Contacts of the helix formed by residues 242 - 256 (chain B) in PDB entry 1PXV
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 TRP 242 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240B ASN* 3.0 32.7 + - + +
241B SER* 1.3 74.7 - - - +
243B ALA* 1.3 63.6 + - - +
244B ALA 3.2 3.6 - - - -
245B GLY 2.8 14.5 + - - -
246B PHE* 2.9 26.7 + + + -
263B ALA* 4.4 1.8 - - + -
264B HIS* 3.6 49.4 - + + -
267B MET* 3.4 28.3 - - + +
276B GLU* 5.1 2.5 - - - -
279B LEU* 2.8 44.7 + - + +
280B PRO* 3.5 30.0 - - + +
282B CYS 3.3 17.3 - - - -
284B THR* 5.2 0.2 - - - -
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Residues in contact with ALA 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B GLN* 3.5 18.4 - - - +
241B SER 3.3 3.8 + - - -
242B TRP* 1.3 74.0 - - - +
244B ALA* 1.3 56.5 + - - +
246B PHE* 3.3 6.7 + - - +
247B SER* 2.9 31.9 + - - -
340B HIS* 3.3 39.7 - - + +
341B ALA* 3.5 13.4 - - - +
361B PRO* 3.8 1.2 - - + +
98D GLY* 4.2 9.6 - - - -
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Residues in contact with ALA 244 (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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241B SER 4.9 0.8 + - - -
242B TRP 3.2 1.0 - - - -
243B ALA* 1.3 75.6 - - - +
245B GLY* 1.3 59.5 + - - +
248B MET* 2.8 41.2 + - + +
284B THR* 3.3 38.3 + - + +
289B MET* 3.9 11.4 - - + -
323B MET* 4.0 6.3 - - - -
341B ALA* 3.6 20.7 - - + +
97D ILE 4.7 3.6 + - - +
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Residues in contact with GLY 245 (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 TRP 2.8 8.4 + - - -
244B ALA* 1.3 75.1 - - - +
246B PHE* 1.3 64.9 + - - +
248B MET* 4.3 0.9 - - - +
249B ALA* 3.0 27.4 + - - +
263B ALA* 3.7 11.2 - - - -
266B ILE* 3.6 20.5 - - - +
267B MET* 4.0 20.5 - - - -
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Residues in contact with PHE 246 (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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235B GLU* 3.6 48.3 - - + +
236B GLN 3.5 30.3 - - - -
237B GLN* 3.6 25.4 - - + -
240B ASN* 3.6 24.2 - - - -
242B TRP* 2.9 34.0 + + + -
243B ALA 3.3 7.2 + - - +
245B GLY* 1.3 77.6 - - - +
247B SER* 1.3 55.7 + - - +
249B ALA* 3.8 1.9 - - - +
250B ALA* 3.0 23.4 + - - +
263B ALA* 3.5 15.8 - - + +
359B TRP* 3.6 14.5 - + + -
361B PRO* 3.6 16.8 - - + -
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Residues in contact with SER 247 (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 ALA 2.9 16.9 + - - -
246B PHE* 1.3 74.2 - - - +
248B MET* 1.4 64.5 + - - +
250B ALA* 3.3 1.9 + - - +
251B LEU* 3.0 30.1 + - - +
323B MET* 3.8 21.1 - - - -
341B ALA 3.3 2.4 + - - -
342B LEU* 3.2 37.8 - - - -
343B ALA* 3.6 9.0 + - - -
359B TRP* 4.4 4.0 - - - -
361B PRO* 3.6 5.4 - - - +
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Residues in contact with MET 248 (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 ALA* 2.8 38.7 + - + +
245B GLY 4.3 0.4 - - - +
247B SER* 1.4 72.5 - - - +
249B ALA* 1.3 57.9 + - - +
251B LEU* 3.3 6.1 + - - +
252B LEU* 2.9 39.5 + - + +
266B ILE* 3.9 30.3 - - + -
270B LEU* 5.0 1.8 - - + -
284B THR* 4.5 13.0 - - + -
289B MET* 4.0 12.8 - - - +
292B TYR* 4.0 17.0 - - + -
323B MET* 3.6 20.6 - - + -
393B TYR* 3.5 39.3 - - + -
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B GLU* 4.1 4.9 - - - +
245B GLY 3.0 20.0 + - - +
246B PHE 3.8 3.1 - - - +
248B MET* 1.3 75.5 - - - +
250B ALA* 1.3 58.2 + - - +
253B ASN* 2.9 36.9 + - - +
261B TYR* 3.7 12.0 - - - +
262B ASN* 3.7 37.9 - - - +
263B ALA 3.9 1.3 - - - +
266B ILE* 3.7 6.6 - - + +
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Residues in contact with ALA 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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231B PHE* 3.6 32.1 - - + -
232B LYS 4.7 11.0 + - - +
233B ILE* 5.9 0.9 - - - -
234B ARG 6.2 0.2 - - - +
246B PHE 3.0 17.1 + - - +
247B SER 3.9 3.4 - - - +
249B ALA* 1.3 76.8 - - - +
251B LEU* 1.3 60.6 + - - +
253B ASN* 3.8 7.2 - - - +
254B ALA* 3.1 23.6 + - - +
343B ALA* 5.1 0.2 - - + -
359B TRP* 3.8 15.5 - - + -
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Residues in contact with LEU 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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228B LEU* 4.1 9.0 - - + -
231B PHE* 4.4 3.8 - - + -
247B SER 3.0 22.4 + - - +
248B MET* 3.8 3.6 - - - +
250B ALA* 1.3 75.3 - - - +
252B LEU* 1.3 58.5 + - - +
254B ALA* 3.2 4.4 + - - +
255B THR* 2.9 34.6 + - - +
321B GLY* 4.0 7.4 - - - -
322B ILE 3.4 42.0 - - - +
323B MET* 3.6 15.9 - - + +
343B ALA* 3.9 14.1 - - + -
344B VAL 3.5 24.9 - - - +
393B TYR* 3.8 23.8 - - + -
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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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248B MET 2.9 23.2 + - - +
251B LEU* 1.3 72.7 - - - +
253B ASN* 1.3 60.8 + - - +
255B THR* 3.8 2.9 - - - -
256B LYS* 2.9 47.8 + - - +
261B TYR* 3.7 31.4 - - + -
292B TYR* 3.7 30.5 - - + -
293B GLY* 5.5 0.7 - - - -
296B GLN* 4.4 8.3 - - + -
298B ARG* 3.9 21.8 - - + +
393B TYR* 3.5 37.9 - - + +
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Residues in contact with ASN 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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230B ASN 4.6 3.8 - - - +
234B ARG* 3.7 24.8 - - - +
249B ALA* 2.9 25.7 + - - +
250B ALA* 3.8 7.4 - - - +
252B LEU* 1.3 76.6 - - - +
254B ALA* 1.3 57.6 + - - +
257B ASN* 3.0 8.1 + - - -
258B THR* 2.9 48.1 + - - +
259B ASP* 3.8 6.0 + - - +
260B THR 3.3 4.7 + - - -
261B TYR* 2.9 51.5 + - - +
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Residues in contact with ALA 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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228B LEU* 4.1 11.0 - - + -
229B LYS 3.3 18.2 - - - +
230B ASN* 3.5 18.8 + - - +
231B PHE* 3.7 34.3 - - + +
250B ALA 3.1 15.4 + - - +
251B LEU 3.5 7.9 - - - +
252B LEU 3.1 0.4 - - - -
253B ASN* 1.3 77.6 - - - +
255B THR* 1.3 62.9 + - - +
257B ASN 3.2 9.5 + - - -
319B ASN* 4.2 1.4 + - - +
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Residues in contact with THR 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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228B LEU* 4.3 10.5 - - + -
230B ASN* 5.7 0.3 + - - -
251B LEU 2.9 22.9 + - - +
252B LEU* 3.7 4.9 + - - -
254B ALA* 1.3 72.0 - - - +
256B LYS* 1.3 59.0 + - - +
257B ASN* 3.8 0.9 + - - +
298B ARG* 3.0 22.2 + - - -
319B ASN* 3.0 53.4 + - - +
321B GLY 3.9 8.7 - - - +
393B TYR* 2.6 34.7 + - - +
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Residues in contact with LYS 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 LEU* 2.9 24.1 + - - +
255B THR* 1.3 77.7 - - - +
257B ASN* 1.3 71.9 + - - +
258B THR* 3.4 13.4 + - + -
261B TYR* 3.1 32.0 + - + +
296B GLN* 2.8 31.6 + - - +
298B ARG* 3.5 32.1 - - - +
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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