Contacts of the helix formed by residues 219 - 240 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A PHE 4.6 5.4 - - - +
218A PRO* 1.3 77.5 - - - +
220A PHE* 1.3 57.3 + - - +
221A LEU 3.4 0.7 - - - -
222A THR* 3.6 3.4 - - - -
223A TRP* 2.8 36.1 + - + +
425A PHE* 3.9 2.6 - - + -
433A GLY 3.9 5.4 - - - +
434A HIS* 2.9 30.3 + - + +
440A MET* 5.2 1.3 - - + -
449A ASN* 3.2 33.7 - - - +
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Residues in contact with PHE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A SER 3.3 23.3 - - - +
215A HIS* 4.1 6.3 - + - -
217A GLY 3.2 14.8 + - - +
218A PRO 3.1 2.2 - - - -
219A ALA* 1.3 76.2 - - - +
221A LEU* 1.3 90.3 + - + +
224A HIS* 2.9 48.6 + + + +
356A ARG* 3.9 5.6 - - - -
360A GLU* 3.6 49.8 - - + +
377A HIS* 3.5 48.7 - + - -
404A HIS* 4.1 5.4 - + - -
407A THR* 4.2 6.3 - - + -
434A HIS* 4.1 1.4 - - - -
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Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A PRO 4.2 2.6 + - - -
219A ALA 3.4 0.4 - - - -
220A PHE* 1.3 101.4 - - + +
222A THR* 1.3 59.0 + - - +
224A HIS* 3.9 3.0 - - + +
225A ARG* 3.0 27.4 + - - +
342A PHE* 3.7 30.7 - - + -
355A PHE* 3.8 7.4 - - + -
356A ARG* 4.1 9.0 - - + -
359A VAL* 3.8 22.9 - - + -
407A THR* 3.9 20.6 - - + +
408A ASP* 4.5 1.9 - - - +
411A PHE* 3.8 43.1 - - + -
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Residues in contact with THR 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A PRO 4.8 0.6 + - - -
219A ALA* 3.4 8.5 + - - -
221A LEU* 1.3 73.8 - - + +
223A TRP* 1.3 64.3 + - - +
225A ARG* 3.5 6.9 - - - +
226A TYR 3.1 17.7 + - - -
342A PHE* 5.5 0.7 - - + -
411A PHE* 4.1 9.2 - - + -
425A PHE* 4.1 5.8 - - + -
440A MET* 3.5 9.7 - - - +
449A ASN* 2.6 51.5 + - - +
452A MET* 3.7 22.4 - - + +
453A PHE* 4.0 25.8 - - + +
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Residues in contact with TRP 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A THR 3.6 18.2 - - - -
192A HIS* 3.5 37.2 - + - -
195A SER* 3.7 6.6 - - - -
213A PHE 3.9 10.3 - - - -
214A SER* 3.4 25.3 - - - -
219A ALA* 2.8 25.6 + - + +
220A PHE 4.0 2.0 - - - +
222A THR* 1.3 73.5 + - - +
224A HIS* 1.3 76.9 + + - +
226A TYR* 3.2 5.2 + - - +
227A HIS* 3.0 50.6 + + + +
440A MET* 3.6 25.9 - - + -
441A VAL 2.6 26.9 + - - -
443A PHE* 3.4 29.3 - + - -
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Residues in contact with HIS 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A HIS* 3.2 3.0 + - - -
214A SER 3.3 16.1 + - - -
215A HIS* 3.3 14.1 - + - -
220A PHE* 2.9 35.5 + + + +
221A LEU* 4.3 3.6 - - + +
223A TRP* 1.3 98.4 - + - +
225A ARG* 1.3 61.6 + - - +
227A HIS* 3.4 5.0 - - - +
228A LEU* 3.1 29.9 + - + +
400A PHE* 3.9 10.8 - + - -
404A HIS* 3.0 38.6 - + + +
407A THR* 6.4 0.7 - - + -
408A ASP* 5.9 0.7 - - - -
512A ZN 2.1 34.9 - - - -
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Residues in contact with ARG 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 5.5 0.9 + - - -
221A LEU 3.0 19.8 + - - +
222A THR 3.5 5.8 - - - +
223A TRP 3.2 0.2 - - - -
224A HIS* 1.3 74.9 - - - +
226A TYR* 1.3 67.4 + - - +
228A LEU* 3.3 5.7 + - - +
229A LEU* 3.0 21.7 + - + +
408A ASP* 2.8 36.7 + - - +
411A PHE* 3.6 20.0 - - - -
412A ASP* 3.0 37.9 + - - +
415A LEU* 3.6 4.2 - - - +
452A MET* 3.2 35.1 + - - -
454A VAL 2.7 29.5 + - - -
456A ALA* 4.3 0.8 - - - +
460A LEU* 3.7 17.0 - - + +
462A TYR* 3.3 18.9 + - - +
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Residues in contact with TYR 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A THR 3.1 4.2 + - - +
223A TRP 3.2 4.2 + - - +
225A ARG* 1.3 79.0 - - - +
227A HIS* 1.3 53.6 + - - +
229A LEU* 3.0 13.0 + - + +
230A ARG* 2.8 64.9 + - + -
440A MET* 3.7 24.2 - - + -
443A PHE* 3.3 42.2 - + + -
444A TRP 4.1 11.5 + - - -
445A PRO* 4.9 4.2 + - - +
447A VAL* 4.1 23.0 - - + +
452A MET* 3.9 26.5 - - + -
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Residues in contact with HIS 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PHE* 2.9 73.5 + + - -
191A THR* 3.7 17.8 + - - -
192A HIS* 4.0 6.5 - - + -
223A TRP* 3.0 41.9 + + + +
224A HIS* 3.4 14.0 + - - +
226A TYR* 1.3 77.6 - - - +
228A LEU* 1.3 63.2 + - - +
230A ARG* 3.5 3.9 + - + +
231A LEU 3.3 14.9 + - - -
395A PRO* 4.6 0.4 - - + -
400A PHE* 3.4 26.4 - + - -
404A HIS* 6.0 0.2 - - - -
443A PHE* 3.9 11.9 - + + -
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 4.3 11.7 - - - +
188A PHE* 4.5 13.7 - - + -
224A HIS* 3.1 17.7 + - + +
225A ARG* 3.7 3.4 - - - +
226A TYR 3.3 0.2 - - - -
227A HIS* 1.3 77.2 - - + +
229A LEU* 1.3 67.6 + - - +
231A LEU* 3.1 2.6 + - - -
232A GLU* 2.9 20.1 + - - +
246A LEU* 3.6 21.6 - - + +
400A PHE* 5.5 0.4 - - + -
401A VAL* 3.7 29.2 - - + +
404A HIS* 3.3 40.8 - - + +
405A THR* 3.6 17.5 - - + +
408A ASP* 4.1 12.1 - - + -
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Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PRO* 4.2 27.4 - - + -
130A ARG* 3.8 11.0 - - - +
225A ARG* 3.0 12.7 + - + +
226A TYR* 3.0 16.0 + - + +
228A LEU* 1.3 75.5 - - - +
230A ARG* 1.3 62.4 + - - +
232A GLU* 3.5 8.7 + - - +
233A LYS* 3.1 24.7 + - + +
452A MET* 4.2 27.4 - - + -
460A LEU* 4.4 17.0 - - + +
462A TYR* 3.8 29.8 - - + -
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Residues in contact with ARG 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A HIS* 5.1 0.4 - - - -
158A LEU* 5.0 8.3 - - - +
159A PHE* 3.8 33.6 - - - -
187A TYR* 3.9 26.5 - - + +
188A PHE* 6.3 0.2 - - + -
226A TYR* 2.8 50.2 + - + +
227A HIS* 3.7 6.7 - - + +
229A LEU* 1.3 78.1 - - - +
231A LEU* 1.3 57.4 + - - +
233A LYS* 3.5 26.6 + - - +
234A ASP* 3.0 56.6 + - - +
237A GLU* 5.4 3.0 + - - -
443A PHE* 5.3 3.4 - - + -
444A TRP 4.1 5.8 + - - -
445A PRO* 5.3 3.0 - - - +
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Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU* 5.1 1.1 - - + -
151A ALA* 5.2 0.2 - - + -
184A ILE* 4.2 17.9 - - + +
185A TYR* 4.2 20.0 - - + -
188A PHE* 3.7 38.1 - - + -
227A HIS 3.3 3.0 + - - +
228A LEU 3.1 6.8 + - - +
230A ARG* 1.3 77.6 - - - +
232A GLU* 1.3 60.5 + - - +
234A ASP* 3.3 5.0 + - - +
235A MET* 2.9 55.9 + - + +
246A LEU* 4.4 5.4 - - + -
401A VAL* 3.9 35.9 - - + -
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Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE* 3.2 25.8 - - - +
130A ARG* 2.9 36.3 + - - +
228A LEU 2.9 17.1 + - - +
229A LEU* 3.8 13.6 - - + +
231A LEU* 1.3 74.9 - - - +
233A LYS* 1.3 57.2 + - - +
235A MET* 3.3 3.2 + - - +
236A GLN* 2.9 47.2 + - - +
244A PHE* 3.9 8.1 - - + +
245A SER* 3.4 3.5 - - - -
246A LEU* 2.8 44.7 + - + +
462A TYR* 4.6 1.2 - - - +
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Residues in contact with LYS 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A THR* 2.6 41.5 + - - +
113A CYS* 4.4 8.9 + - - +
229A LEU* 3.1 18.4 + - + +
230A ARG* 3.7 28.3 - - - +
231A LEU 3.2 0.2 - - - -
232A GLU* 1.3 77.6 - - - +
234A ASP* 1.3 62.1 + - - +
236A GLN* 3.3 19.3 + - - +
237A GLU* 3.1 43.9 + - + +
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Residues in contact with ASP 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A HIS* 2.7 37.1 + - - +
157A PRO* 5.7 1.0 - - + +
184A ILE* 3.8 23.8 - - + +
187A TYR* 4.3 3.8 - - - -
230A ARG* 3.0 55.7 + - - +
231A LEU* 3.7 6.7 - - - +
233A LYS* 1.3 74.9 - - - +
235A MET* 1.3 57.9 + - - +
237A GLU* 3.4 10.4 + - - +
238A MET* 2.8 28.7 + - - +
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Residues in contact with MET 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A PHE* 5.0 0.7 - - + -
147A ALA* 3.8 33.9 - - + +
148A LEU* 3.8 19.5 - - + +
151A ALA* 4.3 13.9 - - + -
184A ILE* 4.6 2.7 - - + -
231A LEU* 2.9 48.8 + - + +
232A GLU 3.8 0.4 - - - +
234A ASP* 1.3 76.2 - - - +
236A GLN* 1.3 59.4 + - - +
238A MET* 4.0 9.2 - - + -
239A LEU* 2.8 38.2 + - + +
244A PHE* 3.4 38.6 - - + -
246A LEU* 4.2 8.7 - - + -
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Residues in contact with GLN 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ILE* 3.6 13.1 - - - +
232A GLU* 2.9 35.3 + - - +
233A LYS* 3.5 22.1 - - + +
235A MET* 1.3 76.5 - - - +
237A GLU* 1.3 57.6 + - + +
240A GLN* 2.9 22.9 + - - -
241A GLU 2.9 33.6 + - - +
242A PRO* 3.5 19.4 + - + +
244A PHE* 3.0 32.8 + - + +
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Residues in contact with GLU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A THR* 4.5 4.7 + - - -
157A PRO* 5.2 10.9 - - + +
230A ARG* 5.4 2.5 + - - -
233A LYS* 3.1 49.9 + - + +
234A ASP* 3.8 10.3 - - - +
236A GLN* 1.3 74.2 - - + +
238A MET* 1.3 67.4 + - - +
240A GLN* 3.3 17.7 + - - +
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Residues in contact with MET 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ALA 3.5 22.4 - - - +
150A MET* 3.7 37.2 - - + +
151A ALA* 3.5 30.3 - - - +
154A THR* 4.1 7.4 - - + -
184A ILE* 3.7 20.9 - - + -
234A ASP 2.8 19.1 + - - +
235A MET* 3.6 15.7 - - + +
237A GLU* 1.3 77.8 - - - +
239A LEU* 1.3 88.8 + - + +
240A GLN* 3.6 4.0 + - - +
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Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A HIS* 4.3 13.0 - - + +
147A ALA* 3.9 20.0 - - + -
150A MET* 4.5 11.0 - - - -
235A MET 2.8 24.2 + - - +
238A MET* 1.3 90.1 - - + +
240A GLN* 1.3 69.2 + - - +
241A GLU* 3.3 34.2 + - + +
244A PHE* 3.5 43.5 - - + -
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Residues in contact with GLN 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A GLN 2.9 8.9 + - - -
237A GLU* 3.3 15.4 + - - +
238A MET 4.5 3.4 - - - +
239A LEU* 1.3 79.8 - - - +
241A GLU* 1.3 59.5 + - - +
242A PRO* 3.6 11.3 - - - +
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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
------------------------------------------------------------
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