Contacts of the helix formed by residues 238 - 260 (chain B) in PDB entry 5H1C
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 LEU 238 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A VAL* 4.8 2.5 - - + -
232B TYR* 4.6 1.0 - - - +
234B GLY* 4.2 7.0 - - - +
235B ARG* 3.5 36.8 - - + +
237B GLU* 1.3 74.5 - - - +
239B SER* 1.3 55.6 + - - +
240B ALA 3.0 0.4 - - - -
241B ARG* 2.7 53.2 + - - +
242B GLN* 2.7 25.6 + - + +
3D T 3.2 47.3 - - + +
4D T 3.7 34.5 - - + +
5D T 4.7 6.5 - - - +
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Residues in contact with SER 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B GLY 5.3 0.2 - - - -
237B GLU 2.2 27.4 + - - -
238B LEU* 1.3 72.8 - - - +
240B ALA* 1.3 57.2 + - - +
242B GLN* 4.4 1.7 - - - +
243B MET* 3.2 24.0 + - - +
2D T 4.2 13.9 - - - -
3D T 3.3 35.5 + - - +
7E A 5.1 0.9 - - - -
8E A 4.4 14.7 + - - -
9E A 5.3 5.2 + - - -
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Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TYR* 4.9 14.3 + - + -
237B GLU* 3.4 15.8 + - - +
238B LEU 3.0 0.4 - - - -
239B SER* 1.3 83.4 + - - +
241B ARG* 1.3 57.9 + - - +
243B MET* 3.1 15.6 + - - +
244B HIS* 2.9 28.9 + - - +
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Residues in contact with ARG 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B TYR* 3.3 40.0 - - + +
229B ARG* 5.3 1.7 - - - +
232B TYR* 3.5 38.1 + - + -
238B LEU* 2.7 30.7 + - - +
240B ALA* 1.3 79.4 - - - +
242B GLN* 1.3 86.4 + - - +
244B HIS* 3.1 4.3 + - - +
245B LEU* 2.9 36.7 + - + +
287B ILE* 4.1 11.7 - - - +
288B GLY* 3.8 18.2 - - - +
4D T 3.5 2.4 + - - -
5D T 3.2 36.4 + - - -
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Residues in contact with GLN 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B LEU* 2.7 22.4 + - + +
239B SER 4.5 1.8 - - - +
241B ARG* 1.3 112.1 - - - +
243B MET* 1.3 57.2 + - - +
245B LEU* 3.8 8.3 - - - +
246B ALA* 3.0 32.7 + - - +
288B GLY* 2.9 29.3 + - - +
289B GLY 4.5 0.4 - - - +
291B ILE* 3.3 34.6 - - + +
3D T 3.4 39.1 + - + +
4D T 4.1 5.1 + - - -
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Residues in contact with MET 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A SER* 3.4 48.4 - - - +
234A GLY 5.3 3.6 - - - +
239B SER 3.2 17.8 + - - +
240B ALA* 3.1 19.5 - - - +
241B ARG 3.1 0.4 - - - -
242B GLN* 1.3 79.7 - - - +
244B HIS* 1.3 59.2 + - - +
246B ALA* 4.0 5.2 + - - +
247B ARG* 3.8 32.6 + - - +
3D T 5.3 5.8 + - - -
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Residues in contact with HIS 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B THR* 3.8 16.8 - - - -
198B ASP* 3.6 22.2 + - - -
201B THR* 3.8 23.8 - - + +
228B TYR* 2.7 37.8 + + + -
232B TYR* 4.5 14.6 - - - +
240B ALA 2.9 11.8 + - - +
241B ARG* 3.1 7.6 + - - +
243B MET* 1.3 76.5 - - - +
245B LEU* 1.3 65.8 + - - +
246B ALA 3.2 1.6 - - - -
247B ARG* 3.1 13.4 + - + +
248B PHE* 3.0 23.2 + + + +
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Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ALA* 4.8 3.6 - - + +
225B THR* 5.3 9.2 - - + -
228B TYR* 3.4 41.1 - - + +
241B ARG* 2.9 44.2 + - + +
242B GLN* 3.9 13.0 - - - +
244B HIS* 1.3 77.0 - - - +
246B ALA* 1.3 63.6 + - - +
248B PHE* 3.1 13.7 + - + +
249B LEU* 2.9 39.0 + - + +
287B ILE* 5.8 0.4 - - + -
288B GLY* 4.4 14.4 - - - -
291B ILE* 5.1 4.5 - - + -
292B ILE* 4.6 12.1 - - + -
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Residues in contact with ALA 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ARG* 5.1 7.4 - - + +
230A THR* 3.4 37.0 - - + +
242B GLN 3.0 16.6 + - - +
243B MET* 4.2 6.5 - - - +
244B HIS 3.2 0.2 - - - -
245B LEU* 1.3 76.9 - - - +
247B ARG* 1.3 59.2 + - + +
249B LEU* 3.9 2.5 - - - +
250B ARG 3.0 22.5 + - - -
291B ILE* 4.0 24.6 - - + +
3D T 5.7 2.2 - - - +
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Residues in contact with ARG 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A THR 4.0 18.6 + - - +
231A ASP 5.3 3.4 + - - -
233A SER* 2.3 42.9 + - - +
237A GLU* 5.4 2.2 + - - -
243B MET* 3.8 22.4 + - - +
244B HIS* 3.1 14.4 + - + +
246B ALA* 1.3 75.7 - - + +
248B PHE* 1.3 66.7 + - - +
250B ARG* 3.2 6.8 + - - +
251B MET* 2.9 31.3 + - + +
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Residues in contact with PHE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ILE* 6.4 0.2 - - + -
200B GLN* 3.9 36.8 - - + -
201B THR* 5.2 7.9 - - + -
204B LEU* 3.6 31.2 - - + -
221B VAL* 5.0 10.5 - - + -
224B ALA* 3.8 26.2 - - + -
228B TYR* 4.3 11.4 - + - +
244B HIS* 3.0 15.3 + - + +
245B LEU* 3.1 17.9 + - + +
247B ARG* 1.3 76.2 - - - +
249B LEU* 1.3 74.0 + - + +
251B MET* 3.0 10.3 + - - +
252B LEU* 3.0 54.1 + - + +
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 4.3 5.5 - - + +
224B ALA* 6.1 1.1 - - + -
245B LEU* 2.9 25.6 + - + +
246B ALA* 4.0 3.4 - - - +
248B PHE* 1.3 89.9 - - + +
250B ARG* 1.3 66.4 + - - +
252B LEU* 3.1 17.5 + - + +
253B LEU* 2.9 26.5 + - - +
265B ILE* 4.3 19.1 - - + -
291B ILE* 3.8 31.4 - - + +
292B ILE* 3.8 27.1 - - + +
295B ALA* 4.1 17.7 - - + -
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Residues in contact with ARG 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A PHE* 3.1 25.9 + - - +
196A ASN* 4.2 9.9 + - - -
227A LEU* 3.5 23.2 - - - +
230A THR* 3.0 39.4 + - + +
231A ASP* 3.0 28.8 + - - -
54B TYR 4.6 5.7 + - - -
56B PRO* 4.7 6.9 - - - +
246B ALA 3.0 19.3 + - - +
247B ARG* 3.2 6.9 + - - +
249B LEU* 1.3 76.9 - - - +
251B MET* 1.3 62.3 + - + +
253B LEU* 3.1 17.9 + - + +
254B ARG* 2.9 35.7 + - + +
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Residues in contact with MET 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLU* 5.8 0.4 - - - +
204B LEU* 3.7 27.1 - - + -
205B TYR* 4.5 29.6 - - + +
208B SER* 6.4 2.2 - - - -
247B ARG* 2.9 22.3 + - + +
248B PHE* 3.0 8.3 + - - +
250B ARG* 1.3 78.8 - - - +
252B LEU* 1.3 59.8 + - - +
254B ARG* 2.8 72.2 + - + +
255B LEU* 3.0 22.7 + - + +
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 4.0 11.9 - - + -
204B LEU* 3.8 28.3 - - + -
219B LEU* 4.7 6.7 - - + -
221B VAL* 5.6 10.1 - - + -
224B ALA* 5.9 0.2 - - + -
248B PHE* 3.0 45.4 + - + +
249B LEU* 3.1 22.0 + - + +
251B MET* 1.3 76.5 - - - +
253B LEU* 1.3 58.0 + - - +
255B LEU* 3.3 11.5 + - + +
256B ALA* 2.9 30.8 + - - +
263B VAL* 4.3 25.7 - - + +
265B ILE* 4.4 10.8 - - + -
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLU* 5.4 16.8 - - + +
193A ARG* 5.5 2.0 - - - +
121B SER* 6.1 1.3 - - - -
122B ILE* 3.9 24.2 - - + -
249B LEU* 2.9 17.8 + - + +
250B ARG* 3.3 17.7 - - + +
252B LEU* 1.3 76.0 - - - +
254B ARG* 1.3 60.0 + - - +
256B ALA* 4.4 4.3 - - + +
257B ASP* 2.9 57.5 + - - +
295B ALA* 5.1 17.0 - - + +
297B THR* 5.8 6.1 - - + -
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Residues in contact with ARG 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B GLY 6.1 0.2 - - - -
46B PHE* 3.2 29.5 - - - -
51B ALA* 5.0 13.9 + - + -
54B TYR* 5.2 14.7 + - + +
55B ALA* 5.1 1.3 - - - +
56B PRO* 4.4 12.5 - - - +
59B GLU* 2.9 32.1 + - - -
205B TYR* 5.0 4.9 - - - -
250B ARG* 2.9 21.8 + - + +
251B MET* 2.8 52.3 + - - +
253B LEU* 1.3 76.4 - - - +
255B LEU* 1.3 62.5 + - + +
257B ASP* 4.6 2.1 - - - +
258B GLU* 3.0 47.7 + - - +
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 4.4 22.4 - - + +
207B ALA* 4.7 10.1 - - + -
208B SER* 3.9 31.4 - - - -
211B MET* 4.7 13.0 - - + -
219B LEU* 3.5 31.4 - - + -
251B MET* 3.0 21.9 + - + +
252B LEU* 3.8 9.0 - - + +
254B ARG* 1.3 84.1 - - + +
256B ALA* 1.3 60.5 + - - +
258B GLU* 3.1 12.6 + - - +
259B PHE* 3.0 35.1 + - + +
260B GLY 4.4 1.0 + - - +
263B VAL* 6.1 0.9 - - + -
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Residues in contact with ALA 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLY* 3.3 37.1 - - - +
121B SER* 4.2 2.5 - - - +
122B ILE* 5.2 2.0 - - + -
252B LEU 2.9 18.2 + - - +
253B LEU* 4.2 6.1 - - + +
255B LEU* 1.3 79.0 - - - +
257B ASP* 1.3 62.7 + - - +
258B GLU 3.1 1.3 + - - -
260B GLY 3.6 18.8 + - - +
263B VAL* 3.4 27.1 - - + -
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Residues in contact with ASP 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLU 5.5 0.3 - - - +
193A ARG* 2.6 32.7 + - - -
195A PHE* 3.5 23.2 - - + -
50B GLU* 5.2 0.3 - - - +
54B TYR* 4.6 12.4 + - + -
120B GLY 4.1 9.9 - - - +
253B LEU* 2.9 44.2 + - - +
254B ARG* 4.6 3.1 - - - +
255B LEU 3.2 0.2 - - - -
256B ALA* 1.3 78.2 - - - +
258B GLU* 1.3 62.0 + - + +
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Residues in contact with GLU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PRO* 4.7 5.7 - - - +
48B THR* 3.9 4.8 + - - -
50B GLU* 4.2 16.1 - - - +
51B ALA* 3.1 38.3 - - - +
54B TYR* 4.0 20.1 - - + -
254B ARG* 3.0 31.4 - - - +
255B LEU* 3.5 8.0 - - - +
257B ASP* 1.3 84.3 - - - +
259B PHE* 1.3 99.9 + - + +
260B GLY 3.5 2.1 + - - -
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Residues in contact with PHE 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PRO* 3.6 30.7 - - + -
48B THR* 3.4 31.2 - - + -
50B GLU* 4.7 2.2 - - - -
208B SER* 5.1 3.6 - - - -
211B MET* 3.4 59.9 - - + -
215B ARG* 5.7 8.2 + - - +
255B LEU* 3.0 16.9 + - + +
258B GLU* 1.3 112.4 - - + +
260B GLY* 1.3 68.3 + - - +
261B VAL* 2.9 13.4 + - + +
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Residues in contact with GLY 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B THR* 4.2 4.5 - - - -
120B GLY* 3.5 27.8 + - - -
255B LEU 4.7 0.9 - - - +
256B ALA* 3.6 16.1 + - - -
258B GLU 3.5 4.0 + - - -
259B PHE* 1.3 77.0 - - - +
261B VAL* 1.3 68.6 + - - +
262B ALA* 3.1 6.8 + - - -
263B VAL* 5.6 0.2 - - - +
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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