Contacts of the helix formed by residues 239 - 254 (chain B) in PDB entry 6F3T
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 LEU 239 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B LEU* 4.3 17.7 - - + -
225B ILE* 4.2 12.3 - - + -
235B GLU 5.5 0.7 - - - +
236B LEU* 3.1 34.1 + - + +
237B SER 3.0 1.0 - - - -
238B GLN* 1.3 79.7 - - - +
240B PHE* 1.3 64.6 + - - +
241B TYR 3.4 0.2 - - - -
242B PRO* 3.4 7.3 - - + +
243B LEU* 3.1 47.3 + - + +
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Residues in contact with PHE 240 (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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218B TYR* 3.1 32.9 + + - +
221B LEU* 5.1 3.6 - - + -
222B LYS* 3.8 41.5 - - + -
225B ILE* 3.8 32.5 - - + -
226B GLU* 4.6 10.3 - - + -
233B ARG* 6.3 0.2 - - + -
237B SER* 3.2 41.7 + - - +
239B LEU* 1.3 77.8 - - + +
241B TYR* 1.3 65.0 + - - +
243B LEU* 6.4 0.2 - - + -
244B PHE* 2.9 21.8 + - - +
270B ASP* 5.3 10.3 - - + +
271B GLN* 3.3 13.7 - - - +
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Residues in contact with TYR 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B SER 4.6 0.8 + - - -
238B GLN 4.3 1.3 + - - +
240B PHE* 1.3 81.2 - - - +
242B PRO* 1.3 77.5 - - + +
244B PHE* 3.6 1.4 - + - +
245B VAL* 3.1 51.3 + - + +
271B GLN* 3.2 15.9 + - + +
275B TYR* 3.4 69.5 - + + +
278B ASP* 2.7 35.0 + - + +
279B LEU* 5.3 4.7 - - + -
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Residues in contact with PRO 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLN 3.1 23.8 - - - +
239B LEU* 3.4 14.4 - - + +
241B TYR* 1.3 103.7 - - + +
243B LEU* 1.3 57.4 + - + +
245B VAL* 3.4 4.0 + - + +
246B HIS* 3.0 47.3 + - + +
275B TYR* 5.8 0.2 - - - +
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B TYR* 4.2 15.0 - - + -
221B LEU* 3.4 33.4 - - + -
239B LEU* 3.1 38.5 + - + +
240B PHE* 4.1 1.6 - - - +
242B PRO* 1.3 74.6 - - + +
244B PHE* 1.3 66.4 + - - +
246B HIS* 4.6 6.1 - - + +
247B MET* 2.9 44.2 + - + +
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Residues in contact with PHE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B TYR* 3.8 8.9 - - - +
240B PHE 2.9 20.7 + - - +
241B TYR* 3.6 3.1 - + - +
243B LEU* 1.3 76.8 - - - +
245B VAL* 1.3 66.0 + - + +
248B TYR* 2.9 33.9 + - + +
263B PHE* 3.4 37.0 - + - -
264B PHE* 3.5 32.5 - + - -
267B PHE* 3.7 29.6 - - + -
268B HIS* 3.8 16.6 - - + -
271B GLN* 3.8 16.8 - - + +
279B LEU* 3.5 30.3 - - + -
282B LEU* 4.5 5.6 - - + -
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Residues in contact with VAL 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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241B TYR* 3.1 49.2 + - + +
242B PRO* 4.0 4.3 - - + +
244B PHE* 1.3 80.9 - - + +
246B HIS* 1.3 63.6 + - + +
248B TYR* 3.8 2.6 - - - +
249B LEU* 2.8 57.5 + - + +
282B LEU* 3.9 28.3 - - + -
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Residues in contact with HIS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PRO* 3.0 34.2 + - + +
243B LEU* 4.2 6.8 - - + +
245B VAL* 1.3 79.1 - - + +
247B MET* 1.3 60.0 + - + +
249B LEU* 3.9 10.4 - - + +
250B GLU* 3.0 31.5 + - - +
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Residues in contact with MET 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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214B TYR* 3.4 60.2 - - + +
217B TYR* 4.3 14.6 - - + -
218B TYR* 4.0 22.0 - - + -
243B LEU* 2.9 36.4 + - + +
246B HIS* 1.3 75.3 - - + +
248B TYR* 1.3 65.9 + - - +
250B GLU* 3.4 4.9 + - - +
251B LEU* 3.2 28.9 + - - +
263B PHE* 3.8 14.8 - - + -
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Residues in contact with TYR 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 PHE* 2.9 25.3 + - + +
245B VAL* 3.8 3.4 - - - +
247B MET* 1.3 77.7 - - - +
249B LEU* 1.3 67.5 + - + +
251B LEU* 3.3 6.4 + - - +
252B VAL* 3.1 32.3 + - + +
260B ALA* 3.3 40.6 - - + +
261B LYS* 4.5 1.9 - - - -
263B PHE* 3.9 14.9 - + + -
264B PHE* 3.8 25.3 - + + -
282B LEU* 3.1 47.8 + - + -
283B SER* 4.6 2.1 + - - -
285B LEU* 2.4 29.5 + - + -
286B THR* 4.3 8.1 - - - +
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Residues in contact with LEU 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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245B VAL* 2.8 42.9 + - + +
246B HIS* 4.1 9.9 - - + +
248B TYR* 1.3 79.9 - - + +
250B GLU* 1.3 56.8 + - - +
252B VAL* 3.7 9.8 - - + +
253B TYR* 2.8 32.6 + - - +
282B LEU* 3.8 24.9 - - + -
285B LEU* 4.6 15.3 - - + -
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Residues in contact with GLU 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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209B GLY 6.0 0.2 + - - -
214B TYR* 3.2 29.1 + - + +
246B HIS* 3.0 20.8 + - - +
247B MET* 3.7 7.5 - - - +
248B TYR 3.2 0.4 - - - -
249B LEU* 1.3 75.2 - - - +
251B LEU* 1.3 67.3 + - + +
253B TYR* 4.0 3.1 - - - -
254B ASN* 2.9 48.3 + - - +
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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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211B PRO* 4.1 18.8 - - + -
214B TYR* 3.5 46.0 - - + -
247B MET 3.2 18.1 + - - +
248B TYR* 3.3 2.4 + - - +
250B GLU* 1.3 80.2 - - + +
252B VAL* 1.3 60.7 + - - +
254B ASN* 3.6 0.9 + - - +
255B GLN 3.1 3.6 + - - -
256B HIS* 2.8 43.0 + - + +
259B GLU* 4.2 17.7 - - + +
260B ALA* 3.7 28.0 - - + -
263B PHE* 4.1 20.0 - - + -
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Residues in contact with VAL 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 TYR* 3.1 39.2 + - + +
249B LEU* 3.7 11.9 - - + +
251B LEU* 1.3 77.4 - - - +
253B TYR* 1.3 65.5 + - - +
255B GLN* 2.9 14.7 + - - +
256B HIS 5.0 1.6 - - - +
257B GLU* 5.8 0.9 - - - +
260B ALA* 3.8 17.0 - - + -
285B LEU* 3.8 14.1 - - + +
286B THR* 3.9 16.9 - - - +
287B LYS 3.6 27.8 - - - +
288B LYS 3.9 9.4 + - - +
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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 LEU 2.8 21.9 + - - +
250B GLU* 4.1 5.2 - - - +
252B VAL* 1.3 76.0 - - - +
254B ASN* 1.3 69.6 + - - +
255B GLN* 3.4 10.9 + - - +
287B LYS 6.1 0.4 - - - -
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Residues in contact with ASN 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 GLU* 2.9 44.8 + - - +
251B LEU* 6.1 0.2 - - - +
253B TYR* 1.3 87.0 - - - +
255B GLN* 1.3 70.7 + - - +
256B HIS* 3.3 30.8 + - + +
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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