Contacts of the helix formed by residues 282 - 303 (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 MET 282 (chain B).
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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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Residues in contact with PHE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B VAL* 6.0 1.3 - - + -
208B ALA* 4.0 26.7 - - + -
279B PHE 3.7 12.9 + - - +
280B PHE* 3.1 22.4 + + + +
282B MET* 1.3 80.1 - - - +
284B ASN* 1.3 69.4 + - - +
286B GLY* 3.2 2.8 + - - -
287B LEU* 2.9 50.1 + - + +
701B 3PE 3.6 46.4 - - + +
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Residues in contact with ASN 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B THR* 3.7 15.5 + - - +
258B LEU* 3.7 35.8 - - - +
260B THR* 5.1 5.4 - - + -
280B PHE* 2.9 55.2 + - - +
281B MET* 3.9 9.8 - - - +
282B MET 3.3 0.6 - - - -
283B PHE* 1.3 82.6 - - - +
285B LEU* 1.3 63.0 + - - +
287B LEU* 3.7 6.5 - - - +
288B THR* 3.2 28.8 + - + +
259C THR* 6.3 1.6 - - - -
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B MET 3.7 7.5 + - - +
282B MET* 3.6 12.9 + - + +
283B PHE 3.3 0.4 - - - -
284B ASN* 1.3 78.7 - - - +
286B GLY* 1.3 61.0 + - - +
288B THR* 4.0 4.2 + - - +
289B ALA* 3.3 26.3 + - + +
205C THR* 5.1 8.3 - - - +
209C ILE* 5.6 1.6 - - + -
255C ILE* 4.8 4.9 - - + -
258C LEU* 3.8 19.5 - - + -
259C THR* 3.7 35.6 - - + +
288C THR* 4.5 17.9 - - + -
291C LEU* 4.0 27.9 - - + +
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Residues in contact with GLY 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B MET 3.6 4.6 + - - -
283B PHE 3.2 7.1 + - - -
285B LEU* 1.3 78.8 - - - +
287B LEU* 1.3 62.3 + - - +
289B ALA* 4.1 4.1 - - - +
290B TYR* 3.3 20.3 + - - +
701B 3PE 3.6 32.4 - - - +
295C MET* 4.8 12.3 - - - +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B VAL* 4.0 25.4 - - + -
205B THR* 4.4 11.2 - - + -
208B ALA* 4.3 7.2 - - + -
258B LEU* 3.9 40.2 - - + -
283B PHE* 2.9 43.4 + - + +
284B ASN* 4.1 6.7 - - - +
285B LEU 3.3 0.4 - - - -
286B GLY* 1.3 76.8 - - - +
288B THR* 1.3 62.4 + - + +
290B TYR* 3.0 10.3 + - + +
291B LEU* 3.0 38.1 + - + +
701B 3PE 4.2 13.0 - - + -
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Residues in contact with THR 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 4.6 17.3 - - + -
258B LEU* 3.6 23.1 - - + +
259B THR* 5.4 1.3 - - - -
260B THR* 5.4 6.2 - - + +
284B ASN* 3.2 19.6 + - - +
285B LEU* 4.0 4.9 + - - +
287B LEU* 1.3 81.4 - - + +
289B ALA* 1.3 58.5 + - - +
290B TYR 3.2 0.2 - - - -
291B LEU* 4.0 10.5 - - + +
292B ILE* 3.3 40.9 + - - +
292C ILE* 5.4 3.6 - - - +
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU* 3.3 18.6 + - + +
286B GLY* 4.3 4.0 - - - +
287B LEU 3.2 1.0 - - - -
288B THR* 1.3 80.3 + - - +
290B TYR* 1.3 57.2 + - - +
292B ILE* 4.8 0.9 - - - -
293B GLY* 3.6 15.7 + - - -
291C LEU* 4.4 7.9 - - + +
292C ILE* 4.0 29.1 - - + +
295C MET* 3.3 37.0 - - + +
296C THR 4.9 0.3 + - - -
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Residues in contact with TYR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ARG* 4.5 2.3 + - - -
200B LYS* 4.7 5.7 - - - +
201B LEU* 3.7 24.2 - - + +
204B VAL* 4.7 12.5 - - + +
286B GLY 3.3 19.1 + - - +
287B LEU* 3.0 8.2 + - + +
289B ALA* 1.3 78.2 - - - +
291B LEU* 1.3 71.7 + - + +
293B GLY* 4.0 1.2 - - - -
294B ASN* 2.9 57.4 + - - +
701B 3PE 3.6 77.1 + - + -
295C MET* 4.5 10.5 - - + -
299C VAL* 4.7 10.0 - - + +
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 4.0 30.7 - - + +
289A ALA* 4.4 8.0 - - + +
201B LEU* 4.0 27.6 - - + +
204B VAL* 5.5 0.7 - - + -
205B THR* 3.7 34.1 - - + -
258B LEU* 5.8 0.2 - - + -
287B LEU* 3.0 28.2 + - + +
288B THR* 3.9 8.0 + - + +
290B TYR* 1.3 93.5 - - + +
292B ILE* 1.3 60.9 + - + +
294B ASN* 3.4 2.9 + - - +
295B MET* 2.9 31.0 + - - +
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Residues in contact with ILE 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A THR* 5.0 4.5 - - - +
289A ALA* 4.1 25.6 - - + +
292A ILE* 3.7 45.8 - - + -
288B THR* 3.3 25.8 + - - +
289B ALA* 4.8 0.9 - - - -
291B LEU* 1.3 78.2 - - + +
293B GLY* 1.3 54.8 + - - +
295B MET* 3.9 0.7 - - - +
296B THR* 2.5 41.9 + - - +
292C ILE* 3.7 36.3 - - + -
296C THR* 5.1 0.7 - - - +
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Residues in contact with GLY 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ALA 3.6 16.3 + - - -
290B TYR 3.8 1.1 + - - -
291B LEU 3.3 0.2 - - - -
292B ILE* 1.3 78.2 - - - +
294B ASN* 1.3 60.4 + - - +
296B THR* 4.0 2.1 - - - -
297B ASN* 3.4 14.4 + - - +
292C ILE* 5.4 0.2 - - - +
295C MET 4.6 1.3 - - - -
296C THR* 3.6 35.7 + - - +
299C VAL* 3.5 20.1 - - - +
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Residues in contact with ASN 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ARG* 3.0 32.5 - - - +
201B LEU* 3.8 24.0 - - + -
290B TYR* 2.9 49.1 + - - +
291B LEU 3.9 0.4 - - - +
292B ILE 3.2 0.2 - - - -
293B GLY* 1.3 77.4 - - - +
295B MET* 1.3 60.4 + - - +
296B THR 3.2 0.7 - - - -
297B ASN* 3.2 10.2 + - - +
298B LEU* 3.0 32.3 + - + +
701B 3PE 4.7 0.6 + - - -
299C VAL* 3.4 24.3 - - - +
303C THR* 5.0 1.6 - - - +
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Residues in contact with MET 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLY* 4.8 18.6 - - - +
289A ALA* 3.3 35.7 - - + +
290A TYR* 4.5 9.6 - - + -
701A 3PE 6.4 0.9 - - + -
198B CYS* 4.6 13.0 - - + -
201B LEU* 4.6 13.8 - - + +
291B LEU 2.9 18.1 + - - +
292B ILE 4.2 0.9 - - - +
294B ASN* 1.3 74.5 - - - +
296B THR* 1.3 60.1 + - - +
298B LEU* 3.8 22.6 - - - +
299B VAL* 2.9 39.7 + - + +
302B TRP* 6.0 2.9 - - - -
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Residues in contact with THR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ILE* 5.0 0.5 - - - +
293A GLY* 3.6 22.2 - - - +
296A THR* 3.8 36.3 + - + -
292B ILE* 2.5 31.1 + - - +
293B GLY* 4.0 0.8 - - - -
294B ASN 3.2 0.2 - - - -
295B MET* 1.3 76.3 - - - +
297B ASN* 1.3 61.0 + - - +
299B VAL* 4.2 0.5 - - - +
300B VAL* 3.3 31.4 + - + +
296C THR* 3.8 24.9 + - + +
300C VAL* 6.1 0.4 - - - -
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Residues in contact with ASN 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B TYR* 5.1 4.4 + - - -
197B ARG* 6.0 1.2 - - - +
293B GLY 3.4 12.9 + - - +
294B ASN* 3.2 14.6 + - - +
296B THR* 1.3 79.1 - - - +
298B LEU* 1.3 64.3 + - - +
300B VAL* 3.8 6.1 + - - +
301B HIS* 3.2 23.7 + - - +
296C THR* 5.4 0.4 - - - +
299C VAL* 4.2 9.9 - - + +
300C VAL* 4.1 19.1 - - + +
303C THR* 2.9 28.7 + - - +
307C ARG* 2.9 37.4 + - - +
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B TYR* 4.6 12.6 - - + +
194B PHE* 4.0 24.8 - - + +
197B ARG* 4.1 32.8 - - + +
198B CYS* 3.7 29.8 - - - -
201B LEU* 4.8 5.4 - - + -
294B ASN* 3.0 20.5 + - + +
295B MET* 3.3 19.0 + - - +
296B THR 3.2 0.2 - - - -
297B ASN* 1.3 84.0 - - + +
299B VAL* 1.3 54.7 + - - +
301B HIS* 3.2 4.9 + - + +
302B TRP* 2.6 47.9 + - + +
307C ARG* 6.2 0.4 - - - -
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A TYR* 4.7 10.3 - - + +
293A GLY* 3.5 26.0 - - - +
294A ASN* 3.4 41.1 - - - +
297A ASN* 4.2 9.0 - - + -
701A 3PE 6.1 0.2 - - - +
295B MET* 2.9 31.3 + - + +
296B THR 4.2 1.1 - - - +
298B LEU* 1.3 73.4 - - + +
300B VAL* 1.3 60.8 + - - +
302B TRP* 3.3 13.6 - - + +
303B THR* 2.9 40.1 + - + +
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A THR 6.0 0.2 - - - -
297A ASN* 4.1 28.3 - - + +
296B THR* 3.3 25.5 + - + +
297B ASN* 4.0 6.5 - - - +
299B VAL* 1.3 77.0 - - - +
301B HIS* 1.3 60.2 + - - +
303B THR* 4.8 0.7 - - - -
304B SER* 3.2 28.1 + - - -
307B ARG* 4.3 13.6 + - - +
307C ARG* 5.0 12.6 - - - +
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Residues in contact with HIS 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B TYR* 3.8 28.0 - + + -
194B PHE* 3.2 38.3 - + + -
297B ASN 3.2 18.2 + - - +
298B LEU* 3.2 8.8 + - + +
300B VAL* 1.3 74.3 - - - +
302B TRP* 1.3 66.0 + - - +
304B SER* 4.2 4.8 + - - -
307C ARG* 3.6 36.7 + - + +
310C ARG* 4.6 10.3 - - + -
311C ASP* 2.6 38.8 + - - -
314C ARG* 3.8 15.4 + - - -
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Residues in contact with TRP 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A 3PE 3.9 42.7 - - - +
194B PHE* 3.9 47.5 - + + +
195B TRP* 4.4 26.5 - + - -
295B MET* 6.0 2.9 - - - -
298B LEU* 2.6 36.3 + - + +
299B VAL* 3.3 19.3 - - + +
301B HIS* 1.3 76.7 - - - +
303B THR* 1.3 70.2 + - + +
304B SER 3.5 3.0 + - - -
305B ARG* 4.7 5.7 + - - +
314C ARG* 5.0 4.3 + - - -
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Residues in contact with THR 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TYR* 4.5 11.4 - - - +
197A ARG* 4.4 18.8 - - - +
294A ASN* 4.9 0.2 - - - +
297A ASN* 2.9 27.0 + - - +
701A 3PE 4.2 23.8 - - - +
299B VAL* 2.9 21.7 + - + +
300B VAL* 4.0 2.0 - - - -
302B TRP* 1.3 83.8 - - + +
304B SER* 1.3 59.2 + - - +
305B ARG 3.4 2.0 - - - +
306B THR* 4.4 9.9 - - - +
307B ARG* 3.3 25.7 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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