Contacts of the helix formed by residues 248 - 266 (chain B) in PDB entry 1JPP
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 VAL 248 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B VAL* 4.5 31.2 - - + -
212B ARG* 5.3 0.7 - - + -
246B SER* 3.0 16.2 + - - +
247B PRO* 1.3 89.3 - - + +
249B ASP* 1.3 65.3 + - - +
250B SER* 3.4 23.1 - - - +
251B VAL* 3.5 18.2 - - + -
252B LEU* 3.0 24.9 + - - +
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Residues in contact with ASP 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 PRO 4.1 8.0 - - - +
248B VAL* 1.3 70.2 - - - +
250B SER* 1.3 58.5 + - - +
252B LEU* 3.0 6.2 + - - -
253B PHE* 2.8 71.7 + - + -
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Residues in contact with SER 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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212B ARG* 3.3 29.7 - - - +
248B VAL* 3.4 12.5 - - - +
249B ASP* 1.3 75.6 - - - +
251B VAL* 1.3 63.3 + - - +
253B PHE* 3.6 5.9 + - - +
254B TYR* 2.6 45.3 + - - -
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL* 4.9 2.0 - - + +
211B ALA* 4.6 12.1 - - + -
212B ARG* 4.0 29.8 - - + +
215B ALA* 4.6 15.8 - - + +
243B MET* 4.7 23.2 - - + +
246B SER* 4.0 17.7 - - - +
248B VAL* 3.5 30.9 + - + +
249B ASP 3.2 0.4 - - - -
250B SER* 1.3 75.1 - - - +
252B LEU* 1.3 62.5 + - - +
254B TYR* 3.5 6.7 + - - +
255B ALA* 3.3 23.2 + - - +
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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
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243B MET 4.1 5.8 - - - +
244B LEU* 3.5 39.0 - - + +
246B SER* 3.8 20.2 - - - +
247B PRO 6.1 0.4 - - - -
248B VAL 3.0 17.7 + - - +
249B ASP* 3.0 6.8 + - - +
251B VAL* 1.3 75.5 - - - +
253B PHE* 1.3 69.2 + - + +
254B TYR 3.0 9.4 + - - -
255B ALA* 3.5 2.6 + - - +
256B ILE* 3.5 22.2 + - - +
285B LEU* 4.2 10.5 - - + -
288B LYS* 4.0 28.5 - - - +
293B PHE* 4.0 23.1 - - + -
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Residues in contact with PHE 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 ASP* 2.8 61.9 + - + +
250B SER* 3.9 5.2 - - - +
252B LEU* 1.3 80.1 - - + +
254B TYR* 1.3 56.0 + - - +
256B ILE* 3.7 7.0 - - - +
257B THR* 3.3 24.9 + - - +
288B LYS* 5.9 4.3 - - + -
290B ASN* 4.6 21.3 - - + -
293B PHE* 3.1 52.9 - + + -
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Residues in contact with TYR 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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176B HIS* 5.5 5.4 + - - -
212B ARG* 4.7 19.0 + - + -
215B ALA* 4.4 15.7 - - + -
216B GLY* 3.8 23.7 - - - -
219B HIS* 4.0 34.0 - + + -
220B ASN* 5.7 1.6 - - - -
250B SER* 2.6 41.4 + - - +
251B VAL* 3.7 7.0 - - - +
252B LEU 3.0 0.8 + - - -
253B PHE* 1.3 76.5 - - + +
255B ALA* 1.3 67.7 + - - +
256B ILE 3.3 1.3 - - - -
257B THR* 2.6 24.4 + - - -
258B THR* 3.3 10.2 + - - -
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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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215B ALA* 5.3 5.3 - - + +
240B LEU* 4.1 29.8 - - + +
243B MET* 4.1 15.7 - - + +
244B LEU* 4.7 7.4 - - + -
251B VAL* 3.3 14.1 + - + +
252B LEU 4.1 2.7 - - - +
254B TYR* 1.3 78.4 - - - +
256B ILE* 1.3 62.6 + - - +
258B THR* 3.2 10.3 + - - -
259B LEU* 3.1 27.7 + - - +
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Residues in contact with ILE 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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244B LEU* 4.0 25.2 - - + +
252B LEU 3.5 11.4 + - - +
253B PHE* 3.7 20.6 - - - +
255B ALA* 1.3 79.0 - - - +
257B THR* 1.3 69.0 + - + +
259B LEU* 3.4 9.9 + - + +
260B HIS* 3.0 27.1 + - - +
282B MET* 4.5 24.0 - - + -
285B LEU* 5.3 2.5 - - + -
293B PHE* 4.3 14.6 - - + -
296B ILE* 4.0 20.9 - - + +
297B THR* 4.3 24.5 - - + +
300B CYS* 4.6 6.7 - - - -
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Residues in contact with THR 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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219B HIS* 3.1 25.7 - - - +
253B PHE 3.3 19.3 + - - +
254B TYR 2.6 19.1 + - - -
256B ILE* 1.3 85.3 - - + +
258B THR* 1.3 62.4 + - - +
260B HIS* 3.6 8.1 + - - +
261B ASN* 3.1 29.9 + - - +
296B ILE* 3.8 24.0 - - + -
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Residues in contact with THR 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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215B ALA 4.8 1.9 + - - -
218B LEU* 4.3 13.2 - - + +
219B HIS* 3.5 22.0 + - - +
222B SER* 4.2 21.9 - - - -
231B ILE* 4.8 7.0 - - + -
240B LEU* 4.2 25.5 - - + +
254B TYR 3.3 12.2 + - - -
255B ALA* 3.2 10.6 + - - -
257B THR* 1.3 77.5 + - - +
259B LEU* 1.3 63.1 + - - +
261B ASN* 3.4 7.4 + - - +
262B LEU* 3.1 27.6 + - + +
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Residues in contact with LEU 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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237B ILE* 4.3 9.9 - - + -
240B LEU* 4.1 32.5 - - + -
241B VAL* 4.6 9.2 - - + +
244B LEU* 4.0 30.3 - - + -
255B ALA 3.1 15.7 + - - +
256B ILE* 3.6 14.6 - - + +
258B THR* 1.3 74.5 - - - +
260B HIS* 1.3 59.0 + - - +
262B LEU* 3.1 10.5 + - + +
263B LEU* 2.9 38.7 + - + +
273B VAL* 4.0 26.9 - - + -
282B MET* 4.8 11.9 - - + -
300B CYS* 5.2 4.7 - - - -
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Residues in contact with HIS 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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256B ILE 3.0 17.4 + - - +
257B THR* 3.7 10.3 - - - +
259B LEU* 1.3 76.1 - - - +
261B ASN* 1.3 67.4 + - - +
263B LEU* 3.5 3.5 + - - +
264B LEU* 3.2 56.3 + - + +
296B ILE* 3.8 25.4 - - + -
299B ASP* 2.9 30.8 + - - +
300B CYS* 3.7 28.0 - - - -
303B ILE* 5.2 2.6 - - + +
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Residues in contact with ASN 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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222B SER* 3.4 39.4 + - - +
223B HIS* 4.0 16.8 + - - +
228B LEU* 4.5 6.6 - - + +
257B THR* 3.1 18.8 + - - +
258B THR 3.5 8.7 - - - +
259B LEU 3.2 0.4 - - - -
260B HIS* 1.3 84.6 + - - +
262B LEU* 1.3 61.3 + - - +
264B LEU* 3.2 11.3 + - - +
265B HIS* 3.1 31.2 + - - +
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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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228B LEU* 4.3 32.3 - - + +
231B ILE* 4.5 14.1 - - + -
232B PHE* 5.0 4.7 - - + +
237B ILE* 3.8 25.1 - - + -
240B LEU* 3.7 31.0 - - + -
258B THR* 3.1 19.9 + - + +
259B LEU* 3.1 11.0 + - + +
261B ASN* 1.3 76.0 - - - +
263B LEU* 1.3 62.6 + - + +
266B GLN* 3.3 44.6 + - + +
269B ALA* 3.3 20.2 - - + +
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Residues in contact with LEU 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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259B LEU* 2.9 20.9 + - + +
260B HIS 3.8 3.8 - - - +
262B LEU* 1.3 76.6 - - - +
264B LEU* 1.3 62.3 + - - +
266B GLN 5.0 3.5 + - - +
269B ALA* 4.2 14.7 - - + +
270B LYS* 4.5 14.0 - - + +
273B VAL* 3.7 30.7 - - + -
282B MET* 5.6 2.0 - - + -
300B CYS* 3.7 45.8 - - + +
303B ILE* 4.4 25.5 - - + +
304B LEU* 4.1 26.0 - - + -
672B GOL 5.5 1.7 + - - -
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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 HIS* 3.2 43.7 - - + +
261B ASN* 3.2 7.4 + - - +
263B LEU* 1.3 81.4 - - - +
265B HIS* 1.3 85.4 + - + +
266B GLN 3.9 0.4 + - - -
299B ASP* 5.3 1.3 - - - +
303B ILE* 3.8 22.7 - - + -
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Residues in contact with HIS 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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228B LEU* 4.0 21.9 - - + +
261B ASN* 3.1 14.6 + - - +
264B LEU* 1.3 104.8 - - + +
266B GLN* 1.3 60.7 + - - +
267B GLU 4.3 0.9 + - - -
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Residues in contact with GLN 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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225B ARG 4.9 1.4 - - - +
228B LEU* 3.9 9.1 - - + +
229B LEU* 3.5 48.9 + - - +
232B PHE* 4.0 32.7 - - + -
261B ASN 4.7 0.2 + - - -
262B LEU* 3.3 34.0 + - + +
263B LEU 5.0 2.6 - - - +
264B LEU 3.9 1.6 + - - -
265B HIS* 1.3 78.1 - - - +
267B GLU* 1.3 84.8 + - - +
268B GLY 3.0 8.1 + - - -
269B ALA* 3.6 9.4 + - + +
672B GOL 4.1 9.1 + - - -
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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