Contacts of the helix formed by residues 248 - 269 (chain B) in PDB entry 3ZVU
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 HIS 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B GLU* 6.0 2.9 - - + -
202B MET 3.8 22.2 - - - +
203B GLU* 4.0 13.9 - - + +
247B GLY* 1.3 72.7 - - - -
249B LYS* 1.3 91.4 + - + +
250B VAL 3.4 3.3 + - - -
251B ALA* 3.5 4.3 + - - +
252B ASP* 3.0 56.2 + - - +
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Residues in contact with LYS 249 (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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247B GLY 3.6 1.4 - - - -
248B HIS* 1.3 106.6 - - + +
250B VAL* 1.3 58.0 + - - +
252B ASP* 3.9 4.4 - - - +
253B TYR* 3.0 27.0 + - - +
320B VAL* 3.7 27.8 - - + +
321B ALA* 3.9 20.2 - - + -
325B VAL* 4.3 2.6 - - + +
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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 HIS 3.4 0.4 - - - -
249B LYS* 1.3 75.6 - - - +
251B ALA* 1.3 62.3 + - - +
253B TYR* 3.2 5.3 + - - +
254B CYS* 2.9 29.0 + - - -
301B ILE* 3.7 41.1 - - + -
320B VAL* 5.0 0.9 - - + -
321B ALA* 4.2 7.4 - - + -
322B SER 5.6 0.2 - - - +
325B VAL* 3.6 36.2 - - + +
326B GLY 3.9 10.8 - - - +
327B SER* 3.8 12.6 - - - -
400B ILE* 3.8 24.9 - - + +
401B GLY* 4.7 0.9 - - - -
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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
----------------------------------------------------------
203B GLU 3.4 25.6 - - - +
205B ALA* 3.8 11.5 - - + +
242B TYR* 3.6 18.2 - - + +
244B GLY* 3.7 5.8 - - - +
248B HIS 3.5 5.7 + - - +
250B VAL* 1.3 79.9 - - - +
252B ASP* 1.3 56.2 - - - +
254B CYS* 3.3 3.7 + - - +
255B ARG* 2.9 26.9 + - - +
326B GLY 4.6 1.0 + - - -
327B SER* 3.5 23.6 - - - +
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Residues in contact with ASP 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLU 5.6 0.9 - - - +
204B ASP 4.9 2.4 - - - +
205B ALA* 3.9 7.3 - - - +
248B HIS* 3.0 45.2 + - - +
249B LYS* 3.9 5.8 - - - +
251B ALA* 1.3 75.0 - - - +
253B TYR* 1.3 58.1 + - - +
255B ARG* 3.2 39.6 + - - +
256B ASP* 3.0 36.3 + - - +
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Residues in contact with TYR 253 (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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249B LYS 3.0 19.5 + - - +
250B VAL* 3.2 6.2 + - - +
252B ASP* 1.3 72.9 - - - +
254B CYS* 1.3 66.0 + - - +
256B ASP* 3.3 6.5 + - + -
257B ARG* 2.9 53.8 + - + +
297B VAL* 4.1 11.2 - - + -
300B GLU* 2.4 46.0 + - + +
301B ILE* 3.5 29.2 - - + -
307B ARG* 3.7 21.4 - - + +
308B ALA 6.2 0.2 - - - -
320B VAL* 3.7 30.3 - - + -
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Residues in contact with CYS 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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242B TYR* 3.5 36.6 + - + -
250B VAL* 2.9 20.3 + - - +
251B ALA* 3.3 9.9 - - - +
253B TYR* 1.3 75.7 - - - +
255B ARG* 1.3 65.8 + - - +
258B LEU* 3.1 36.2 + - + +
259B HIS* 4.7 0.5 + - - -
297B VAL* 4.3 11.9 - - - -
301B ILE* 5.0 0.2 - - - -
327B SER* 4.8 3.6 - - - -
329B ALA* 5.0 0.2 - - - -
400B ILE* 4.0 33.7 - - - -
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Residues in contact with ARG 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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204B ASP 5.4 1.0 + - - -
205B ALA* 4.0 19.5 - - + +
206B PHE* 3.4 26.7 - - - +
207B ALA* 3.8 6.6 - - + +
242B TYR* 3.6 12.3 - - + -
251B ALA 2.9 14.1 + - - +
252B ASP* 3.4 43.8 + - - +
253B TYR 3.2 0.4 - - - -
254B CYS* 1.3 77.6 - - - +
256B ASP* 1.3 80.1 + - - +
259B HIS* 3.3 19.1 + - - -
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Residues in contact with ASP 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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252B ASP* 3.0 18.3 + - - +
253B TYR* 4.0 7.1 - - + +
255B ARG* 1.3 102.2 + - - +
257B ARG* 1.3 57.6 + - + +
259B HIS* 3.9 2.3 - - - -
260B PHE* 3.4 24.6 - - - -
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Residues in contact with ARG 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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253B TYR* 2.9 43.2 + - + +
254B CYS 3.3 0.6 + - - -
256B ASP* 1.3 76.6 - - + +
258B LEU* 1.3 68.7 + - - +
259B HIS 3.3 2.0 - - - -
260B PHE* 2.9 36.7 + - - +
261B ALA* 3.0 25.6 + - - +
264B GLU* 3.0 42.0 + - - -
296B THR* 4.7 2.6 - - - +
297B VAL* 4.6 5.6 - - + -
300B GLU* 2.8 44.3 + - - +
307B ARG* 5.9 1.0 - - - +
315B LYS* 5.9 5.4 - - - +
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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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238B PHE* 3.8 25.1 - - + -
242B TYR* 3.9 23.6 - - + +
254B CYS* 3.1 30.8 + - - +
257B ARG* 1.3 78.4 - - - +
259B HIS* 1.3 57.4 + - - +
261B ALA* 3.2 2.1 + - - +
262B LEU* 2.9 25.9 + - + +
290B PHE* 5.5 1.1 - - + -
293B CYS* 3.9 13.9 - - - -
294B PHE* 4.1 24.7 - - + -
297B VAL* 4.1 27.4 - - + -
329B ALA* 4.6 3.6 - - + -
331B VAL* 4.1 9.6 - - + -
400B ILE* 5.6 1.8 - - + -
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Residues in contact with HIS 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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207B ALA* 4.3 8.6 - - + +
209B SER* 4.1 14.4 + - - -
212B PHE* 3.3 44.3 - + + -
213B LEU* 4.7 0.2 - - - +
238B PHE* 3.5 51.0 - + + -
254B CYS 4.7 0.8 + - - -
255B ARG 3.3 26.6 + - - -
256B ASP* 3.9 13.2 - - - -
258B LEU* 1.3 80.2 + - - +
260B PHE* 1.3 77.8 + + - +
262B LEU* 3.3 3.9 + - - +
263B ALA 2.9 24.3 + - - -
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Residues in contact with PHE 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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212B PHE* 3.7 26.5 - + - -
256B ASP 3.4 23.8 - - - -
257B ARG* 2.9 25.1 + - - +
259B HIS* 1.3 104.4 - + - +
261B ALA* 1.3 56.6 + - - +
263B ALA* 3.3 4.4 + - + +
264B GLU* 3.0 34.9 + - - +
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Residues in contact with ALA 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 ARG* 3.0 33.0 + - - +
258B LEU 3.6 7.0 - - - +
260B PHE* 1.3 75.9 - - - +
262B LEU* 1.3 63.1 + - - +
264B GLU* 3.4 6.0 + - - +
265B GLU* 3.0 22.9 + - - +
268B ARG* 5.0 1.4 + - - -
293B CYS* 4.2 12.5 - - - +
296B THR* 4.8 9.2 - - + -
297B VAL* 3.9 24.9 - - + -
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Residues in contact with LEU 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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213B LEU* 3.9 14.6 - - + -
238B PHE* 3.9 12.6 - - + -
258B LEU 2.9 14.0 + - - +
259B HIS* 3.4 8.7 - - - +
260B PHE 3.2 0.2 - - - -
261B ALA* 1.3 77.2 - - - +
263B ALA* 1.3 63.2 + - - +
265B GLU* 3.1 3.0 + - - -
266B ILE* 3.0 31.1 + - + +
286B TRP* 5.2 0.7 - - + -
289B VAL* 3.8 26.2 - - + -
290B PHE* 3.8 30.5 - - + -
293B CYS* 3.7 16.9 - - + -
333B LEU* 3.6 33.4 - - + -
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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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212B PHE* 3.9 12.3 - - + +
213B LEU* 3.6 26.4 - - + +
259B HIS 2.9 15.2 + - - +
260B PHE* 3.3 5.8 + - + +
262B LEU* 1.3 74.1 - - - +
264B GLU* 1.3 64.2 + - + +
266B ILE* 3.2 6.0 + - - +
267B GLU* 2.9 24.8 + - - +
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Residues in contact with GLU 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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257B ARG* 3.0 41.9 + - - -
260B PHE* 3.0 15.5 + - - +
261B ALA* 3.7 7.8 - - - +
263B ALA* 1.3 75.9 - - + +
265B GLU* 1.3 56.6 + - - +
267B GLU* 3.4 7.1 + - - +
268B ARG* 2.8 54.9 + - - +
315B LYS* 5.8 2.2 + - - -
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Residues in contact with GLU 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 ALA 3.0 14.4 + - - +
262B LEU* 3.1 9.1 + - - +
264B GLU* 1.3 74.8 - - - +
266B ILE* 1.3 64.8 + - - +
268B ARG* 2.7 41.0 + - - +
269B ILE* 3.2 42.4 + - - +
288B LYS 5.0 0.3 - - - +
289B VAL* 3.6 38.4 - - + +
292B SER* 3.5 27.9 + - - -
293B CYS* 4.7 4.5 - - + +
296B THR* 5.3 1.4 + - - -
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Residues in contact with ILE 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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213B LEU* 4.3 14.8 - - + -
214B LYS 4.2 7.4 - - - +
215B LEU* 4.0 24.0 - - + -
216B PRO* 3.9 32.7 - - + +
219B MET* 4.5 8.1 - - - -
262B LEU* 3.0 34.0 + - + +
263B ALA* 3.7 7.2 - - - +
265B GLU* 1.3 76.2 - - - +
267B GLU* 1.3 64.0 + - - +
268B ARG 3.5 0.2 + - - -
269B ILE* 3.5 23.8 + - - +
270B LYS* 4.9 0.7 - - - -
286B TRP* 4.3 12.6 - - + -
289B VAL* 4.0 16.8 - - + -
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Residues in contact with GLU 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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263B ALA 2.9 16.4 + - - +
264B GLU* 3.6 7.2 - - - +
266B ILE* 1.3 79.3 - - - +
268B ARG* 1.3 65.8 + - - +
269B ILE 3.3 0.7 + - - -
270B LYS* 3.5 30.8 + - - +
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Residues in contact with ARG 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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261B ALA 5.0 1.2 + - - -
264B GLU* 2.8 43.5 + - - +
265B GLU* 2.7 56.8 + - - +
267B GLU* 1.3 73.9 - - - +
269B ILE* 1.3 60.4 + - + +
270B LYS* 2.9 16.3 + - - +
296B THR* 5.3 8.3 + - - +
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Residues in contact with ILE 269 (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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216B PRO* 5.7 3.5 - - - +
219B MET* 4.1 21.2 - - + +
265B GLU* 3.2 33.0 + - + +
266B ILE* 3.5 13.9 - - - +
267B GLU 3.3 0.2 - - - -
268B ARG* 1.3 75.3 - - + +
270B LYS* 1.3 65.0 + - - +
285B GLN* 4.2 16.8 - - + +
289B VAL* 3.7 26.9 - - + -
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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