Contacts of the helix formed by residues 249 - 270 (chain A) in PDB entry 2PZI
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 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A LYS 4.1 4.3 - - - +
248A LEU* 1.3 88.6 - - + +
250A VAL* 1.3 66.6 + - + +
251A ALA* 4.6 3.4 - - + +
252A GLU* 3.3 41.7 + - + +
253A ALA* 3.2 17.0 + - - +
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Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU 5.0 0.4 - - - +
249A PRO* 1.3 73.8 - - + +
251A ALA* 1.3 65.9 + - - +
253A ALA* 3.3 1.0 + - - +
254A ILE* 3.0 34.0 + - + +
339A THR* 3.9 14.8 - - + +
359A VAL* 3.5 32.5 - - + -
363A TYR* 3.7 23.6 + - + -
366A TYR* 4.0 21.5 - - + -
399A VAL* 3.5 33.4 - - + -
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Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL* 4.1 9.6 - - + -
249A PRO* 3.3 3.9 - - + +
250A VAL* 1.3 80.7 - - - +
252A GLU* 1.3 63.0 + - + +
254A ILE 3.4 0.2 + - - -
255A ALA* 2.9 24.3 + - - +
396A LEU* 3.6 23.4 - - + +
399A VAL* 3.8 19.6 - - + +
400A VAL* 4.1 11.9 - - + -
403A ASP* 4.9 7.6 + - - +
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Residues in contact with GLU 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL* 4.2 10.7 - - + +
80A ILE* 3.6 31.9 - - + +
248A LEU* 3.4 24.1 - - + +
249A PRO* 3.3 35.4 + - + +
251A ALA* 1.3 78.0 - - + +
253A ALA* 1.3 62.8 + - - +
255A ALA* 3.3 4.9 + - - +
256A TYR* 3.1 39.6 + - + +
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Residues in contact with ALA 253 (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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248A LEU* 4.0 20.1 - - + +
249A PRO 3.2 5.4 + - - +
250A VAL 3.3 2.2 + - - +
252A GLU* 1.3 75.5 - - - +
254A ILE* 1.3 66.3 + - - +
256A TYR* 3.4 4.4 + - - +
257A LEU* 3.0 29.1 + - - +
335A LEU* 4.0 8.5 - - + -
338A LEU* 4.2 13.9 - - + -
339A THR* 3.5 32.1 - - + -
366A TYR* 5.2 0.2 - - - +
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Residues in contact with ILE 254 (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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250A VAL* 3.0 29.1 + - + +
251A ALA 3.7 3.1 - - - +
253A ALA* 1.3 74.3 - - - +
255A ALA* 1.3 54.3 + - - +
257A LEU* 3.1 3.5 + - - +
258A LEU* 2.8 36.3 + - + +
335A LEU* 4.2 7.9 - - + -
366A TYR* 3.8 33.9 - - + -
392A LEU* 3.6 33.0 - - + +
395A VAL* 3.9 18.4 - - + -
396A LEU* 3.6 32.8 - - + +
399A VAL* 4.4 6.1 - - + -
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Residues in contact with ALA 255 (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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73A LEU* 3.7 28.0 - - + +
74A GLY* 4.3 4.8 + - - +
78A VAL* 3.8 20.4 - - + -
251A ALA 2.9 14.0 + - - +
252A GLU 3.3 9.8 + - - +
254A ILE* 1.3 79.2 - - - +
256A TYR* 1.3 62.9 + - - +
258A LEU* 3.2 7.6 + - - +
259A GLU* 3.2 26.0 + - - +
396A LEU* 4.5 5.6 - - - +
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Residues in contact with TYR 256 (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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73A LEU* 3.7 22.7 - - + -
80A ILE* 3.6 29.0 - - + +
240A LEU* 3.7 39.9 - - + -
248A LEU* 3.5 36.4 - - + +
252A GLU* 3.1 25.5 + - + -
253A ALA* 3.6 6.1 - - - +
255A ALA* 1.3 73.0 - - - +
257A LEU* 1.3 65.1 + - + +
259A GLU* 3.1 17.5 + - - +
260A ILE* 3.6 8.0 + - - +
282A ILE* 5.3 0.8 - - - +
284A LEU* 4.0 18.0 - - + +
289A LEU* 3.5 32.2 - - + +
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Residues in contact with LEU 257 (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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240A LEU* 5.0 0.2 - - + -
253A ALA 3.0 19.7 + - - +
254A ILE 3.9 2.2 - - - +
256A TYR* 1.3 80.2 - - + +
258A LEU* 1.3 62.1 + - - +
260A ILE* 3.1 19.5 + - + +
261A LEU* 3.1 29.1 + - + +
277A LEU* 3.9 16.2 - - + -
282A ILE* 4.5 7.6 - - + -
331A VAL* 3.9 25.1 - - + +
334A THR* 3.7 24.2 - - + -
335A LEU* 3.5 29.4 - - + -
338A LEU* 3.7 23.3 - - + -
392A LEU* 4.6 7.2 - - + -
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Residues in contact with LEU 258 (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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74A GLY* 4.5 12.1 - - - -
254A ILE* 2.8 19.6 + - + +
255A ALA* 3.5 10.3 - - - +
257A LEU* 1.3 71.6 - - - +
259A GLU* 1.3 62.9 + - + +
261A LEU* 4.3 3.5 - - + +
262A PRO* 3.3 19.4 - - - +
389A SER* 3.4 47.1 + - - +
392A LEU* 4.0 16.1 - - + +
393A THR* 3.5 25.4 - - + +
396A LEU* 3.9 28.5 - - + -
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Residues in contact with GLU 259 (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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72A MET 4.7 2.6 - - - +
73A LEU* 3.5 34.1 - - + +
74A GLY* 4.0 14.6 + - - -
75A GLY 5.1 1.6 + - - -
209A SER* 4.1 14.4 + - - -
255A ALA 3.4 13.6 - - - +
256A TYR 3.1 8.7 + - - +
257A LEU 3.1 1.4 - - - -
258A LEU* 1.3 81.7 - - - +
260A ILE* 1.3 60.1 + - - +
262A PRO* 3.5 12.5 - - - +
263A ALA 5.0 0.2 + - - -
289A LEU* 3.7 22.8 + - + +
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Residues in contact with ILE 260 (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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209A SER* 5.0 3.8 - - - +
256A TYR 4.1 7.2 - - - +
257A LEU* 3.6 27.6 - - + +
259A GLU* 1.3 78.5 - - - +
261A LEU* 1.3 65.7 + - + +
262A PRO 3.2 2.9 - - - -
263A ALA* 2.8 31.2 + - + +
264A LEU* 3.1 27.1 + - + +
277A LEU* 4.1 20.4 - - + -
282A ILE* 4.3 12.1 - - + -
289A LEU* 4.1 30.3 - - + +
290A LYS 4.6 1.1 - - - -
291A LEU* 3.7 29.8 - - + +
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Residues in contact with LEU 261 (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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257A LEU 3.1 21.7 + - - +
258A LEU* 4.3 4.9 - - + +
260A ILE* 1.3 79.4 - - + +
262A PRO* 1.4 61.0 - - + +
264A LEU* 3.2 21.3 + - + +
265A SER* 2.8 32.0 + - - -
328A ILE* 5.5 0.4 - - + -
331A VAL* 4.1 20.0 - - + -
385A ALA* 3.9 29.9 - - + +
388A MET* 4.7 9.0 - - + -
389A SER* 4.0 32.8 - - - +
392A LEU* 3.9 26.7 - - + -
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Residues in contact with PRO 262 (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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207A HIS* 3.9 12.3 + - + +
258A LEU 3.3 19.7 - - - +
259A GLU* 3.5 10.1 - - - +
260A ILE 3.3 4.7 - - - -
261A LEU* 1.4 88.3 - - + +
263A ALA* 1.3 58.7 + - - +
265A SER* 3.7 9.1 - - - +
266A TYR* 2.9 28.9 + - - +
389A SER* 5.6 3.4 - - - +
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Residues in contact with ALA 263 (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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207A HIS* 3.8 23.3 - - + +
209A SER* 4.2 9.2 - - - -
210A ILE* 4.1 14.1 - - + +
259A GLU 5.0 0.6 + - - -
260A ILE* 2.8 22.2 + - - +
262A PRO* 1.3 72.4 - - - +
264A LEU* 1.3 55.1 + - - +
266A TYR* 3.2 6.3 + - - +
267A LEU* 2.9 32.3 + - - +
291A LEU* 3.8 22.7 - - + -
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Residues in contact with LEU 264 (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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260A ILE* 3.1 26.7 + - + +
261A LEU* 3.2 14.6 + - + +
263A ALA* 1.3 72.0 - - - +
265A SER* 1.3 59.7 + - - +
267A LEU* 3.1 7.6 + - + +
268A HIS* 2.8 50.0 + - + -
274A TYR* 3.7 37.2 - - + -
277A LEU* 4.3 7.6 - - + -
291A LEU* 4.1 14.4 - - + -
327A ASP* 4.6 12.3 - - + +
330A THR* 5.7 0.2 - - - +
331A VAL* 3.8 29.8 - - + -
385A ALA* 4.4 3.8 - - + -
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Residues in contact with SER 265 (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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261A LEU 2.8 21.8 + - - -
262A PRO* 3.7 9.3 - - - +
264A LEU* 1.3 70.7 - - - +
266A TYR* 1.3 62.7 + - - +
268A HIS* 3.3 10.7 + - - +
269A SER* 3.0 25.3 + - - -
385A ALA* 3.3 17.4 - - - +
386A GLU* 3.5 32.4 + - - +
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Residues in contact with TYR 266 (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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204A GLU 4.1 4.0 + - - -
205A VAL* 3.9 20.5 - - + -
206A VAL* 3.3 39.3 + - + +
207A HIS* 3.7 29.4 - + + -
210A ILE* 4.2 1.1 - - + -
262A PRO 2.9 15.5 + - - +
263A ALA 3.3 10.8 - - - +
265A SER* 1.3 75.9 - - - +
267A LEU* 1.3 71.8 + - + +
269A SER* 2.7 27.8 + - - -
270A ILE* 3.3 40.1 + - + +
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Residues in contact with LEU 267 (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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205A VAL* 3.8 29.8 - - + -
210A ILE* 4.3 12.1 - - + -
263A ALA 2.9 17.1 + - - +
264A LEU* 3.1 13.2 + - + +
266A TYR* 1.3 81.6 - - + +
268A HIS* 1.3 66.4 + - + +
270A ILE* 3.1 15.4 + - + +
272A LEU* 3.1 46.5 + - + +
273A VAL 4.7 0.7 - - - -
274A TYR* 3.9 44.4 - - + +
291A LEU* 5.3 0.7 - - + -
294A LEU* 5.3 1.8 - - + -
297A VAL* 4.7 9.6 - - + -
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Residues in contact with HIS 268 (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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264A LEU* 2.8 41.2 + - + +
265A SER* 3.7 6.6 + - - +
267A LEU* 1.3 74.8 - - + +
269A SER* 1.3 56.6 + - - +
271A GLY* 2.9 19.4 + - - -
272A LEU 3.1 19.7 - - - +
273A VAL* 4.5 2.5 - - + -
300A ILE* 4.5 6.9 - - + +
324A VAL* 3.9 47.3 - - + +
327A ASP* 2.9 33.8 + - + +
328A ILE* 5.4 1.8 - - + -
385A ALA* 4.1 16.8 + - + +
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Residues in contact with SER 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A SER 3.0 14.0 + - - -
266A TYR* 2.7 26.6 + - - -
268A HIS* 1.3 76.3 - - - +
270A ILE* 1.3 66.2 + - - +
271A GLY 3.7 0.3 + - - -
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Residues in contact with ILE 270 (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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204A GLU 5.6 0.7 - - - +
205A VAL* 4.2 8.3 - - + -
266A TYR* 3.5 46.9 - - + +
267A LEU* 3.1 17.3 - - - +
269A SER* 1.3 88.3 + - - +
271A GLY* 1.3 58.6 + - - +
272A LEU* 3.7 27.8 + - + +
299A ARG* 6.0 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
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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