Contacts of the helix formed by residues 282 - 303 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A ILE* 3.1 20.8 + - + +
279A PHE* 3.8 35.7 - - + +
281A MET* 1.3 75.2 - - - +
283A PHE* 1.3 64.6 + - - +
284A ASN 3.3 0.2 - - - -
285A LEU* 3.6 10.2 + - + +
286A GLY 3.6 12.8 + - - -
701A 3PE 1.8 110.8 - - + +
206B LEU* 4.9 0.2 - - + -
209B ILE* 4.5 2.5 - - + -
255B ILE* 3.8 18.4 - - + -
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Residues in contact with PHE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A VAL* 6.0 1.1 - - + -
208A ALA* 4.0 26.5 - - + -
279A PHE 3.7 12.1 + - - +
280A PHE* 3.1 22.4 + + + +
282A MET* 1.3 79.6 - - - +
284A ASN* 1.3 70.5 + - - +
286A GLY* 3.2 2.9 + - - -
287A LEU* 2.9 50.2 + - + +
701A 3PE 3.7 43.0 - - + +
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Residues in contact with ASN 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A THR* 3.7 15.3 + - - +
258A LEU* 3.7 34.1 - - - +
260A THR* 5.1 5.6 - - + -
280A PHE* 2.9 55.4 + - - +
281A MET* 3.9 10.2 - - + +
282A MET 3.3 0.4 - - - -
283A PHE* 1.3 82.5 - - - +
285A LEU* 1.3 64.6 + - - +
287A LEU* 3.7 6.1 - - - +
288A THR* 3.2 28.5 + - + +
259B THR* 6.3 1.1 - - - -
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A MET 3.7 6.9 + - - +
282A MET* 3.6 13.1 + - + +
283A PHE 3.3 0.6 - - - -
284A ASN* 1.3 79.4 - - - +
286A GLY* 1.3 62.3 + - - +
288A THR* 4.0 4.1 + - - +
289A ALA* 3.3 27.1 + - + +
701A 3PE 6.3 1.6 - - + -
205B THR* 5.1 9.6 - - + +
209B ILE* 5.6 1.1 - - + -
255B ILE* 4.9 4.9 - - + -
258B LEU* 3.8 19.3 - - + -
259B THR* 3.8 34.5 - - + +
288B THR* 4.6 17.9 - - + -
291B LEU* 4.0 27.3 - - + +
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Residues in contact with GLY 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A MET 3.6 5.4 + - - -
283A PHE 3.2 7.1 + - - -
285A LEU* 1.3 77.8 - - - +
287A LEU* 1.3 61.7 + - - +
289A ALA* 4.1 4.4 - - - +
290A TYR* 3.3 20.8 + - - +
701A 3PE 3.6 31.1 - - - +
295B MET* 4.8 12.8 - - - +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 4.0 25.8 - - + -
205A THR* 4.4 12.6 - - + -
208A ALA* 4.3 6.7 - - + -
258A LEU* 3.9 39.7 - - + -
283A PHE* 2.9 44.5 + - + +
284A ASN* 4.1 6.3 - - - +
285A LEU 3.3 0.2 - - - -
286A GLY* 1.3 75.9 - - - +
288A THR* 1.3 63.7 + - + +
290A TYR* 3.0 9.8 + - + +
291A LEU* 3.0 37.3 + - + +
701A 3PE 4.1 12.6 - - + -
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Residues in contact with THR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LEU* 3.6 23.3 - - + +
259A THR* 5.4 1.3 - - - -
260A THR* 5.4 6.0 - - + +
284A ASN* 3.2 20.4 + - - +
285A LEU* 4.0 4.7 + - - +
287A LEU* 1.3 81.1 - - + +
289A ALA* 1.3 60.3 + - - +
291A LEU* 4.0 10.3 - - + +
292A ILE* 3.3 39.4 + - - +
292B ILE* 5.4 3.4 - - - +
285D LEU* 4.6 17.7 - - + -
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 3.3 18.8 + - + +
286A GLY* 4.5 3.8 - - - +
287A LEU 3.2 1.0 - - - -
288A THR* 1.3 79.5 + - - +
290A TYR* 1.3 58.3 + - - +
292A ILE* 4.8 0.9 - - - -
293A GLY* 3.6 15.4 + - - -
291B LEU* 4.4 11.7 - - + +
292B ILE* 4.1 26.7 - - + +
295B MET* 3.3 36.2 - - + +
296B THR 4.8 0.2 + - - -
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Residues in contact with TYR 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ARG* 4.5 2.9 + - - -
200A LYS* 4.7 5.0 - - - +
201A LEU* 3.7 23.3 - - + +
204A VAL* 4.7 11.9 - - + +
286A GLY 3.3 18.3 + - - +
287A LEU* 3.0 8.8 + - + +
289A ALA* 1.3 79.7 - - - +
291A LEU* 1.3 73.0 + - + +
292A ILE 3.4 0.2 - - - -
293A GLY* 4.0 1.1 - - - -
294A ASN* 2.9 57.8 + - - +
701A 3PE 3.6 78.4 + - + -
295B MET* 4.5 9.9 - - + -
299B VAL* 4.7 9.8 - - + +
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 4.0 28.2 - - + +
204A VAL* 5.5 0.7 - - + -
205A THR* 3.7 33.7 - - + -
287A LEU* 3.0 26.7 + - + +
288A THR* 3.9 8.2 + - + +
290A TYR* 1.3 93.7 - - + +
292A ILE* 1.3 61.5 + - + +
294A ASN* 3.8 3.7 - - - +
295A MET* 2.9 31.0 + - - +
285D LEU* 4.0 31.0 - - + +
289D ALA* 4.4 8.2 - - + +
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Residues in contact with ILE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A THR* 3.3 25.6 + - - +
289A ALA* 4.8 0.4 - - - -
291A LEU* 1.3 78.4 - - + +
293A GLY* 1.3 54.7 + - - +
295A MET* 3.5 1.2 + - - +
296A THR* 2.5 41.6 + - - +
292B ILE* 3.7 42.0 - - + -
296B THR* 5.0 0.9 - - - +
288D THR* 5.0 3.4 - - - +
289D ALA* 4.1 24.8 - - + +
292D ILE* 3.7 40.8 - - + -
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Residues in contact with GLY 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ALA 3.6 16.8 + - - -
290A TYR 3.8 0.9 + - - -
291A LEU 3.3 0.4 - - - -
292A ILE* 1.3 79.7 - - - +
294A ASN* 1.3 59.4 + - - +
296A THR* 4.0 1.9 - - - -
297A ASN* 3.4 14.2 + - - +
292B ILE* 5.4 0.2 - - - +
295B MET 4.6 1.6 - - - -
296B THR* 3.6 35.5 + - - +
299B VAL* 3.5 19.5 - - - +
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Residues in contact with ASN 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ARG* 3.0 31.5 - - - +
201A LEU* 3.8 25.5 - - + +
290A TYR* 2.9 48.8 + - - +
291A LEU 3.9 0.4 - - - +
292A ILE 3.2 0.2 - - - -
293A GLY* 1.3 76.5 - - - +
295A MET* 1.3 60.5 + - - +
296A THR 3.2 0.2 - - - -
297A ASN* 3.2 10.8 + - - +
298A LEU* 3.0 31.4 + - + +
701A 3PE 4.8 0.8 + - - -
299B VAL* 3.4 24.1 - - - +
303B THR* 4.9 2.0 - - - +
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Residues in contact with MET 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A CYS* 4.6 13.7 - - + -
201A LEU* 4.6 14.3 - - + +
291A LEU 2.9 18.0 + - - +
292A ILE 4.2 1.1 - - - +
294A ASN* 1.3 74.1 - - - +
296A THR* 1.3 59.8 + - - +
298A LEU* 4.2 22.2 - - - +
299A VAL* 2.9 40.5 + - + +
302A TRP* 6.0 2.9 - - - -
286D GLY* 4.7 18.6 - - - +
289D ALA* 3.3 35.4 - - + +
290D TYR* 4.5 9.4 - - + -
701D 3PE 6.2 2.2 - - + -
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Residues in contact with THR 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ILE* 2.5 31.5 + - - +
293A GLY* 4.0 0.8 - - - -
295A MET* 1.3 76.2 - - - +
297A ASN* 1.3 60.9 + - - +
299A VAL* 4.2 0.7 - - - +
300A VAL* 3.3 31.1 + - + +
296B THR* 3.8 29.2 + - + +
292D ILE* 4.8 0.3 - - - +
293D GLY* 3.6 22.1 - - - +
296D THR* 3.8 33.6 + - + +
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Residues in contact with ASN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A TYR* 5.1 4.6 + - - -
197A ARG* 6.0 1.2 - - - +
293A GLY 3.4 12.9 + - - +
294A ASN* 3.2 14.0 + - - +
296A THR* 1.3 80.0 - - - +
298A LEU* 1.3 64.1 + - - +
300A VAL* 3.8 5.6 + - - +
301A HIS* 3.2 23.9 + - - +
296B THR* 5.4 0.4 - - - +
299B VAL* 4.2 9.7 - - + +
300B VAL* 4.1 19.6 - - + +
303B THR* 2.9 28.4 + - - -
307B ARG* 2.9 38.1 + - - +
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A TYR* 4.6 12.3 - - + +
194A PHE* 4.0 25.1 - - + +
197A ARG* 4.1 33.2 - - + +
198A CYS* 3.7 30.5 - - - -
201A LEU* 4.8 5.8 - - + -
294A ASN* 3.0 20.2 + - + +
295A MET* 3.3 19.5 + - - +
296A THR 3.2 0.2 - - - -
297A ASN* 1.3 83.1 - - + +
299A VAL* 1.3 55.0 + - - +
301A HIS* 3.2 5.5 + - + +
302A TRP* 2.6 47.6 + - + +
307B ARG* 6.2 0.4 - - - -
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Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A MET* 2.9 30.9 + - + +
296A THR 4.2 1.1 - - - +
298A LEU* 1.3 73.5 - - - +
300A VAL* 1.3 60.6 + - - +
302A TRP* 3.3 14.4 - - + +
303A THR* 2.9 41.1 + - + +
290D TYR* 4.7 10.1 - - + +
293D GLY* 3.5 27.1 - - - +
294D ASN* 3.4 40.6 - - - +
297D ASN* 4.2 8.1 - - + -
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Residues in contact with VAL 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A THR* 3.3 25.2 + - + +
297A ASN* 4.0 7.6 - - - +
299A VAL* 1.3 75.1 - - - +
301A HIS* 1.3 60.8 + - - +
303A THR* 4.8 0.7 - - - -
304A SER* 3.2 27.1 + - - -
307A ARG* 4.3 13.4 + - - +
307B ARG* 5.0 12.8 - - - +
297D ASN* 4.1 30.1 - - + +
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Residues in contact with HIS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TYR* 3.8 26.9 - + + -
194A PHE* 3.2 38.9 - + + -
297A ASN 3.2 17.1 + - - +
298A LEU* 3.2 10.5 + - + +
300A VAL* 1.3 75.5 - - - +
302A TRP* 1.3 65.5 + - - +
304A SER* 4.2 5.4 + - - -
307B ARG* 3.6 36.3 + - + +
310B ARG* 4.6 10.3 - - + -
311B ASP* 2.6 39.3 + - - -
314B ARG* 3.8 16.8 + - - -
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Residues in contact with TRP 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A PHE* 4.1 43.7 - + + +
195A TRP* 4.4 26.5 - + - -
295A MET* 6.0 2.8 - - - -
298A LEU* 2.6 36.6 + - + +
299A VAL* 3.1 20.1 + - + +
301A HIS* 1.3 76.6 - - - +
303A THR* 1.3 69.1 + - + +
304A SER 3.5 3.0 + - - -
305A ARG* 4.7 6.1 + - - +
314B ARG* 5.0 4.7 + - - -
290D TYR* 6.6 0.2 - + - -
701D 3PE 3.9 43.6 - - - +
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Residues in contact with THR 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 2.9 20.0 + - + +
300A VAL* 4.0 2.2 - - - -
302A TRP* 1.3 84.4 - - + +
304A SER* 1.3 59.5 + - - +
305A ARG 3.4 2.0 - - - +
306A THR* 4.4 9.0 - - - +
307A ARG* 3.3 26.5 + - - +
193D TYR* 4.5 11.2 - - - +
197D ARG* 4.4 17.7 - - - +
294D ASN* 4.9 0.2 - - - +
297D ASN* 2.9 27.4 + - - +
701D 3PE 4.2 24.2 - - - +
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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) + - + + + + + -
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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