Contacts of the helix formed by residues 270 - 282 (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 ASN 270 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219B ILE 4.9 2.0 + - - -
223B TYR* 3.3 60.2 - - + +
228B LYS* 4.0 7.9 - - + +
229B THR* 4.0 4.2 - - - +
269B GLU* 1.3 75.2 + - - +
271B PRO* 1.3 66.9 - - + +
272B ARG* 3.1 12.0 + - - +
273B GLU* 3.1 48.4 + - - +
274B MET* 3.3 13.1 + - - +
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Residues in contact with PRO 271 (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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223B TYR* 4.8 4.3 - - - +
269B GLU 4.5 2.0 - - - +
270B ASN* 1.3 86.0 - - + +
272B ARG* 1.3 60.5 + - + +
274B MET* 3.9 18.4 - - + +
275B LEU* 3.7 24.8 + - - +
235C TYR* 5.8 2.2 - - - +
246C ARG* 6.2 3.8 - - + -
248C VAL* 5.1 10.7 - - + +
249C THR* 6.1 0.7 - - - +
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Residues in contact with ARG 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ILE* 3.8 26.6 + - + +
222B ARG* 3.3 28.5 + - - +
223B TYR* 3.8 29.7 - - + -
224B PRO* 3.5 21.6 - - - +
270B ASN* 3.1 7.4 - - + +
271B PRO* 1.3 77.7 - - - +
273B GLU* 1.3 63.6 + - - +
274B MET 3.3 0.4 - - - -
275B LEU* 3.5 8.6 + - - +
276B PHE* 3.3 18.9 + - - +
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Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ASN* 4.2 12.8 - - - +
219B ILE* 3.7 18.0 - - + +
220B ALA* 4.3 6.4 - - - -
229B THR* 3.5 18.2 - - - +
230B TRP* 3.2 47.9 + - + +
268B ALA* 3.7 13.3 - - + -
269B GLU 3.6 9.2 + - - -
270B ASN* 3.1 24.9 + - - +
272B ARG* 1.3 75.2 - - - +
274B MET* 1.3 60.7 + - - +
275B LEU 3.3 0.4 - - - -
276B PHE* 3.7 6.1 - - - +
277B ASP* 3.0 36.4 + - - +
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Residues in contact with MET 274 (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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268B ALA* 3.9 25.1 - - + +
269B GLU 4.5 4.5 - - - +
270B ASN 3.3 13.3 + - - +
271B PRO* 4.2 15.0 - - + -
272B ARG 3.3 1.0 - - - -
273B GLU* 1.3 77.7 - - - +
275B LEU* 1.3 61.2 + - - +
277B ASP* 3.8 1.0 + - - +
278B ILE* 3.2 29.5 + - - +
235C TYR* 4.0 21.8 - - + +
248C VAL* 4.0 15.7 - - + -
249C THR* 3.8 33.9 - - + +
252C TYR* 4.0 25.1 - - + -
266C PHE* 4.0 25.4 - - + -
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PRO 3.7 14.6 + - - +
272B ARG* 3.5 10.8 + - - +
273B GLU 3.3 0.4 - - - -
274B MET* 1.3 78.5 - - - +
276B PHE* 1.3 64.2 + - - +
278B ILE* 3.4 7.5 + - + +
279B PHE* 3.2 49.9 + - + -
246C ARG* 3.5 31.4 - - - +
248C VAL* 4.0 15.7 - - + -
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Residues in contact with PHE 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ALA* 4.2 15.5 - - + -
215B PHE* 3.9 39.5 - + + -
216B ASN* 3.2 38.1 - - + +
219B ILE* 4.9 11.4 - - + -
253B TRP* 4.1 9.6 - + - -
272B ARG 3.3 13.9 + - - +
273B GLU* 3.5 6.7 + - - +
275B LEU* 1.3 78.7 - - - +
277B ASP* 1.3 64.3 + - - +
279B PHE* 3.5 9.0 + + + -
280B PHE* 2.9 38.9 + + + +
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Residues in contact with ASP 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ASN* 4.4 2.9 + - - +
253B TRP* 3.3 36.3 + - - -
268B ALA* 4.2 9.0 + - - +
273B GLU* 3.0 20.5 + - - +
274B MET 4.3 0.2 - - - +
276B PHE* 1.3 79.0 - - - +
278B ILE* 1.3 60.8 + - - +
280B PHE* 3.8 5.4 - - - -
281B MET* 2.9 40.7 + - + +
252C TYR* 3.8 31.1 + - + -
263C TYR* 3.7 16.2 + - - -
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Residues in contact with ILE 278 (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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274B MET 3.2 20.0 + - - +
275B LEU* 3.8 8.7 - - + +
276B PHE 3.2 0.6 - - - -
277B ASP* 1.3 79.3 - - - +
279B PHE* 1.3 72.9 + - + +
281B MET 4.0 0.5 - - - -
282B MET* 3.1 41.4 + - + +
209C ILE* 6.2 2.7 - - + -
248C VAL* 3.7 22.7 - - + +
251C LEU* 3.9 32.5 - - + +
252C TYR* 3.9 9.9 - - + +
255C ILE* 3.9 26.8 - - + +
701C 3PE 5.5 5.6 - - + -
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Residues in contact with PHE 279 (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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275B LEU* 3.2 43.5 + - + +
276B PHE* 4.1 11.2 - + + +
278B ILE* 1.3 84.6 - - + +
280B PHE* 1.3 58.8 + - - +
282B MET* 3.8 26.1 - - + +
283B PHE* 3.7 16.5 + - - +
701B 3PE 5.5 8.6 - - + +
701C 3PE 5.7 6.5 - - + -
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Residues in contact with PHE 280 (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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208B ALA 4.4 3.6 - - - -
212B ALA* 3.6 33.0 - - + -
253B TRP* 4.0 24.7 - + - -
254B SER* 4.4 8.3 - - - -
257B THR* 3.2 26.9 - - - -
258B LEU* 4.2 16.6 - - + -
276B PHE* 2.9 29.8 + + + +
277B ASP* 4.1 5.2 - - - +
279B PHE* 1.3 75.9 - - - +
281B MET* 1.3 62.5 + - + +
282B MET 3.2 1.8 - - - -
283B PHE* 3.1 18.9 + + + -
284B ASN* 2.9 56.6 + - - +
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Residues in contact with MET 281 (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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257B THR* 5.0 11.2 - - - +
277B ASP* 2.9 45.0 + - + +
280B PHE* 1.3 76.5 - - + +
282B MET* 1.3 60.5 + - - +
284B ASN* 3.9 14.6 - - + +
285B LEU* 3.7 10.2 + - - +
252C TYR* 4.1 8.3 - - + -
255C ILE* 3.7 36.8 - - + +
256C THR* 3.9 13.2 - - - +
259C THR* 3.4 28.7 - - + +
261C THR* 3.6 31.6 - - - +
263C TYR* 4.3 15.5 - - + +
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Residues in contact with MET 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ILE* 3.1 23.9 + - + +
279B PHE* 3.8 33.2 - - + +
280B PHE 3.2 0.2 - - - -
281B MET* 1.3 76.1 - - - +
283B PHE* 1.3 63.8 + - - +
284B ASN 3.3 0.4 - - - -
285B LEU* 3.6 11.0 + - + +
286B GLY 3.6 12.3 + - - -
701B 3PE 3.6 72.7 - - + +
206C LEU* 4.0 4.5 - - - -
209C ILE* 4.5 11.2 - - + -
255C ILE* 3.8 18.6 - - + -
701C 3PE 5.4 4.0 - - + -
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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