Contacts of the helix formed by residues 247 - 259 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75C TRP* 3.5 26.2 + + - -
79C PHE* 4.2 21.5 - + + -
83C PHE* 3.5 49.6 - + + -
210C HIS* 3.6 12.3 + + - -
214C CYS* 4.5 10.5 - - - -
244C TRP 4.5 5.4 - - - +
245C ASN* 4.3 11.9 - - - -
246C ARG* 1.3 76.8 - - - +
248C VAL* 1.3 59.6 + - + +
249C THR* 3.1 4.5 - - - -
250C ALA* 3.0 21.5 + - + +
251C LEU* 3.5 40.6 + - + +
701C 3PE 5.2 2.9 - - - +
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Residues in contact with VAL 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B PRO* 5.1 9.9 - - + +
274B MET* 4.0 22.9 - - + +
275B LEU* 4.0 19.5 - - + -
278B ILE* 3.7 20.4 - - + -
246C ARG* 3.2 49.7 + - + +
247C TYR* 1.3 73.8 - - + +
249C THR* 1.3 57.3 + - - +
250C ALA 3.3 0.2 - - - -
251C LEU* 3.4 7.6 + - + +
252C TYR* 2.8 29.0 + - - +
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Residues in contact with THR 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B PRO* 6.1 0.3 - - - +
274B MET* 3.8 19.9 - - + +
230C TRP* 4.0 3.6 - - + -
231C ILE* 4.0 22.9 - - + -
235C TYR* 4.3 15.4 - - + -
246C ARG 5.2 2.6 + - - -
247C TYR* 3.1 2.2 - - - -
248C VAL* 1.3 78.5 - - - +
250C ALA* 1.3 60.4 + - - +
252C TYR* 3.8 3.1 - - - +
253C TRP* 3.2 22.0 + - - +
266C PHE* 3.7 34.9 - - + -
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Residues in contact with ALA 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C PHE* 4.1 16.4 - - + -
213C GLY* 3.3 35.4 - - - +
217C TYR* 4.7 7.2 - - + -
230C TRP* 3.8 20.8 - - + -
231C ILE* 5.8 0.6 - - + +
247C TYR* 3.0 12.7 + - + +
249C THR* 1.3 79.3 - - - +
251C LEU* 1.3 63.9 + - - +
253C TRP* 3.8 4.9 + - - +
254C SER* 3.5 14.0 + - - -
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Residues in contact with LEU 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B ILE* 3.9 22.4 - - + +
209C ILE* 3.8 32.5 - - + +
210C HIS* 4.5 8.5 - - - +
213C GLY* 4.6 5.8 - - - -
247C TYR* 3.5 42.4 + - + +
248C VAL* 3.4 7.0 + - - +
249C THR 3.3 0.2 - - - -
250C ALA* 1.3 81.2 - - - +
252C TYR* 1.3 58.9 + - - +
253C TRP 3.2 0.4 - - - -
254C SER* 3.2 3.3 + - - +
255C ILE* 3.0 32.1 + - - +
701C 3PE 3.9 32.1 - - + -
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Residues in contact with TYR 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B HIS* 3.8 3.1 - - - +
268B ALA* 3.4 29.3 + - + -
274B MET* 4.0 30.3 - - + -
277B ASP* 3.8 32.0 + - + -
278B ILE* 3.9 7.3 - - + +
281B MET* 4.1 12.3 - - + -
248C VAL 2.8 18.1 + - - +
249C THR* 3.4 5.4 + - - +
250C ALA 3.4 0.2 - - - -
251C LEU* 1.3 76.3 - - - +
253C TRP* 1.3 54.5 + - - +
255C ILE* 3.5 6.4 - - - +
256C THR* 2.3 39.3 + - + -
263C TYR* 3.2 28.3 - + - -
265C ASP* 3.9 7.4 + - - -
266C PHE* 3.7 35.2 - + - -
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Residues in contact with TRP 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C ALA 3.6 5.4 - - - -
213C GLY* 5.1 0.2 - - - -
216C ASN* 3.3 43.7 - - + +
230C TRP* 3.8 30.8 - + + +
249C THR 3.2 8.2 + - - +
250C ALA 4.0 6.5 - - - +
252C TYR* 1.3 81.9 - - - +
254C SER* 1.3 88.3 + - - +
256C THR* 3.3 8.9 + - - -
257C THR* 3.2 33.6 - - + +
266C PHE* 3.5 42.0 + - + -
267C HIS* 4.8 3.4 - - - +
276C PHE* 4.1 4.5 - + - -
277C ASP* 3.3 34.1 + - - -
280C PHE* 4.0 24.9 - + - -
263D TYR* 4.5 3.0 + - - -
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Residues in contact with SER 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C ILE* 3.8 26.5 - - - -
212C ALA* 3.1 27.0 + - - +
213C GLY* 3.2 9.2 + - - -
250C ALA 3.5 8.6 + - - -
251C LEU 3.2 6.0 + - - -
253C TRP* 1.3 90.1 - - - +
255C ILE* 1.3 60.8 + - - +
257C THR* 3.5 4.4 + - - -
258C LEU* 3.1 31.7 + - - +
280C PHE* 4.4 5.3 - - - -
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Residues in contact with ILE 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B ILE* 3.9 23.8 - - + +
281B MET* 3.7 37.5 - - + +
282B MET* 3.8 21.8 - - + -
285B LEU* 4.8 3.1 - - + -
209C ILE* 3.7 32.9 - - + +
251C LEU 3.0 19.7 + - - +
252C TYR* 3.5 9.4 - - - +
254C SER* 1.3 75.9 - - - +
256C THR* 1.3 61.6 + - - +
258C LEU* 4.6 2.9 - - + -
259C THR* 2.8 44.1 + - + +
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Residues in contact with THR 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B MET* 3.9 13.0 - - - +
252C TYR* 2.3 36.2 + - + -
253C TRP* 3.3 8.2 + - - -
254C SER 3.2 1.0 - - - -
255C ILE* 1.3 77.7 - - - +
257C THR* 1.3 61.2 + - + +
259C THR* 4.2 2.0 - - - -
261C THR* 2.9 29.6 + - - -
262C GLY* 3.2 27.3 + - - +
263C TYR* 3.6 34.5 - - + +
265C ASP* 5.7 1.3 - - - +
263D TYR* 5.9 1.3 - - + -
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Residues in contact with THR 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C TRP* 3.2 36.2 + - + +
254C SER 3.7 1.2 + - - -
256C THR* 1.3 80.5 - - - +
258C LEU* 1.3 64.5 + - - +
259C THR 3.4 0.4 - - - -
260C THR* 3.2 19.4 + - - +
280C PHE* 3.2 29.4 - - - -
281C MET* 5.0 8.7 - - - +
284C ASN* 3.7 8.9 + - - +
261D THR* 4.3 12.5 + - - -
263D TYR* 3.2 31.6 - - + +
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Residues in contact with LEU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B LEU* 3.8 28.0 - - + -
205C THR* 4.8 4.0 - - - +
208C ALA* 4.0 17.5 - - + +
209C ILE* 3.9 28.0 - - + -
254C SER 3.1 15.8 + - - +
255C ILE* 4.5 2.5 - - + +
257C THR* 1.3 81.2 + - - +
259C THR* 1.3 61.2 + - + +
260C THR* 3.2 3.3 + - - +
280C PHE* 4.2 11.2 - - + -
284C ASN* 3.7 30.5 - - - +
287C LEU* 3.9 25.4 - - + -
288C THR* 3.6 22.7 - - + +
291C LEU* 5.8 0.2 - - + -
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Residues in contact with THR 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B THR* 3.6 18.7 - - - +
281B MET* 3.4 29.2 - - - +
284B ASN* 6.3 1.6 - - - -
285B LEU* 3.7 29.6 - - + -
255C ILE* 2.8 31.3 + - + +
256C THR 3.9 0.2 + - - -
258C LEU* 1.3 75.5 - - - +
260C THR* 1.3 73.1 + - - +
261C THR* 2.8 21.7 + - - -
288C THR* 5.4 1.1 - - - -
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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