Contacts of the helix formed by residues 247 - 259 (chain B) in PDB entry 7CAL
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 TYR 247 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B TRP* 3.5 25.9 + + - -
79B PHE* 4.2 23.1 - + - -
83B PHE* 3.5 50.5 - + + -
210B HIS* 3.6 12.3 + + - -
214B CYS* 4.5 10.1 - - - -
244B TRP 4.5 4.7 - - - +
245B ASN 4.3 11.2 - - - -
246B ARG* 1.3 77.1 - - - +
248B VAL* 1.3 59.1 + - + +
249B THR* 3.1 4.0 - - - +
250B ALA* 3.0 20.5 + - + +
251B LEU* 3.5 39.6 + - + +
701B 3PE 5.1 3.1 - - - +
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Residues in contact with VAL 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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271A PRO* 5.0 10.3 - - + +
274A MET* 4.0 23.3 - - + +
275A LEU* 4.0 19.7 - - + -
278A ILE* 3.8 21.3 - - + -
246B ARG* 3.2 50.4 + - + +
247B TYR* 1.3 73.5 - - + +
249B THR* 1.3 57.9 + - - +
251B LEU* 3.4 7.6 + - + +
252B TYR* 2.8 28.1 + - - +
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Residues in contact with THR 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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271A PRO* 6.1 0.5 - - - +
274A MET* 3.8 20.7 - - + +
230B TRP* 4.0 2.4 - - + -
231B ILE* 4.0 24.0 - - + -
235B TYR* 4.3 13.8 - - + -
246B ARG 5.2 3.0 + - - -
247B TYR* 3.1 1.9 - - - -
248B VAL* 1.3 79.2 - - - +
250B ALA* 1.3 60.1 + - - +
252B TYR* 3.4 2.8 + - - +
253B TRP* 3.2 22.5 + - - +
266B PHE* 3.7 35.6 - - + -
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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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83B PHE* 4.1 16.2 - - + -
213B GLY* 3.3 35.5 - - - +
217B TYR* 4.7 7.4 - - + -
230B TRP* 3.8 21.2 - - + -
231B ILE* 5.8 0.4 - - + +
247B TYR* 3.0 13.6 + - + +
249B THR* 1.3 79.4 - - - +
251B LEU* 1.3 61.5 + - - +
253B TRP* 3.8 4.9 + - - +
254B SER* 3.5 13.7 + - - -
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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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278A ILE* 3.9 21.9 - - + +
209B ILE* 3.8 33.8 - - + +
210B HIS* 4.5 7.9 - - - +
213B GLY* 4.6 6.1 - - - -
247B TYR* 3.5 43.8 + - + +
248B VAL* 3.4 7.5 + - + +
249B THR 3.3 0.4 - - - -
250B ALA* 1.3 79.8 - - - +
252B TYR* 1.3 59.5 + - - +
253B TRP 3.2 0.4 - - - -
254B SER* 3.2 3.3 + - - +
255B ILE* 3.0 31.9 + - - +
701B 3PE 3.8 30.1 - - + -
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Residues in contact with TYR 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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267A HIS* 3.8 2.6 - - - +
268A ALA* 3.4 30.7 + - + -
274A MET* 4.0 33.9 - - + -
277A ASP* 3.8 32.6 + - + -
278A ILE* 3.9 5.1 - - + +
281A MET* 4.1 11.9 - - + -
248B VAL 2.8 18.5 + - - +
249B THR* 3.8 4.5 - - - +
250B ALA 3.4 0.2 - - - -
251B LEU* 1.3 76.7 - - - +
253B TRP* 1.3 56.3 + - - +
255B ILE* 3.5 6.8 - - + +
256B THR* 2.3 38.8 + - + -
263B TYR* 3.2 28.2 - + - -
265B ASP* 4.1 7.6 - - - -
266B PHE* 3.7 36.6 - + - -
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Residues in contact with TRP 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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212B ALA 3.6 5.2 - - - -
216B ASN* 3.3 43.7 - - + +
230B TRP* 3.8 31.0 - + + +
249B THR 3.2 7.8 + - - +
250B ALA 4.0 5.8 - - - +
251B LEU 3.2 0.2 - - - -
252B TYR* 1.3 82.2 - - - +
254B SER* 1.3 88.9 + - - +
256B THR* 3.3 9.6 + - - -
257B THR* 3.2 35.7 + - + +
266B PHE* 3.5 42.3 + - + -
267B HIS* 4.8 3.4 - - - +
276B PHE* 4.1 4.5 - + - -
277B ASP* 3.3 33.2 + - - -
280B PHE* 4.0 25.4 - + - -
263C TYR* 4.5 3.2 + + - -
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Residues in contact with SER 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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209B ILE* 3.8 26.7 - - - -
212B ALA* 3.1 27.5 + - - +
213B GLY* 3.2 9.2 + - - -
250B ALA 3.5 8.5 + - - -
251B LEU* 3.2 5.6 + - - -
253B TRP* 1.3 88.8 - - - +
255B ILE* 1.3 61.6 + - - +
257B THR* 3.5 4.0 + - - -
258B LEU* 3.1 32.2 + - - +
280B PHE* 4.4 6.7 - - - -
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Residues in contact with ILE 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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278A ILE* 3.9 22.7 - - + +
281A MET* 3.7 36.5 - - + +
282A MET* 3.8 18.2 - - + -
285A LEU* 4.9 3.1 - - + -
209B ILE* 3.7 33.1 - - + +
251B LEU 3.0 20.6 + - - +
252B TYR* 3.5 14.6 - - - +
254B SER* 1.3 76.7 - - - +
256B THR* 1.3 61.6 + - - +
258B LEU* 4.6 2.9 - - + -
259B THR* 2.8 44.7 + - + +
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Residues in contact with THR 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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281A MET* 3.9 13.7 - - - +
252B TYR* 2.3 35.3 + - + -
253B TRP* 3.3 8.0 + - - -
254B SER 3.2 1.0 - - - -
255B ILE* 1.3 79.2 - - - +
257B THR* 1.3 61.0 + - + +
259B THR* 4.3 1.8 - - - -
260B THR* 3.8 0.2 - - - -
261B THR* 2.9 29.3 + - - -
262B GLY* 3.2 27.7 + - - +
263B TYR* 3.6 35.2 - - + +
265B ASP* 5.7 0.9 - - - +
263C TYR* 5.9 1.3 - - + -
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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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253B TRP* 3.2 35.1 + - + +
254B SER 3.7 1.0 + - - -
255B ILE 3.4 0.2 - - - -
256B THR* 1.3 80.4 - - - +
258B LEU* 1.3 64.4 + - - +
259B THR 3.4 0.7 - - - -
260B THR* 3.2 20.4 + - - +
280B PHE* 3.2 29.6 - - - -
281B MET* 5.0 8.2 - - - +
284B ASN* 3.7 8.8 + - - +
261C THR* 4.3 12.1 + - - -
263C TYR* 3.2 32.5 - - + +
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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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285A LEU* 3.8 27.4 - - + -
205B THR* 4.8 4.5 - - + +
208B ALA* 4.0 16.4 - - + +
209B ILE* 3.9 30.1 - - + -
254B SER 3.1 14.7 + - - +
255B ILE* 4.5 2.7 - - + +
257B THR* 1.3 80.4 + - - +
259B THR* 1.3 62.7 + - + +
260B THR* 3.2 3.9 + - - +
280B PHE* 4.2 11.0 - - + -
284B ASN* 3.7 30.7 - - - +
287B LEU* 3.9 25.1 - - + -
288B THR* 3.6 22.2 - - + +
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Residues in contact with THR 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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260A THR* 3.6 20.5 - - - +
281A MET* 3.4 29.1 - - - +
284A ASN* 6.3 0.9 - - - -
285A LEU* 3.8 26.0 - - + -
255B ILE* 2.8 36.0 + - + +
256B THR 3.9 0.2 + - - -
258B LEU* 1.3 74.2 - - - +
260B THR* 1.3 72.4 + - - +
261B THR* 2.8 22.6 + - - -
288B THR* 5.4 1.6 - - - -
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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