Contacts of the helix formed by residues 249 - 270 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B LYS 4.2 4.7 - - - +
248B LEU* 1.4 87.5 - - + +
250B VAL* 1.3 67.0 + - - +
251B ALA* 3.0 6.5 + - + +
252B GLU* 3.0 43.9 + - + +
253B ALA* 3.2 9.0 + - - +
403B ASP* 6.2 0.2 - - - +
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Residues in contact with VAL 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU 3.5 2.2 + - - +
249B PRO* 1.3 71.1 - - - +
251B ALA* 1.3 57.2 + - - +
253B ALA* 3.4 2.3 + - - +
254B ILE* 3.1 49.5 + - + +
339B THR* 3.9 12.7 - - + +
359B VAL* 3.6 21.1 - - + -
363B TYR* 3.5 38.5 + - + -
366B TYR* 3.9 26.9 - - + -
399B VAL* 4.1 13.9 - - + -
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 3.5 12.5 - - + +
249B PRO* 3.1 4.1 - - + +
250B VAL* 1.3 75.1 - - - +
252B GLU* 1.3 65.4 + - - +
255B ALA* 3.1 24.9 + - - +
396B LEU* 3.7 6.6 - - - +
399B VAL* 3.6 26.7 - - + +
400B VAL* 4.1 15.7 - - + -
403B ASP* 4.0 15.1 + - - +
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Residues in contact with GLU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 4.3 11.6 - - + +
80B ILE* 4.1 22.9 - - + -
248B LEU* 3.5 18.1 - - + +
249B PRO* 3.0 41.0 + - + +
251B ALA* 1.3 76.8 - - - +
253B ALA* 1.3 59.7 + - - +
255B ALA* 3.2 3.6 + - - +
256B TYR* 2.9 56.3 + - + +
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Residues in contact with ALA 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU* 4.0 14.0 - - + +
249B PRO 3.2 5.2 + - - +
250B VAL 3.7 2.2 - - - +
252B GLU* 1.3 73.5 - - - +
254B ILE* 1.3 66.4 + - - +
256B TYR* 3.1 6.9 + - - +
257B LEU* 2.9 26.5 + - - +
335B LEU* 4.0 8.1 - - + -
338B LEU* 4.1 22.2 - - + -
339B THR* 3.5 31.6 - - + -
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Residues in contact with ILE 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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250B VAL* 3.1 36.6 + - + +
251B ALA 4.0 4.0 - - - +
253B ALA* 1.3 78.5 - - - +
255B ALA* 1.3 57.7 + - - +
257B LEU* 3.2 2.6 + - - +
258B LEU* 2.8 31.9 + - + +
335B LEU* 3.8 10.1 - - + -
366B TYR* 3.8 28.7 - - + -
392B LEU* 3.7 38.2 - - + +
395B VAL* 3.9 18.8 - - + -
396B LEU* 3.8 19.7 - - + +
399B VAL* 4.2 8.1 - - + -
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Residues in contact with ALA 255 (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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73B LEU* 4.1 7.4 - - + -
74B GLY* 3.9 18.2 - - - +
78B VAL* 3.8 26.0 - - + -
251B ALA 3.1 20.3 + - - +
252B GLU 3.2 4.5 + - - +
254B ILE* 1.3 77.5 - - - +
256B TYR* 1.3 64.2 + - - +
258B LEU* 3.3 9.2 + - - +
259B GLU* 3.1 29.1 + - - +
396B LEU* 4.5 1.3 - - + -
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Residues in contact with TYR 256 (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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73B LEU* 3.6 22.4 - - + -
80B ILE* 4.0 17.1 - - + +
240B LEU* 3.8 29.8 - - + -
248B LEU* 3.6 32.1 - - + -
252B GLU* 2.9 40.8 + - + -
253B ALA* 3.1 5.1 + - - +
255B ALA* 1.3 75.8 - - - +
257B LEU* 1.3 63.0 + - + +
259B GLU* 3.0 16.6 + - - +
260B ILE* 3.5 7.6 + - - +
282B ILE* 5.4 0.4 - - - -
284B LEU* 4.0 28.4 - - + +
289B LEU* 3.6 39.9 - - + +
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Residues in contact with LEU 257 (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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240B LEU* 5.2 0.2 - - + -
253B ALA 2.9 13.0 + - - +
254B ILE 3.8 3.4 - - - +
256B TYR* 1.3 76.9 - - + +
258B LEU* 1.3 61.7 + - - +
260B ILE* 3.2 18.6 + - + +
261B LEU* 3.2 28.5 + - - +
277B LEU* 3.8 23.3 - - + -
282B ILE* 4.3 10.3 - - + -
331B VAL* 3.7 24.9 - - + -
334B THR* 3.8 16.6 - - + -
335B LEU* 3.6 26.7 - - + -
338B LEU* 3.6 30.7 - - + -
392B LEU* 4.7 7.6 - - + -
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Residues in contact with LEU 258 (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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74B GLY* 4.3 9.4 - - - -
254B ILE* 2.8 27.0 + - + +
255B ALA 3.5 6.1 - - - +
257B LEU* 1.3 72.4 - - - +
259B GLU* 1.3 66.7 + - - +
260B ILE 3.3 0.2 - - - -
261B LEU* 3.7 6.4 + - + +
262B PRO* 3.4 18.4 - - - +
389B SER* 3.6 30.8 + - - +
392B LEU* 4.1 21.7 - - + +
393B THR* 3.5 28.5 - - + +
396B LEU* 3.5 31.9 - - + -
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Residues in contact with GLU 259 (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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72B MET 4.8 0.9 - - - +
73B LEU* 3.6 19.7 - - + +
74B GLY* 3.0 28.2 + - - -
75B GLY 4.1 4.2 + - - -
209B SER* 4.4 14.0 + - - -
255B ALA 3.1 14.3 - - - +
256B TYR 3.0 9.3 + - - +
258B LEU* 1.3 80.3 - - - +
260B ILE* 1.3 61.3 + - - +
262B PRO* 3.8 9.5 - - - +
289B LEU* 3.7 32.9 - - + +
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Residues in contact with ILE 260 (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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209B SER* 5.2 2.9 - - - +
256B TYR 4.1 6.5 - - - +
257B LEU* 3.5 34.1 - - + +
259B GLU* 1.3 79.6 - - - +
261B LEU* 1.3 68.6 + - + +
262B PRO* 3.4 3.1 - - - -
263B ALA* 3.0 22.7 + - + +
264B LEU* 3.4 22.5 + - + +
277B LEU* 4.0 18.4 - - + -
282B ILE* 4.1 14.8 - - + -
289B LEU* 4.0 24.7 - - + +
290B LYS* 4.4 7.0 - - - -
291B LEU* 3.9 29.8 - - + +
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Residues in contact with LEU 261 (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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257B LEU 3.2 19.8 + - - +
258B LEU* 4.1 6.3 - - - +
260B ILE* 1.3 78.8 - - + +
262B PRO* 1.3 68.1 - - + +
263B ALA 3.2 0.3 + - - -
264B LEU* 3.3 29.2 + - + +
265B SER* 3.0 25.2 + - - -
331B VAL* 4.1 17.9 - - + -
385B ALA* 4.1 18.2 - - + +
388B MET* 4.7 7.9 - - + -
389B SER* 4.0 35.0 - - - +
392B LEU* 3.8 28.0 - - + -
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Residues in contact with PRO 262 (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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207B HIS* 4.0 16.2 + - + +
209B SER* 5.8 0.4 - - - +
258B LEU 3.4 16.6 - - - +
259B GLU* 3.8 8.7 - - - +
260B ILE 3.5 3.6 - - - -
261B LEU* 1.3 91.6 - - + +
263B ALA* 1.3 54.8 + - - +
265B SER* 3.6 9.3 + - - -
266B TYR* 3.2 25.6 + - - +
389B SER* 5.2 4.3 - - - +
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Residues in contact with ALA 263 (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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207B HIS* 4.1 17.8 - - - +
209B SER* 4.2 11.0 - - - -
210B ILE* 3.9 20.8 - - + +
259B GLU 5.2 0.4 + - - -
260B ILE 3.0 14.3 + - - +
262B PRO* 1.3 75.5 - - - +
264B LEU* 1.3 65.5 + - - +
266B TYR* 3.3 5.1 + - - +
267B LEU* 3.2 27.5 + - - +
291B LEU* 3.9 20.0 - - + -
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Residues in contact with LEU 264 (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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260B ILE* 3.8 19.3 - - + +
261B LEU* 3.3 29.8 + - + +
263B ALA* 1.3 75.5 - - - +
265B SER* 1.3 59.3 + - - +
267B LEU* 3.4 5.8 + - + +
268B HIS* 2.9 52.3 + - + -
274B TYR* 3.7 33.4 - - + -
277B LEU* 4.5 7.4 - - + -
291B LEU* 3.9 17.5 - - + -
327B ASP* 4.4 9.9 - - + +
330B THR* 5.7 0.2 - - - +
331B VAL* 3.7 19.7 - - + -
385B ALA* 4.4 3.1 - - + -
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Residues in contact with SER 265 (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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261B LEU 3.0 13.9 + - - -
262B PRO* 3.8 10.6 - - - +
263B ALA 3.3 0.4 - - - -
264B LEU* 1.3 76.3 - - - +
266B TYR* 1.3 56.2 + - - +
268B HIS* 3.5 8.7 + - - +
269B SER* 2.9 28.4 + - - -
385B ALA* 3.4 20.4 + - - +
386B GLU* 3.6 26.3 + - - +
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Residues in contact with TYR 266 (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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204B GLU 4.0 6.2 + - - -
205B VAL* 4.2 9.0 - - + -
206B VAL* 3.1 47.5 + - - +
207B HIS* 3.8 30.3 - + + -
210B ILE* 4.6 0.4 - - + -
262B PRO 3.2 14.1 + - - +
263B ALA 3.5 9.2 - - - +
264B LEU 3.2 0.2 - - - -
265B SER* 1.3 74.1 - - - +
267B LEU* 1.3 72.9 + - + +
269B SER* 2.5 30.2 + - - -
270B ILE* 3.1 41.0 + - + +
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Residues in contact with LEU 267 (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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205B VAL* 3.5 31.4 - - + -
210B ILE* 4.1 15.7 - - + -
263B ALA 3.2 15.5 + - - +
264B LEU* 3.4 11.9 + - + +
266B TYR* 1.3 81.9 - - + +
268B HIS* 1.3 64.0 + - + +
270B ILE* 3.0 16.6 + - + +
272B LEU* 2.9 45.7 + - + +
273B VAL 4.7 0.7 - - - -
274B TYR* 3.8 44.9 - - + +
291B LEU* 5.3 0.2 - - + -
294B LEU* 5.0 3.6 - - + -
297B VAL* 4.7 7.4 - - + -
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Residues in contact with HIS 268 (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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264B LEU* 2.9 39.6 + - + +
265B SER* 3.8 5.7 - - - +
267B LEU* 1.3 77.4 - - + +
269B SER* 1.3 60.7 + - - +
271B GLY* 3.2 13.2 + - - -
272B LEU 3.1 19.7 + - - +
273B VAL* 4.2 4.9 - - + +
300B ILE* 4.2 7.7 - - - +
324B VAL* 3.7 40.3 - - + +
327B ASP* 2.6 43.4 + - + +
328B ILE* 5.6 1.6 - - + -
385B ALA* 4.1 16.7 + - + +
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Residues in contact with SER 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B SER 2.9 13.6 + - - -
266B TYR* 2.5 32.3 + - - -
268B HIS* 1.3 76.1 - - - +
270B ILE* 1.3 62.9 + - - +
271B GLY 3.4 1.6 + - - -
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Residues in contact with ILE 270 (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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204B GLU 5.6 0.7 - - - +
205B VAL* 4.4 10.3 - - + -
266B TYR* 3.1 46.4 + - + +
267B LEU* 3.0 15.4 + - + +
269B SER* 1.3 88.4 - - - +
271B GLY* 1.3 58.9 + - - +
272B LEU* 3.5 28.4 + - + +
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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
------------------------------------------------------------
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