Contacts of the helix formed by residues 299 - 321 (chain A) in PDB entry 4J15
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 TYR 299 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A PHE* 3.5 17.7 - - + -
298A HIS* 1.3 87.2 + + - +
300A HIS* 1.3 71.5 + + - +
301A GLU 3.0 1.6 - - - -
302A VAL* 2.8 20.3 + - - +
303A MET* 2.9 11.6 + - + -
392A ASP* 2.6 27.4 + - - -
393A LYS* 2.9 21.4 + - - +
414A ASN* 3.4 42.3 - - + -
416A TYR* 3.5 38.1 - + - -
430A GLN* 3.7 20.4 - - + -
467A ALA* 4.2 6.1 - - + +
37B SER* 3.0 29.9 + - - +
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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
----------------------------------------------------------
298A HIS* 3.0 23.3 + + + +
299A TYR* 1.3 101.5 + + - +
301A GLU* 1.3 56.3 + - - +
302A VAL 3.2 0.2 - - - -
303A MET* 3.5 22.9 - - + +
304A GLU* 2.9 45.6 + - - +
345A ARG* 3.7 23.7 + - - -
392A ASP* 2.8 26.0 + - - -
393A LYS* 5.1 4.3 - - - -
40B LYS* 2.9 31.7 + - - +
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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
----------------------------------------------------------
293A MET* 4.4 6.4 - - + +
295A PHE* 3.3 10.0 - - + +
296A ASN* 2.7 42.2 + - - +
297A TYR* 3.0 23.8 + - - +
298A HIS* 2.8 24.8 + - + +
300A HIS* 1.3 78.1 - - - +
302A VAL* 1.3 60.6 + - - +
304A GLU* 4.3 5.7 - - - +
305A GLU* 3.3 26.9 + - - +
40B LYS* 6.1 0.5 - - - -
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Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ILE* 5.3 1.1 - - + -
293A MET* 3.4 51.6 - - + +
295A PHE* 3.6 26.5 - - + -
299A TYR 2.8 8.3 + - - +
301A GLU* 1.3 76.1 - - - +
303A MET* 1.3 57.9 + - - +
305A GLU* 2.8 21.7 + - - +
306A ILE* 2.9 28.3 + - + +
416A TYR* 4.1 0.9 - - - +
467A ALA* 3.6 31.2 - - + +
468A GLY* 3.9 3.8 - - - +
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Residues in contact with MET 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A TYR 2.9 14.2 + - - +
300A HIS* 3.5 33.0 - - + -
302A VAL* 1.3 76.0 - - - +
304A GLU* 1.3 67.1 + - + +
306A ILE* 3.4 6.4 + - - +
307A ALA* 3.0 29.2 + - - +
345A ARG* 3.4 30.3 - - + -
390A ILE* 3.8 26.9 - - + -
392A ASP* 4.0 14.4 - - - +
416A TYR* 4.0 36.4 + - + -
418A MET* 3.7 12.4 - - + +
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Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A HIS* 2.9 37.6 + - - +
301A GLU* 4.3 5.3 - - - +
303A MET* 1.3 84.5 - - + +
305A GLU* 1.3 60.3 + - + +
307A ALA* 3.8 5.8 - - - +
308A ASP* 2.9 31.5 + - - +
390A ILE* 5.9 1.6 - - + -
40B LYS* 4.5 6.9 + - - -
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Residues in contact with GLU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU* 6.3 0.7 - - + -
213A LYS* 2.9 53.2 + - + +
215A PHE* 4.9 6.3 - - + -
264A LYS* 5.3 2.3 + - - -
291A ILE* 5.9 0.9 - - + -
293A MET* 4.0 29.6 - - + +
301A GLU 3.3 16.1 + - - +
302A VAL 2.8 12.0 + - - +
304A GLU* 1.3 73.8 - - + +
306A ILE* 1.3 58.1 + - + +
308A ASP* 3.2 5.8 + - - +
309A THR* 2.8 34.0 + - - +
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Residues in contact with ILE 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ILE* 4.0 32.3 - - + +
302A VAL* 2.9 23.5 + - + +
303A MET 3.6 7.0 - - - +
305A GLU* 1.3 76.2 - - + +
307A ALA* 1.3 63.7 + - - +
309A THR* 3.0 8.9 + - - -
310A MET* 3.0 26.1 + - + +
416A TYR* 4.1 11.4 - - + +
418A MET* 3.6 14.6 - - + -
426A LEU* 3.5 26.7 - - + -
468A GLY* 3.8 36.6 - - - +
469A GLY* 4.1 7.2 - - - +
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Residues in contact with ALA 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 MET 3.0 16.4 + - - +
304A GLU* 3.8 6.1 - - - +
305A GLU 3.4 0.2 - - - -
306A ILE* 1.3 78.6 - - - +
308A ASP* 1.3 59.8 + - - +
310A MET* 3.2 4.5 + - - +
311A VAL* 2.9 30.7 + - - +
343A THR* 3.5 24.1 + - + +
388A PHE* 4.1 9.3 - - + -
390A ILE* 3.9 20.6 - - + -
418A MET* 4.4 5.8 - - + -
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Residues in contact with ASP 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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213A LYS* 2.7 32.0 + - - +
304A GLU 2.9 18.7 + - - +
305A GLU* 3.6 6.3 - - - +
307A ALA* 1.3 77.1 - - - +
309A THR* 1.3 57.7 + - - +
311A VAL* 3.3 10.8 + - - +
312A GLN* 2.9 47.1 + - - +
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Residues in contact with THR 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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206A PHE* 4.2 13.0 - - + +
209A THR* 4.0 24.2 - - + -
210A LEU* 3.9 28.3 - - + +
213A LYS* 3.5 15.2 - - - +
291A ILE* 4.8 4.0 - - + -
305A GLU 2.8 15.5 + - - -
306A ILE* 3.0 11.4 + - - -
308A ASP* 1.3 75.1 - - - +
310A MET* 1.3 65.4 + - - +
312A GLN* 3.2 3.1 + - - +
313A ILE* 3.1 33.0 + - + +
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Residues in contact with MET 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A PHE* 5.7 3.1 - - - -
306A ILE* 3.0 23.5 + - + +
307A ALA* 3.2 7.6 + - - +
309A THR* 1.3 77.0 - - - +
311A VAL* 1.3 57.0 + - - +
313A ILE* 3.1 21.0 + - + +
314A PHE* 3.0 61.1 + - + -
388A PHE* 3.6 28.7 - - + -
418A MET* 5.0 1.6 - - - -
425A ILE* 4.0 19.1 - - + -
426A LEU* 5.7 0.9 - - + -
471A ILE* 4.1 29.6 - - + -
476A VAL* 4.3 15.7 - - + -
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Residues in contact with VAL 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 ALA 2.9 18.1 + - - +
308A ASP* 3.5 13.2 - - - +
309A THR 3.2 0.2 - - - -
310A MET* 1.3 77.1 - - - +
312A GLN* 1.3 66.1 + - - +
314A PHE* 3.8 7.1 - - + +
315A LYS* 2.9 35.1 + - + +
339A PHE* 4.1 22.9 - - + -
340A LEU 4.2 12.6 - - - +
341A GLU* 4.3 16.8 - - + +
342A PRO* 6.0 0.9 - - + -
343A THR* 3.6 19.1 - - - +
388A PHE* 4.5 10.1 - - + -
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Residues in contact with GLN 312 (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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205A LEU* 4.2 6.7 - - + +
209A THR* 3.5 35.0 - - + +
308A ASP* 2.9 38.6 + - - +
309A THR 3.2 5.1 + - - +
311A VAL* 1.3 82.5 - - - +
313A ILE* 1.3 58.6 - - - +
315A LYS* 3.6 29.4 + - - +
316A GLY* 2.9 27.0 + - - -
341A GLU* 5.5 0.5 - - - +
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Residues in contact with ILE 313 (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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202A ILE* 4.1 31.2 - - + +
205A LEU* 3.7 12.3 - - + +
206A PHE* 3.8 51.1 - - + +
309A THR* 3.1 22.0 + - + +
310A MET* 3.1 25.3 + - + +
312A GLN* 1.3 76.6 - - - +
314A PHE* 1.3 65.7 + - + +
316A GLY* 3.2 1.9 + - - -
317A LEU* 2.9 48.5 + - + +
471A ILE* 5.3 1.8 - - + -
476A VAL* 5.7 2.0 - - + -
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Residues in contact with PHE 314 (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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310A MET* 3.0 52.5 + - + -
311A VAL* 3.4 8.0 + - - +
313A ILE* 1.3 80.0 - - + +
315A LYS* 1.3 63.6 + - - +
317A LEU* 3.3 1.9 + - + +
318A GLN* 3.1 28.1 + - - +
337A PHE* 3.6 26.5 - + - -
339A PHE* 3.6 31.0 - + + -
388A PHE* 3.7 25.6 - + - -
420A MET* 3.6 32.5 - - + -
476A VAL* 4.9 3.6 - - + -
480A PHE* 3.7 26.9 - + + -
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Residues in contact with LYS 315 (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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311A VAL* 2.9 22.8 + - + +
312A GLN* 3.6 31.5 + - - +
314A PHE* 1.3 75.8 - - - +
316A GLY* 1.3 56.9 + - - +
318A GLN* 3.1 7.5 + - - +
319A GLU* 2.9 49.3 + - - +
339A PHE* 3.9 21.3 - - + -
341A GLU* 3.4 34.3 - - - +
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Residues in contact with GLY 316 (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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205A LEU* 3.8 21.8 - - - -
312A GLN 2.9 20.8 + - - -
313A ILE 3.6 1.1 - - - -
315A LYS* 1.3 72.8 - - - +
317A LEU* 1.3 56.8 + - - +
319A GLU* 4.5 6.3 - - - -
320A ARG* 2.8 43.0 + - - +
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Residues in contact with LEU 317 (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 LEU* 3.9 28.9 - - + +
202A ILE* 4.0 29.2 - - + +
205A LEU* 3.7 16.4 - - + -
313A ILE* 2.9 26.2 + - + +
314A PHE 3.7 4.3 - - - +
316A GLY* 1.3 75.9 - - - +
318A GLN* 1.3 59.6 + - - +
321A PHE* 2.9 47.4 + - + +
325A ILE* 3.4 5.9 - - + +
480A PHE* 3.5 43.7 - - + -
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Residues in contact with GLN 318 (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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314A PHE 3.1 14.6 + - - +
315A LYS* 3.8 3.9 - - - +
317A LEU* 1.3 76.2 - - - +
319A GLU* 1.3 61.1 + - + +
321A PHE 4.7 0.2 - - - -
322A GLN* 3.1 32.9 - - - +
325A ILE* 4.2 5.8 - - + -
336A PRO* 4.7 5.4 - - - +
337A PHE* 2.9 36.7 + - - +
339A PHE* 3.3 30.3 - - - -
480A PHE* 3.9 16.0 - - + -
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Residues in contact with GLU 319 (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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315A LYS* 2.9 38.9 + - - +
316A GLY* 3.9 6.1 - - - +
318A GLN* 1.3 80.6 - - + +
320A ARG* 1.3 65.8 + - + +
322A GLN* 4.9 4.8 + - - +
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Residues in contact with ARG 320 (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 HIS* 3.8 24.5 + - - -
205A LEU* 3.9 17.6 - - - +
208A GLU* 3.4 27.9 + - - -
316A GLY* 2.8 24.3 + - - +
319A GLU* 1.3 82.5 + - + +
321A PHE* 1.3 80.7 + - + +
322A GLN 3.6 2.0 + - - -
324A GLU* 4.1 3.5 - - - +
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Residues in contact with PHE 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ARG* 3.7 19.7 - - + -
198A LEU* 4.0 18.8 - - + -
201A GLY* 3.6 28.0 - - - -
204A HIS* 6.2 2.2 - - - -
205A LEU* 4.7 6.3 - - + -
316A GLY 4.2 0.4 - - - -
317A LEU* 2.9 37.4 + - + +
320A ARG* 1.3 100.2 - - + +
322A GLN* 1.3 65.8 + - - +
324A GLU* 3.1 38.7 - - + +
325A ILE* 3.0 23.0 + - - +
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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
------------------------------------------------------------
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