Contacts of the helix formed by residues 270 - 282 (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 ASN 270 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219C ILE 4.9 1.8 + - - -
223C TYR* 3.3 61.9 - - + +
228C LYS* 4.0 7.9 - - + +
229C THR* 4.0 4.0 - - - +
269C GLU* 1.3 76.2 + - - +
271C PRO* 1.3 66.6 - - + +
272C ARG* 3.1 12.1 + - - +
273C GLU* 3.1 47.4 + - - +
274C MET* 3.3 12.8 + - - +
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Residues in contact with PRO 271 (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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223C TYR* 4.8 4.5 - - + +
269C GLU 4.5 1.8 - - - +
270C ASN* 1.3 85.3 - - + +
272C ARG* 1.3 59.7 + - + +
273C GLU 3.5 0.2 - - - -
274C MET* 3.9 19.3 - - + +
275C LEU* 3.7 25.6 + - - +
235D TYR* 5.8 1.6 - - - +
246D ARG* 6.2 4.0 - - + -
248D VAL* 5.1 10.3 - - + +
249D THR* 6.1 0.2 - - - +
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Residues in contact with ARG 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C ILE* 3.8 27.5 + - + +
222C ARG* 3.3 27.5 + - - +
223C TYR* 3.8 29.4 - - + -
224C PRO* 3.5 21.8 - - - +
270C ASN* 3.1 6.8 - - - +
271C PRO* 1.3 78.9 - - + +
273C GLU* 1.3 62.0 + - - +
274C MET 3.3 0.4 - - - -
275C LEU* 3.5 8.7 + - - +
276C PHE* 3.3 19.8 + - - +
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Residues in contact with GLU 273 (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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216C ASN* 4.2 13.0 - - - +
219C ILE* 3.7 17.1 - - + +
220C ALA* 4.3 6.6 - - - -
229C THR* 3.5 18.5 - - - +
230C TRP* 3.2 47.9 + - + +
268C ALA* 3.7 13.2 - - + -
269C GLU 3.6 9.4 + - - -
270C ASN* 3.1 25.4 + - - +
272C ARG* 1.3 75.3 - - - +
274C MET* 1.3 61.5 + - - +
275C LEU 3.3 0.4 - - - -
276C PHE* 3.7 5.6 - - - +
277C ASP* 3.0 36.5 + - - +
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Residues in contact with MET 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C ALA* 3.9 24.9 - - + +
269C GLU 4.5 4.0 - - - +
270C ASN 3.3 13.8 + - - +
271C PRO* 4.2 14.1 - - + -
272C ARG 3.3 0.6 - - - -
273C GLU* 1.3 78.9 - - - +
275C LEU* 1.3 60.2 + - - +
277C ASP* 4.2 0.7 - - - +
278C ILE* 3.2 30.1 + - - +
235D TYR* 4.0 21.5 - - + +
248D VAL* 4.0 16.2 - - + -
249D THR* 3.8 32.3 - - + +
252D TYR* 4.0 25.3 - - + -
266D PHE* 4.1 25.4 - - + -
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Residues in contact with LEU 275 (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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271C PRO 3.7 15.1 + - - +
272C ARG* 3.5 11.3 + - - +
273C GLU 3.3 0.4 - - - -
274C MET* 1.3 78.4 - - - +
276C PHE* 1.3 64.1 + - - +
278C ILE* 3.4 7.8 + - + +
279C PHE* 3.2 49.7 + - + -
246D ARG* 3.5 30.7 - - - +
248D VAL* 4.0 14.6 - - + -
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Residues in contact with PHE 276 (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* 4.2 16.2 - - + -
215C PHE* 3.9 39.5 - + + -
216C ASN* 3.2 38.6 - - + +
219C ILE* 4.9 11.7 - - + -
253C TRP* 4.1 9.4 - + - -
272C ARG 3.3 14.5 + - - +
273C GLU* 3.5 6.9 + - - +
274C MET 3.4 0.2 - - - -
275C LEU* 1.3 80.0 - - - +
277C ASP* 1.3 63.1 + - - +
279C PHE* 3.5 9.4 + + + -
280C PHE* 2.9 39.4 + + + +
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Residues in contact with ASP 277 (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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216C ASN* 4.4 2.9 + - - +
253C TRP* 3.3 35.4 + - - -
268C ALA* 4.2 9.0 + - - +
273C GLU* 3.0 20.6 + - - +
274C MET 4.3 0.2 - - - +
276C PHE* 1.3 79.5 - - - +
278C ILE* 1.3 59.6 + - - +
280C PHE* 3.8 5.4 - - - -
281C MET* 2.9 42.4 + - + +
252D TYR* 3.8 30.7 + - + -
263D TYR* 3.7 15.5 + - - -
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Residues in contact with ILE 278 (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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274C MET 3.2 18.9 + - - +
275C LEU* 3.8 8.7 - - + +
276C PHE 3.2 0.6 - - - -
277C ASP* 1.3 77.8 - - - +
279C PHE* 1.3 73.4 + - + +
281C MET* 4.0 0.5 - - - +
282C MET* 3.1 41.9 + - + +
209D ILE* 6.2 2.5 - - + -
248D VAL* 3.8 23.1 - - + +
251D LEU* 3.9 32.3 - - + +
252D TYR* 3.9 10.5 - - + +
255D ILE* 3.9 26.9 - - + +
701D 3PE 5.9 5.2 - - + -
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Residues in contact with PHE 279 (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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275C LEU* 3.2 42.1 + - + +
276C PHE* 3.5 10.3 + + + +
278C ILE* 1.3 84.5 - - + +
280C PHE* 1.3 59.2 + - - +
282C MET* 3.8 24.7 - - + +
283C PHE* 3.7 16.6 + - - +
701C 3PE 5.3 11.4 - - + -
701D 3PE 6.5 1.3 - - + -
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Residues in contact with PHE 280 (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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208C ALA 4.4 4.3 - - - -
212C ALA* 3.6 34.1 - - + -
253C TRP* 4.0 25.1 - + - -
254C SER* 4.4 8.5 - - - -
257C THR* 3.2 28.5 - - - -
258C LEU* 4.2 15.5 - - + -
276C PHE* 2.9 29.9 + + + +
277C ASP* 4.1 5.2 - - - +
279C PHE* 1.3 76.3 - - - +
281C MET* 1.3 62.2 + - + +
282C MET 3.2 2.0 - - - -
283C PHE* 3.1 17.3 + + + -
284C ASN* 2.9 56.1 + - - +
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Residues in contact with MET 281 (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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257C THR* 5.0 11.7 - - - +
277C ASP* 2.9 44.6 + - + +
278C ILE 4.0 0.2 - - - -
280C PHE* 1.3 79.0 - - + +
282C MET* 1.3 60.0 + - - +
284C ASN* 3.9 13.0 - - + +
285C LEU* 3.7 10.0 + - - +
252D TYR* 4.1 8.5 - - + -
255D ILE* 3.7 35.7 - - + +
256D THR* 3.9 13.9 - - - +
259D THR* 3.4 28.8 - - + +
261D THR* 3.6 30.3 - - - +
263D TYR* 4.3 15.7 - - + +
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Residues in contact with MET 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C ILE* 3.1 24.8 + - + +
279C PHE* 3.8 34.5 - - + +
281C MET* 1.3 75.7 - - - +
283C PHE* 1.3 63.3 + - - +
284C ASN 3.3 0.7 - - - -
285C LEU* 3.6 11.1 + - + +
286C GLY 3.6 13.2 + - - -
701C 3PE 3.8 49.7 - - + +
206D LEU* 4.0 24.2 - - - -
209D ILE* 4.5 10.3 - - + -
255D ILE* 3.8 19.7 - - + -
701D 3PE 5.7 3.8 - - + -
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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