Contacts of the helix formed by residues 225 - 245 (chain D) in PDB entry 6CP3
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 PRO 225 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C LYS* 4.5 5.4 - - - +
302C TYR* 3.6 18.8 - - + +
19D ALA* 5.2 5.2 - - + -
63D ALA* 4.7 9.4 - - + -
64D MET* 3.9 5.6 - - - +
65D ASP* 3.2 43.3 - - - +
66D GLY* 4.3 2.5 - - - +
67D THR* 5.8 2.2 - - + +
223D ASN 4.2 2.9 - - - +
224D GLU* 1.3 98.2 - - + +
226D PRO* 1.3 74.9 - - + +
227D GLY 3.0 3.3 + - - +
228D ALA* 3.1 13.2 + - - +
229D ARG* 3.7 5.4 + - - -
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Residues in contact with PRO 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ASP* 5.3 3.4 - - + -
302C TYR* 4.7 11.0 - - + -
19D ALA* 4.6 13.2 - - + +
62D ILE* 5.0 0.9 - - + -
63D ALA* 6.2 0.4 - - + -
225D PRO* 1.3 86.2 - - + +
227D GLY* 1.3 57.0 + - - +
228D ALA 3.3 0.2 - - - -
229D ARG* 3.8 13.7 - - - +
230D ALA* 2.9 29.8 + - - +
264D ALA* 3.3 16.2 - - + +
267D GLU* 3.3 34.3 - - + +
268D VAL* 3.7 26.7 - - + -
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Residues in contact with GLY 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ILE* 3.7 19.2 - - - +
63D ALA* 3.4 21.7 + - - +
64D MET* 3.5 10.1 - - - -
225D PRO 3.0 1.8 + - - -
226D PRO* 1.3 79.5 - - - +
228D ALA* 1.3 57.4 + - - +
230D ALA* 3.1 5.5 + - - -
231D ARG* 3.0 35.8 + - - +
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Residues in contact with ALA 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ALA 4.3 0.8 + - - -
64D MET* 3.7 13.7 - - - +
98D VAL* 3.7 25.7 - - + +
220D GLY* 5.6 1.6 - - - -
224D GLU* 3.4 40.4 - - + +
225D PRO 3.1 3.8 + - - +
227D GLY* 1.3 77.1 - - - +
229D ARG* 1.3 59.6 + - - +
232D VAL* 2.9 36.2 + - + +
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Residues in contact with ARG 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C PHE* 3.2 34.6 - - - -
302C TYR* 3.8 11.1 - - - +
305C SER* 4.8 2.0 - - - -
187D VAL* 3.6 20.9 - - + +
188D GLY* 4.3 10.8 - - - +
220D GLY 4.4 6.7 - - - +
221D GLN 3.5 25.8 - - - +
222D MET* 3.6 19.3 + - - +
224D GLU* 3.6 22.5 + - + -
225D PRO 3.7 1.2 + - - -
226D PRO* 3.4 17.1 + - - +
227D GLY 3.3 0.6 - - - -
228D ALA* 1.3 77.2 - - - +
230D ALA* 1.3 59.3 + - - +
231D ARG 3.3 0.4 + - - -
232D VAL* 4.3 7.6 + - - +
233D ALA 5.0 0.7 + - - -
260D ARG* 4.4 10.2 - - - +
261D PHE* 3.8 11.8 - - - -
264D ALA* 3.8 15.0 - - + -
267D GLU* 2.4 32.7 + - - -
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Residues in contact with ALA 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ILE* 6.3 2.0 - - + -
226D PRO 2.9 18.5 + - - +
227D GLY* 3.1 7.1 + - - +
229D ARG* 1.3 79.8 - - - +
231D ARG* 1.3 86.5 + - - +
233D ALA 5.3 0.2 - - - -
234D LEU* 4.3 0.9 - - - +
261D PHE* 3.1 30.5 - - + +
264D ALA* 3.9 19.3 - - + +
265D GLY* 4.6 2.7 - - - +
268D VAL* 6.2 0.7 - - + -
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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
----------------------------------------------------------
34D LEU* 4.4 10.3 - - - +
49D GLU* 2.5 43.7 + - - +
50D VAL 5.9 0.2 + - - -
51D ALA* 6.0 1.2 - - - +
62D ILE* 4.3 19.3 - - - +
64D MET* 3.7 8.5 - - + -
83D ILE* 5.1 0.4 - - + -
98D VAL* 3.6 17.3 - - + +
117D ILE* 4.3 10.1 - - + +
118D HIS* 3.8 10.4 - - - -
227D GLY* 3.0 18.2 + - - +
230D ALA* 1.3 106.9 + - - +
232D VAL* 1.3 59.4 + - - +
233D ALA 3.2 2.9 - - - -
234D LEU* 2.9 40.3 + - - +
235D THR* 3.1 9.5 + - - -
261D PHE* 4.7 6.3 - - - -
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Residues in contact with VAL 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D VAL* 3.7 25.3 - - + +
185D THR* 3.7 6.5 - - + +
186D GLY 4.6 0.2 - - - +
187D VAL* 3.7 30.7 - - + -
218D VAL* 3.7 20.1 - - + +
219D PHE 4.1 0.2 - - - -
220D GLY* 3.5 39.0 - - - +
228D ALA 2.9 20.8 + - - +
229D ARG* 4.3 1.3 - - - -
231D ARG* 1.3 74.8 - - - +
233D ALA* 1.3 62.6 + - - +
235D THR* 3.2 2.8 + - - -
236D GLY 3.0 22.7 + - - -
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Residues in contact with ALA 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D THR* 4.2 6.0 - - + +
187D VAL* 4.0 21.2 - - + +
229D ARG 5.0 0.8 + - - +
231D ARG* 3.2 0.8 - - - +
232D VAL* 1.3 83.1 - - - +
234D LEU* 1.3 57.1 + - - +
236D GLY* 3.5 0.9 + - - -
237D LEU* 2.9 28.1 + - - +
255D ILE* 5.2 9.4 - - + +
258D ILE* 4.7 8.7 - - + -
261D PHE* 4.8 11.2 - - + -
292D LEU* 3.8 30.1 - - + +
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Residues in contact with LEU 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ILE* 3.7 21.5 - - + +
118D HIS* 3.5 31.4 - - + +
230D ALA 4.3 5.6 - - - +
231D ARG* 2.9 30.9 + - - +
233D ALA* 1.3 76.5 - - - +
235D THR* 1.3 59.2 + - - +
237D LEU* 3.3 26.4 + - + +
238D THR* 2.9 33.4 + - - -
261D PHE* 4.9 9.0 - - + -
291D LEU 5.0 4.3 - - - +
292D LEU* 3.7 19.7 - - + -
295D ARG* 4.3 5.2 - - - +
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Residues in contact with THR 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D VAL* 3.8 22.6 - - + +
96D ILE* 5.2 2.2 - - + -
97D ASN 4.0 9.9 - - - +
98D VAL* 3.2 32.0 + - - +
117D ILE* 3.8 12.9 - - - +
218D VAL* 3.7 25.8 - - + -
231D ARG 3.1 3.9 + - - -
232D VAL* 3.2 11.6 + - - -
234D LEU* 1.3 76.1 - - - +
236D GLY* 1.3 62.9 + - - +
238D THR* 3.1 13.0 + - - -
239D ILE* 3.1 18.0 + - + +
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Residues in contact with GLY 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D VAL* 4.2 10.0 - - - +
185D THR* 3.6 26.0 - - - -
218D VAL* 4.4 6.5 - - - +
232D VAL 3.0 12.6 + - - -
233D ALA 3.8 2.7 - - - -
235D THR* 1.3 77.5 - - - +
237D LEU* 1.3 60.4 + - - +
239D ILE* 3.5 3.5 + - - +
240D ALA* 3.0 24.0 + - - +
253D LEU* 4.4 5.0 - - - +
255D ILE* 6.0 0.9 - - - -
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Residues in contact with LEU 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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233D ALA 2.9 19.2 + - - +
234D LEU* 3.3 24.5 - - + +
236D GLY* 1.3 77.0 - - - +
238D THR* 1.3 57.9 + - - +
240D ALA* 3.3 6.5 + - + +
241D GLU* 2.9 35.1 + - + +
253D LEU* 5.3 4.5 - - - +
255D ILE* 5.8 0.8 - - - +
291D LEU 4.8 0.7 - - - +
292D LEU* 4.2 10.5 - - + +
295D ARG* 3.4 69.1 - - + +
296D ILE* 3.6 22.9 - - + -
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Residues in contact with THR 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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85D VAL* 3.9 11.7 - - + -
87D VAL* 4.5 1.3 - - + -
115D LYS* 3.7 31.3 - - + +
116D PRO 3.4 18.2 + - - +
117D ILE* 3.3 24.8 - - - -
234D LEU 2.9 16.8 + - - -
235D THR 3.1 4.9 + - - -
237D LEU* 1.3 74.6 - - - +
239D ILE* 1.3 61.9 + - - +
241D GLU* 3.2 10.3 + - - +
242D TYR* 2.9 27.7 + - - +
295D ARG* 4.2 6.2 + - - +
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Residues in contact with ILE 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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85D VAL* 5.1 6.5 - - + -
86D PRO 4.2 17.7 - - - +
87D VAL* 4.6 11.9 - - + -
91D THR* 4.7 7.4 - - - +
96D ILE* 4.0 20.6 - - + -
183D VAL* 3.8 22.0 - - + -
216D ALA* 4.5 9.9 - - + -
218D VAL* 3.8 28.7 - - + -
235D THR* 3.1 13.7 + - + +
236D GLY* 3.9 7.4 - - - +
237D LEU 3.4 0.2 - - - -
238D THR* 1.3 73.8 - - - +
240D ALA* 1.3 63.9 + - - +
242D TYR* 3.3 2.6 + - - +
243D PHE* 3.1 40.4 + - + -
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Residues in contact with ALA 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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183D VAL* 4.6 5.8 - - + +
236D GLY 3.0 17.9 + - - +
237D LEU* 3.6 7.9 - - + +
238D THR 3.2 0.2 - - - -
239D ILE* 1.3 77.5 - - - +
241D GLU* 1.3 56.9 + - + +
243D PHE* 3.4 3.3 + - - +
244D ARG* 2.9 27.8 + - - +
251D VAL* 4.2 22.2 - - + +
253D LEU* 4.2 28.5 - - + -
296D ILE* 6.1 0.2 - - + -
304D VAL* 5.0 6.5 - - + +
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Residues in contact with GLU 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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115D LYS* 5.3 9.4 - - - -
119D ALA* 4.4 8.1 - - - +
120D ASP 5.0 3.4 - - - +
122D PRO* 5.3 1.3 - - - +
237D LEU* 2.9 28.6 + - + +
238D THR* 3.2 8.4 + - + +
240D ALA* 1.3 76.9 - - - +
242D TYR* 1.3 57.9 + - - +
244D ARG* 3.3 31.2 + - - +
245D ASP* 2.9 37.3 + - - +
295D ARG* 3.0 55.2 + - - +
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Residues in contact with TYR 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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87D VAL* 3.6 26.0 - - + -
88D GLY* 3.4 38.0 - - - -
112D LYS* 6.1 1.0 - - - -
113D LEU* 3.3 34.1 - - + +
115D LYS* 3.8 17.9 - - + +
238D THR 2.9 15.3 + - - +
239D ILE 3.9 3.1 - - - +
241D GLU* 1.3 77.6 - - - +
243D PHE* 1.3 70.2 + + + +
245D ASP* 5.5 0.2 - - - -
246D GLU* 3.4 55.8 + - + +
247D GLU* 4.0 8.5 + - - +
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Residues in contact with PHE 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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88D GLY* 3.3 42.0 - - - -
89D ARG* 4.3 8.3 - - + -
91D THR* 4.2 5.2 - - - -
92D LEU* 3.7 31.4 - - + -
181D PHE* 3.6 33.4 - + + -
182D SER 5.5 0.2 - - - -
183D VAL* 4.7 13.5 - - + -
216D ALA* 5.0 1.3 - - + -
239D ILE* 3.1 32.1 + - + +
240D ALA 4.0 1.6 - - - +
242D TYR* 1.3 83.5 - + + +
244D ARG* 1.3 63.0 + - - +
247D GLU* 3.3 28.7 - - + +
248D GLY 4.1 1.6 + - - -
249D GLN* 4.3 5.3 + - - +
251D VAL* 3.6 24.3 - - + +
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Residues in contact with ARG 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D PRO* 4.0 13.7 - - - +
240D ALA 2.9 17.8 + - - +
241D GLU* 3.2 38.2 + - - +
243D PHE* 1.3 77.2 - - - +
245D ASP* 1.3 82.8 + - - +
248D GLY* 3.2 18.4 + - - -
249D GLN 4.3 2.4 + - - -
251D VAL* 3.9 6.0 - - - +
295D ARG 3.5 18.2 + - - -
297D THR* 2.4 40.0 + - - +
299D THR* 3.6 26.6 - - - +
301D LYS 3.5 8.5 - - - +
302D GLY* 4.0 21.0 - - - -
304D VAL* 3.6 25.6 - - + +
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Residues in contact with ASP 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D GLU* 2.9 23.4 + - - +
242D TYR* 5.5 0.2 - - - -
244D ARG* 1.3 99.5 + - - +
246D GLU* 1.3 69.8 + - + +
247D GLU 3.0 6.9 + - - -
248D GLY* 3.8 4.2 + - - -
299D THR* 3.9 5.5 + - - +
301D LYS* 3.7 41.9 - - + +
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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) + - + + + + + -
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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