Contacts of the helix formed by residues 219 - 240 (chain C) in PDB entry 5M8L
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 ALA 219 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C PHE 4.6 4.9 - - - +
214C SER 4.5 0.4 - - - -
217C GLY 3.0 0.6 + - - -
218C PRO* 1.3 78.6 - - - +
220C PHE* 1.3 63.1 + - - +
221C LEU 3.4 0.9 - - - -
222C THR* 3.7 10.1 - - - -
223C TRP* 3.0 27.3 + - + +
425C PHE* 3.8 2.2 - - - -
433C GLY 4.0 4.5 - - - +
434C HIS* 3.1 34.6 + - + +
440C MET* 5.6 0.4 - - + -
449C ASN* 3.2 25.1 - - - +
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Residues in contact with PHE 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C SER 3.4 15.9 + - - +
215C HIS* 4.1 4.3 - + - -
217C GLY 3.1 9.4 + - - +
218C PRO 3.1 3.2 + - - -
219C ALA* 1.3 75.9 - - - +
221C LEU* 1.3 92.1 + - + +
224C HIS* 2.9 59.9 + + + +
356C ARG* 3.9 5.8 - - - -
360C GLU* 3.2 53.2 - - + +
377C HIS* 3.5 50.3 - + + -
404C HIS* 3.9 4.7 - + - -
407C THR* 4.0 8.7 - - + -
434C HIS* 4.3 0.6 + - - -
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Residues in contact with LEU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C PRO 4.1 1.8 + - - -
219C ALA 3.4 0.2 - - - -
220C PHE* 1.3 106.7 - - + +
222C THR* 1.3 58.2 + - - +
224C HIS* 3.9 2.4 - - - +
225C ARG* 3.0 28.9 + - - +
342C PHE* 3.7 18.4 - - + -
355C PHE* 3.7 22.4 - - + -
356C ARG* 4.4 6.5 - - + -
359C VAL* 4.0 12.8 - - + -
407C THR* 3.9 18.8 - - + +
408C ASP* 4.4 2.2 - - - +
411C PHE* 3.6 50.9 - - + -
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Residues in contact with THR 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C PRO 4.9 0.6 + - - -
219C ALA* 3.6 9.4 + - - -
221C LEU* 1.3 74.7 - - + +
223C TRP* 1.3 64.2 + - - +
225C ARG* 3.3 4.3 + - - +
226C TYR 3.2 17.5 + - - -
342C PHE* 5.9 0.7 - - + -
411C PHE* 4.1 16.6 - - + -
425C PHE* 4.2 6.8 - - + -
440C MET* 3.7 4.5 - - - +
449C ASN* 2.7 54.4 + - - +
452C MET* 3.7 31.9 - - + +
453C PHE* 4.0 12.6 - - + +
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Residues in contact with TRP 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C THR* 3.6 9.0 - - - -
192C HIS* 3.6 35.9 - + - -
195C SER* 3.5 14.5 - - - -
213C PHE 4.0 9.6 + - - -
214C SER* 3.4 26.1 - - - -
219C ALA* 3.0 23.8 + - + +
220C PHE 4.0 1.6 - - - +
222C THR* 1.3 80.3 + - - +
224C HIS* 1.3 73.2 + + - +
226C TYR* 3.3 0.7 + - - -
227C HIS* 3.0 60.4 + + - -
440C MET* 3.7 30.9 - - + -
441C VAL 2.7 29.2 + - - -
443C PHE* 3.7 19.6 - + - -
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Residues in contact with HIS 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C HIS* 3.2 3.6 + - - -
214C SER 3.5 11.4 + - - -
215C HIS* 3.1 20.4 + + - -
220C PHE* 2.9 35.9 + + + +
221C LEU* 4.3 2.5 - - - +
223C TRP* 1.3 94.5 - + - +
225C ARG* 1.3 64.5 + - - +
227C HIS* 3.3 6.2 - - - +
228C LEU* 3.1 29.9 + - + +
400C PHE* 4.0 9.9 - + - -
404C HIS* 3.1 36.3 - + + +
408C ASP* 6.1 0.2 - - - -
512C ZN 2.2 34.9 - - - -
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Residues in contact with ARG 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ARG* 5.5 1.0 + - - -
221C LEU 3.0 17.6 + - - +
222C THR 3.5 5.4 - - - +
223C TRP 3.2 0.4 - - - -
224C HIS* 1.3 74.6 - - - +
226C TYR* 1.3 65.8 + - - +
228C LEU* 3.2 6.3 + - - +
229C LEU* 3.0 21.2 + - + +
408C ASP* 3.0 34.7 + - - +
411C PHE* 3.4 24.4 - - - -
412C ASP* 3.0 38.5 + - - +
415C LEU* 3.8 2.0 - - - +
452C MET* 3.2 32.5 + - - -
454C VAL 2.7 28.1 + - - -
456C ALA 4.2 0.8 - - - +
460C LEU* 3.6 19.2 - - + +
462C TYR* 3.2 20.9 + - + +
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Residues in contact with TYR 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C THR 3.2 4.8 + - - +
223C TRP 3.9 4.5 - - - +
225C ARG* 1.3 79.8 - - - +
227C HIS* 1.3 56.6 + - - +
229C LEU* 3.2 12.5 + - + -
230C ARG* 2.9 54.2 + - + +
440C MET* 3.8 22.2 - - + -
443C PHE* 3.4 44.6 - + + -
444C TRP 4.1 16.0 + - - -
445C PRO* 4.7 4.7 + - - +
447C VAL* 4.0 24.0 - - + +
452C MET* 3.9 27.8 - - + -
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Residues in contact with HIS 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C PHE* 2.8 76.2 + + - -
191C THR* 3.4 18.0 + - - -
192C HIS* 3.9 10.7 - - + +
223C TRP* 3.0 43.1 + + + +
224C HIS* 3.3 13.8 + - - +
226C TYR* 1.3 76.7 - - - +
228C LEU* 1.3 62.2 + - - +
230C ARG* 3.6 4.6 + - + +
231C LEU 3.2 16.1 + - - -
395C PRO* 4.6 0.4 - - + -
400C PHE* 3.7 18.9 - + - -
443C PHE* 4.0 12.0 - + + -
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Residues in contact with LEU 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ARG* 4.4 11.7 - - - +
188C PHE* 4.5 12.3 - - + -
224C HIS 3.1 15.5 + - - +
225C ARG 3.7 4.7 - - - +
227C HIS* 1.3 75.2 - - + +
229C LEU* 1.3 60.8 + - - +
231C LEU* 3.2 4.7 + - - +
232C GLU* 2.8 31.3 + - - +
246C LEU* 3.7 17.0 - - + +
400C PHE* 5.6 0.2 - - + -
401C VAL* 3.8 20.2 - - + +
404C HIS* 3.4 41.7 - - + +
405C THR* 3.5 25.6 - - + +
408C ASP* 4.2 11.9 - - + -
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Residues in contact with LEU 229 (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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115C PRO* 4.0 27.4 - - + -
130C ARG* 3.9 10.1 - - - +
225C ARG* 3.0 15.7 + - + +
226C TYR* 3.2 14.1 + - + +
228C LEU* 1.3 78.0 - - - +
230C ARG* 1.3 57.0 + - - +
232C GLU* 3.7 9.6 - - - +
233C LYS* 3.0 29.6 + - + +
452C MET* 4.3 25.4 - - + -
460C LEU* 4.3 14.6 - - + +
462C TYR* 3.7 33.0 - - + -
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Residues in contact with ARG 230 (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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107C GLY* 5.9 4.2 - - - -
108C HIS 6.0 0.8 - - - +
156C HIS* 4.9 1.0 - - - -
158C LEU* 5.1 7.1 - - - +
159C PHE* 3.8 28.6 - - - -
187C TYR* 4.0 24.4 + - + +
188C PHE* 6.4 0.4 - - + -
226C TYR* 2.9 48.1 + - + +
227C HIS* 3.8 6.7 - - + +
229C LEU* 1.3 75.0 - - - +
231C LEU* 1.3 64.8 + - - +
233C LYS* 3.6 20.5 + - - +
234C ASP* 2.7 59.1 + - - +
237C GLU* 5.9 0.4 + - - -
443C PHE* 5.2 6.1 - - + -
444C TRP 4.3 7.9 + - - -
445C PRO* 5.2 4.4 - - - +
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Residues in contact with LEU 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C LEU* 5.0 0.7 - - + -
151C ALA* 5.2 0.7 - - + -
184C ILE* 4.4 16.8 - - + +
185C TYR* 4.3 19.3 - - + -
188C PHE* 3.8 37.0 - - + -
227C HIS 3.2 4.7 + - - +
228C LEU 3.2 7.1 + - - +
230C ARG* 1.3 77.1 - - - +
232C GLU* 1.3 65.4 + - - +
234C ASP* 3.3 5.3 + - - +
235C MET* 3.0 51.0 + - + +
246C LEU* 4.3 12.8 - - + -
401C VAL* 3.8 30.5 - - + -
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Residues in contact with GLU 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ILE* 3.2 24.1 - - - +
130C ARG* 2.8 41.1 + - - -
228C LEU 2.8 20.2 + - - +
229C LEU* 3.7 14.6 - - - +
230C ARG 3.3 0.2 - - - -
231C LEU* 1.3 73.8 - - - +
233C LYS* 1.3 56.6 + - - +
235C MET* 3.3 4.7 + - - +
236C GLN* 3.0 45.0 + - - +
244C PHE* 3.8 7.9 - - + +
245C SER* 3.4 5.6 - - - -
246C LEU* 3.0 36.3 + - + +
462C TYR* 4.5 1.6 - - - +
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Residues in contact with LYS 233 (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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112C THR* 2.5 41.6 + - - +
113C CYS* 4.1 10.7 + - - +
229C LEU* 3.0 18.3 + - + +
230C ARG* 4.0 24.7 - - - +
232C GLU* 1.3 75.0 - - - +
234C ASP* 1.3 65.4 + - - +
236C GLN* 3.3 22.9 + - - +
237C GLU* 3.2 46.2 + - + +
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Residues in contact with ASP 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C HIS* 2.9 33.6 + - + -
157C PRO* 6.4 0.2 - - + -
184C ILE* 3.7 24.9 - - + +
187C TYR* 4.4 4.5 - - - -
230C ARG* 2.7 56.8 + - - +
231C LEU* 3.3 7.3 + - - +
233C LYS* 1.3 75.9 - - - +
235C MET* 1.3 57.8 + - - +
237C GLU* 3.6 7.7 + - - +
238C MET* 2.9 28.6 + - - +
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Residues in contact with MET 235 (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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144C PHE* 5.0 0.7 - - + +
147C ALA* 3.6 44.0 - - + +
148C LEU* 3.6 23.8 - - + +
151C ALA* 4.4 7.9 - - + -
184C ILE* 4.8 1.3 - - + -
231C LEU* 3.0 46.9 + - + +
232C GLU 3.8 0.7 - - - +
234C ASP* 1.3 75.7 - - - +
236C GLN* 1.3 65.5 + - - +
238C MET* 4.0 15.7 - - + -
239C LEU* 2.9 33.3 + - + +
244C PHE* 3.6 31.2 - - + -
246C LEU* 4.1 8.3 - - + -
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Residues in contact with GLN 236 (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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128C ILE* 3.8 12.5 - - - +
232C GLU* 3.0 31.4 + - - +
233C LYS* 3.3 27.6 + - - +
235C MET* 1.3 76.3 - - - +
237C GLU* 1.3 59.2 + - + +
240C GLN* 2.8 24.3 + - - -
241C GLU 3.0 24.7 + - - +
242C PRO* 3.5 28.3 + - + +
244C PHE* 3.1 31.1 + - + +
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Residues in contact with GLU 237 (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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112C THR* 4.3 6.2 + - - +
157C PRO* 6.1 1.2 - - - +
230C ARG* 5.9 0.2 + - - -
233C LYS* 3.2 48.1 + - + +
234C ASP* 4.1 7.2 - - - +
236C GLN* 1.3 79.3 - - + +
238C MET* 1.3 66.4 + - - +
240C GLN* 3.5 16.7 + - - +
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Residues in contact with MET 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C ALA 3.4 26.2 - - - +
150C MET* 3.8 36.5 - - + +
151C ALA* 3.6 30.5 - - + +
154C THR* 4.2 7.4 - - + +
184C ILE* 3.8 21.8 - - + -
234C ASP 2.9 19.7 + - - +
235C MET* 3.2 13.4 + - + +
237C GLU* 1.3 79.5 - - - +
239C LEU* 1.3 81.7 + - + +
240C GLN* 4.5 3.8 - - - +
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Residues in contact with LEU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C HIS* 4.3 9.4 - - + +
147C ALA* 3.8 30.5 - - + -
150C MET* 4.4 13.0 - - - -
235C MET* 2.9 21.2 + - + +
236C GLN 4.2 0.2 - - - +
238C MET* 1.3 87.6 - - + +
240C GLN* 1.3 69.7 + - - +
241C GLU* 3.3 35.2 + - + +
244C PHE* 3.7 37.2 - - + -
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Residues in contact with GLN 240 (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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236C GLN 2.8 10.1 + - - -
237C GLU* 3.5 14.8 + - - +
238C MET 3.3 4.4 - - - +
239C LEU* 1.3 80.4 - - - +
241C GLU* 1.3 60.4 + - - +
242C PRO* 3.6 10.2 - - - +
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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