Contacts of the helix formed by residues 289 - 311 (chain A) in PDB entry 3ISL
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 GLY 289 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A VAL 3.0 10.7 + - - -
286A LEU 3.4 8.2 + - - -
287A GLU 3.3 3.4 - - - -
288A GLU* 1.3 78.7 - - - +
290A LEU* 1.3 55.7 + - - -
291A GLU 3.4 2.2 - - - -
292A THR* 4.0 5.6 - - - -
293A ARG* 2.6 38.3 + - - +
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Residues in contact with LEU 290 (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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57A GLU* 3.4 26.2 - - + +
58A LEU* 3.9 19.3 - - + +
60A GLN* 3.9 24.2 - - + +
180A GLY* 5.1 0.7 - - - -
285A VAL* 3.4 31.8 + - + -
286A LEU* 4.2 12.7 - - + +
289A GLY* 1.3 70.1 - - - -
291A GLU* 1.3 62.1 + - - +
293A ARG* 3.1 4.5 + - - -
294A PHE* 2.7 58.9 + - + -
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Residues in contact with GLU 291 (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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60A GLN* 4.6 9.5 + - - +
183A GLU* 4.9 11.6 - - - +
185A LYS* 5.6 3.8 - - - -
289A GLY 3.4 0.6 - - - -
290A LEU* 1.3 81.2 - - - +
292A THR* 1.3 57.0 + - - +
294A PHE* 3.2 25.5 + - + +
295A GLU* 2.9 30.6 + - - +
298A ARG* 4.9 2.7 + - - +
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Residues in contact with THR 292 (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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288A GLU* 3.4 35.3 + - + +
289A GLY* 3.4 4.0 + - - -
291A GLU* 1.3 75.2 - - - +
293A ARG* 1.3 59.5 + - - +
295A GLU* 3.2 7.8 + - + +
296A ARG* 2.8 32.3 + - + +
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Residues in contact with ARG 293 (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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180A GLY 2.9 28.7 + - - +
201A CYS 2.8 23.8 + - - -
202A LEU* 4.4 7.7 + - - +
203A SER* 5.0 1.2 - - - -
284A LEU* 4.4 6.1 + - - +
285A VAL* 3.8 48.3 - - - +
288A GLU* 2.8 46.0 + - + +
289A GLY 2.6 23.0 + - - +
290A LEU* 3.5 4.7 - - - +
292A THR* 1.3 74.2 - - - +
294A PHE* 1.3 62.3 + - + +
296A ARG* 3.0 14.2 + - - +
297A HIS* 2.9 38.7 + - + -
370A GLY* 3.8 12.3 - - - -
371A TYR 4.8 1.2 - - - +
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Residues in contact with PHE 294 (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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58A LEU 5.9 0.9 - - - -
60A GLN* 4.0 12.1 - - - -
180A GLY* 4.2 9.0 - - - -
181A GLY* 3.5 32.9 - - - +
182A CYS* 3.6 16.2 - - - -
183A GLU* 3.6 44.4 - - + +
184A VAL 4.4 2.2 - - - -
290A LEU* 2.7 50.2 + - + -
291A GLU* 3.2 24.9 + - + +
293A ARG* 1.3 74.4 - - + +
295A GLU* 1.3 57.7 + - - +
297A HIS* 3.3 4.0 + - - +
298A ARG* 3.0 47.2 + - - +
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Residues in contact with GLU 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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291A GLU 2.9 16.6 + - - +
292A THR* 3.6 7.0 - - - +
294A PHE* 1.3 74.1 - - - +
296A ARG* 1.3 61.7 + - - +
298A ARG* 2.8 37.4 + - - +
299A HIS* 2.8 39.4 + - + +
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Residues in contact with ARG 296 (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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288A GLU* 2.7 41.8 + - - +
292A THR* 2.8 22.4 + - + +
293A ARG* 3.0 28.6 + - - +
295A GLU* 1.3 75.1 - - - +
297A HIS* 1.3 69.7 + - - +
299A HIS* 3.4 7.4 + - + +
300A HIS* 3.1 42.7 + - + +
370A GLY 2.7 28.5 + - - -
371A TYR* 4.8 1.8 - - - +
373A CYS* 3.0 29.0 + - - +
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Residues in contact with HIS 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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180A GLY 4.0 4.9 + - - -
181A GLY* 3.7 20.5 + - - +
201A CYS* 4.5 0.8 - - - +
293A ARG* 2.9 51.8 + - + +
294A PHE 3.6 7.6 - - - +
296A ARG* 1.3 96.6 - - - +
298A ARG* 1.3 61.9 + - + +
300A HIS* 3.5 0.9 + - - -
301A GLU* 3.1 23.5 + - - +
324A PRO* 4.9 5.8 - - + +
325A VAL* 3.5 29.6 - - + -
368A THR* 3.5 15.9 + - - -
369A MET* 4.0 0.6 - - - -
370A GLY 2.9 25.1 + - - -
373A CYS* 3.7 11.8 - - - +
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Residues in contact with ARG 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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183A GLU* 6.4 0.2 - - - +
291A GLU* 4.9 2.8 + - - +
294A PHE* 3.0 29.0 + - - +
295A GLU* 2.8 51.4 + - - +
297A HIS* 1.3 74.3 - - - +
299A HIS* 1.3 66.1 + - - +
301A GLU* 3.2 19.9 + - - +
302A ALA* 2.9 25.0 + - - +
324A PRO* 4.6 14.1 - - + -
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Residues in contact with HIS 299 (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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295A GLU* 2.8 30.1 + - + +
296A ARG* 3.6 9.5 - - - +
297A HIS 3.3 0.2 - - - -
298A ARG* 1.3 73.8 - - - +
300A HIS* 1.3 75.4 + + - +
302A ALA* 3.0 16.7 + - + +
303A ALA* 3.1 12.6 + - - +
408A VAL* 4.1 20.8 + - + -
409A TYR* 3.5 36.2 + + - -
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Residues in contact with HIS 300 (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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296A ARG* 3.1 36.4 + - + +
298A ARG 3.3 0.4 - - - -
299A HIS* 1.3 84.7 + + - +
301A GLU* 1.3 65.5 + - - +
303A ALA* 3.4 2.0 + - - +
304A LEU* 2.9 26.7 + - - +
368A THR* 5.0 2.5 - - + -
373A CYS* 3.6 40.8 + - - -
374A ARG* 4.0 1.4 - - - +
375A LYS* 3.2 27.4 + - + -
378A VAL* 4.0 13.4 - - + +
409A TYR* 2.6 42.8 + + - +
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Residues in contact with GLU 301 (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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297A HIS 3.1 17.7 + - - +
298A ARG* 3.5 15.3 - - - +
300A HIS* 1.3 78.5 - - - +
302A ALA* 1.3 57.9 + - - +
304A LEU* 3.5 5.8 + - - +
305A ALA* 3.0 31.3 + - + +
322A LYS* 2.5 41.5 + - - +
324A PRO* 3.3 42.7 - - - +
327A THR* 4.7 6.0 + - - +
368A THR* 4.7 8.2 + - - +
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Residues in contact with ALA 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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298A ARG 2.9 12.6 + - - +
299A HIS* 3.4 11.4 - - + +
301A GLU* 1.3 74.7 - - - +
303A ALA* 1.3 60.5 + - - +
305A ALA* 3.4 7.5 + - - +
306A ALA* 2.9 29.6 + - - +
408A VAL* 4.3 10.9 - - + +
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Residues in contact with ALA 303 (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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299A HIS 3.1 7.3 + - - +
300A HIS 3.8 3.1 - - - +
302A ALA* 1.3 74.7 - - - +
304A LEU* 1.4 62.8 + - - +
306A ALA* 3.3 1.6 + - - -
307A GLY 3.0 17.7 + - - -
378A VAL* 4.3 1.6 - - + -
405A ALA* 3.6 18.6 - - + +
408A VAL* 3.6 27.2 - - + +
409A TYR* 3.4 44.2 - - + +
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Residues in contact with LEU 304 (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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300A HIS 2.9 21.0 + - - +
301A GLU* 3.7 4.7 - - - +
303A ALA* 1.4 70.7 - - - +
305A ALA* 1.3 52.3 + - - +
307A GLY* 3.0 3.3 + - - -
308A ILE* 2.8 49.9 + - + +
327A THR* 3.8 29.6 - - + +
366A ILE* 3.8 26.9 - - + +
368A THR* 3.9 16.8 - - + -
378A VAL* 3.9 17.5 - - + +
381A VAL* 3.9 22.4 - - + -
382A LEU* 3.8 22.4 - - + +
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Residues in contact with ALA 305 (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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301A GLU* 3.0 23.9 + - + +
302A ALA* 3.5 8.1 - - - +
304A LEU* 1.3 73.4 - - - +
306A ALA* 1.3 60.7 + - - +
308A ILE* 3.4 6.8 + - - +
309A LYS* 2.9 31.6 + - - +
315A LEU* 5.0 17.8 - - + +
322A LYS* 6.1 1.6 - - - -
327A THR* 5.5 4.9 - - + +
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Residues in contact with ALA 306 (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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302A ALA 2.9 10.2 + - - +
305A ALA* 1.3 75.7 - - - +
307A GLY* 1.3 63.7 + - - +
309A LYS* 3.4 7.6 + - - +
310A ALA* 3.0 26.7 + - - +
404A ALA* 3.8 15.3 - - + +
408A VAL* 3.8 29.4 - - + -
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Residues in contact with GLY 307 (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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303A ALA 3.0 15.0 + - - -
304A LEU 3.0 4.2 + - - -
306A ALA* 1.3 77.6 - - - +
308A ILE* 1.3 61.6 + - - +
311A MET* 3.0 25.3 + - - +
382A LEU* 3.8 18.2 - - - -
401A ALA* 3.6 28.3 - - - +
405A ALA 4.4 1.7 - - - +
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Residues in contact with ILE 308 (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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304A LEU* 2.8 33.6 + - + +
305A ALA* 3.9 5.8 - - - +
307A GLY* 1.3 71.8 - - - +
309A LYS* 1.3 63.1 + - - +
311A MET* 3.3 12.6 - - - +
313A LEU* 3.2 45.1 + - + +
315A LEU* 3.9 24.0 - - + -
327A THR* 4.8 3.6 - - + -
329A VAL* 4.1 21.8 - - + -
366A ILE* 4.2 7.2 - - + -
382A LEU* 3.7 19.3 - - + +
385A LEU* 3.9 26.5 - - + -
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Residues in contact with LYS 309 (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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305A ALA 2.9 18.2 + - - +
306A ALA* 3.8 7.6 - - - +
308A ILE* 1.3 75.4 - - - +
310A ALA* 1.3 58.5 + - - +
311A MET 3.1 1.6 - - - -
312A GLY* 2.8 24.3 + - - -
313A LEU 4.0 11.2 + - - +
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Residues in contact with ALA 310 (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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306A ALA 3.0 17.8 + - - +
307A GLY 3.9 2.9 - - - +
309A LYS* 1.3 77.8 - - - +
311A MET* 1.3 60.6 + - - +
312A GLY* 3.1 1.8 + - - -
397A GLU* 4.7 4.3 + - - +
400A LYS* 3.6 45.2 - - + +
404A ALA* 3.6 12.1 - - + -
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Residues in contact with MET 311 (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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307A GLY 3.0 18.2 + - - +
308A ILE* 3.3 12.6 - - - +
309A LYS 3.1 0.4 - - - -
310A ALA* 1.3 78.3 - - - +
312A GLY* 1.3 57.3 + - - +
313A LEU* 3.4 14.7 + - + +
382A LEU* 4.7 4.5 - - - +
385A LEU* 3.5 10.5 - - + +
386A GLU* 3.4 38.1 - - + +
389A LEU* 3.1 36.8 - - + -
396A ILE* 3.2 47.1 - - + +
397A GLU 5.1 6.3 - - - +
401A ALA* 4.1 17.7 - - + +
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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
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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