY* 1.3 74.6 - - - +
241D MET* 1.3 58.4 + - - +
243D MET* 3.3 4.4 + - - -
244D TYR* 3.0 27.4 + - - +
250D LEU* 3.6 16.9 - - + +
252D TRP* 3.7 28.6 - + - -
271D LYS* 5.3 2.4 - - + +
279D LEU* 4.6 6.7 - - + -
291D LEU* 4.4 6.7 - - + +
295D ARG* 3.0 28.5 + - - -
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Residues in contact with MET 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D LEU* 4.9 0.2 - - + -
149D LEU* 3.7 22.0 - - + -
166D VAL* 4.4 2.9 - - + -
167D LYS* 3.7 8.1 - - - -
168D PRO* 3.5 43.3 - - + -
171D PHE* 3.6 22.0 - - + -
218D TYR* 4.0 14.3 - - + -
237D ALA 3.0 13.4 + - - +
238D LEU* 3.1 16.8 + - + +
240D HIS* 1.3 74.9 - - - +
242D PHE* 1.3 70.1 + - + +
244D TYR* 3.2 7.5 - - + +
245D PHE* 3.1 47.5 + - + -
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Residues in contact with PHE 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D VAL* 4.0 12.6 - - + +
145D ILE* 4.5 2.0 - - + -
146D ALA* 3.5 49.6 - - + -
149D LEU* 4.4 7.4 - - + -
150D ILE* 4.9 1.1 - - + -
238D LEU* 2.8 53.4 + - + -
239D GLY* 3.3 13.9 + - - +
241D MET* 1.3 86.4 - - + +
243D MET* 1.3 64.3 + - - +
245D PHE* 3.4 14.8 + + - +
246D LEU* 3.1 26.8 + - - +
287D MET* 3.8 25.1 - - + -
290D TYR* 4.0 18.2 - + - -
312D PHE* 4.5 5.4 - + - -
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Residues in contact with MET 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D GLY 3.2 16.5 + - - +
240D HIS* 3.8 7.6 - - - +
241D MET 3.3 0.2 - - - -
242D PHE* 1.3 73.9 - - - +
244D TYR* 1.3 61.9 + - - +
246D LEU* 3.9 16.8 - - + +
247D ARG* 2.9 46.7 + - + +
250D LEU* 4.1 12.1 - - + -
279D LEU* 3.9 26.0 - - + +
280D CYS* 4.0 13.7 - - - -
283D PHE* 3.9 26.2 - - + -
287D MET* 3.7 31.4 - - - -
291D LEU* 4.2 18.8 - - + -
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Residues in contact with TYR 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D GLU* 2.9 35.4 + - - -
130D PHE* 3.6 23.2 - + - -
135D ARG* 3.1 15.9 + - - -
168D PRO* 3.8 6.5 - - + -
217D ARG* 3.2 18.5 + - - -
218D TYR* 3.4 26.0 - + + -
240D HIS 3.0 13.9 + - - +
241D MET* 3.2 12.3 - - + +
243D MET* 1.3 75.6 - - - +
245D PHE* 1.3 70.7 + + - +
248D GLY* 2.8 42.5 + - - -
249D SER* 4.1 6.7 - - - -
250D LEU* 3.7 16.4 - - + +
253D GLN* 3.1 30.1 - - - -
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Residues in contact with PHE 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D LEU* 3.9 32.5 - - + -
130D PHE* 3.7 16.6 - + - -
136D THR* 3.7 6.6 - - - -
137D PHE* 3.0 55.9 + + + -
142D VAL* 3.6 18.2 - - + -
145D ILE* 4.4 11.7 - - + -
168D PRO* 4.0 11.2 - - + -
241D MET* 3.1 44.8 + - + -
242D PHE* 3.5 15.5 - + - +
243D MET 3.3 0.2 - - - -
244D TYR* 1.3 102.7 - + - +
246D LEU* 1.3 61.5 + - - +
248D GLY 3.8 0.3 + - - -
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Residues in contact with LEU 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D THR* 4.5 6.8 + - - -
137D PHE 4.1 10.8 - - - +
139D LEU* 4.1 28.0 - - + +
142D VAL* 3.6 27.6 - - + -
242D PHE 3.1 17.7 + - - +
243D MET* 3.3 28.9 + - + +
245D PHE* 1.3 80.9 - - - +
247D ARG* 1.3 60.5 + - - +
283D PHE* 3.4 38.3 - - + -
287D MET* 3.9 25.8 - - + -
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Residues in contact with ARG 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D THR* 5.4 2.1 - - - -
243D MET* 2.9 31.5 + - + +
246D LEU* 1.3 75.5 - - - +
248D GLY* 1.3 58.4 + - - +
249D SER* 3.0 31.4 + - - +
250D LEU* 4.4 0.8 - - - +
251D PRO* 3.7 29.1 - - - +
278D VAL 4.5 5.7 + - - -
279D LEU* 3.5 41.2 + - - +
281D GLU 5.3 3.2 + - - -
283D PHE* 3.6 25.3 - - + -
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Residues in contact with GLY 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D PHE* 4.0 13.3 - - - -
135D ARG* 3.2 35.8 + - - +
136D THR* 4.7 2.9 - - - +
244D TYR* 2.8 19.4 + - - -
245D PHE 3.8 2.5 + - - -
246D LEU 3.4 2.2 - - - -
247D ARG* 1.3 75.9 - - - +
249D SER* 1.3 61.3 + - - +
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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