Contacts of the helix formed by residues 301 - 322 (chain E) in PDB entry 1K7L
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 ASP 301 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300E LEU* 1.3 76.4 - - - +
302E LEU* 1.3 60.8 + - - +
303E ASN* 3.8 27.8 + - - +
304E ASP* 2.7 42.0 + - + +
305E GLN* 2.9 9.7 + - - +
392E LEU* 4.5 18.8 - - + +
393E ASN* 5.6 7.6 - - + +
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Residues in contact with LEU 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298E ALA 5.5 0.7 - - - +
300E LEU 4.2 2.5 - - - +
301E ASP* 1.3 75.6 + - - +
303E ASN* 1.3 59.4 + - - +
305E GLN* 3.1 28.4 + - - +
306E VAL* 2.9 33.8 + - - +
691F HIS* 4.1 18.4 - - + +
694F LEU* 4.0 29.4 - - + +
695F GLN* 3.9 31.9 - - - +
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Residues in contact with ASN 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301E ASP* 3.1 18.0 + - - +
302E LEU* 1.3 78.0 - - - +
304E ASP* 1.3 61.1 + - - +
306E VAL* 3.7 6.1 - - - +
307E THR* 2.8 36.8 + - - +
392E LEU* 6.3 1.3 - - + -
685F GLU* 4.9 14.5 + - - +
691F HIS* 3.8 20.6 + - - -
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Residues in contact with ASP 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300E LEU* 4.2 9.7 - - + +
301E ASP* 2.7 27.6 + - - +
303E ASN* 1.3 78.9 - - - +
305E GLN* 1.3 56.9 + - - -
307E THR* 3.8 1.2 + - - -
308E LEU* 2.9 37.1 + - - +
390E GLY 4.9 0.7 - - - +
391E LEU* 3.9 7.4 - - - +
392E LEU* 2.9 31.3 + - - +
393E ASN* 3.1 28.8 + - - +
397E ILE* 3.2 26.2 - - + +
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Residues in contact with GLN 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292E LYS* 4.7 4.5 - - - +
297E PHE* 3.3 50.3 + - + +
298E ALA* 3.6 19.5 + - - +
300E LEU* 3.4 15.8 + - + +
301E ASP 2.9 12.4 + - - +
302E LEU* 3.1 38.7 - - - +
304E ASP* 1.3 79.1 - - - +
306E VAL* 1.3 63.7 + - - +
308E LEU* 3.5 2.7 - - - +
309E LEU* 3.0 26.3 + - - +
694F LEU* 3.5 28.8 + - + +
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Residues in contact with VAL 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302E LEU 2.9 19.7 + - - +
303E ASN* 3.7 6.5 - - - +
305E GLN* 1.3 76.7 - - - +
307E THR* 1.3 59.7 + - - +
309E LEU* 3.2 1.9 + - - -
310E LYS* 2.8 31.6 + - + +
685F GLU* 5.0 3.6 - - - +
687F HIS* 3.6 39.0 - - + +
690F LEU* 3.8 12.4 - - + +
691F HIS* 3.6 34.3 - - + +
694F LEU* 3.5 22.4 - - + -
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Residues in contact with THR 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303E ASN* 2.8 29.0 + - - +
304E ASP* 4.5 0.2 - - - -
306E VAL* 1.3 74.3 - - - +
308E LEU* 1.3 63.0 + - - +
310E LYS* 3.2 17.6 + - + -
311E TYR* 3.3 23.5 + - + +
388E ARG* 3.9 8.9 - - + +
389E PRO 3.1 28.4 + - - +
390E GLY* 4.6 8.1 + - - -
391E LEU* 3.5 28.2 - - + +
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Residues in contact with LEU 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297E PHE* 3.8 21.1 - - + -
300E LEU* 3.8 28.5 - - + -
304E ASP 2.9 23.0 + - - +
305E GLN 3.5 4.0 - - - +
307E THR* 1.3 77.2 - - - +
309E LEU* 1.3 61.6 + - - +
311E TYR* 4.7 0.3 - - - +
312E GLY* 3.1 22.5 + - - -
383E ILE* 3.5 29.2 - - + +
384E CYS* 4.4 9.9 - - - -
385E CYS 3.5 25.8 - - - +
388E ARG* 4.0 9.1 + - + -
391E LEU* 3.9 20.4 - - + -
397E ILE* 4.3 9.0 - - + -
400E MET* 5.8 0.2 - - - -
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Residues in contact with LEU 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284E VAL* 6.0 1.1 - - + -
287E LEU* 4.0 28.3 - - + +
288E THR* 3.9 21.3 - - + +
291E ALA* 4.3 7.4 - - + -
297E PHE* 4.0 12.8 - - + -
305E GLN 3.0 17.6 + - - +
306E VAL 3.9 2.7 - - - +
308E LEU* 1.3 76.1 - - - +
310E LYS* 1.3 58.5 + - - +
313E VAL* 2.9 44.6 + - + +
383E ILE* 4.5 13.2 - - + -
463E ILE* 5.4 0.8 - - - +
690F LEU* 4.1 19.7 - - + -
694F LEU* 3.3 34.3 - - + -
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Residues in contact with LYS 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306E VAL* 2.8 18.0 + - + +
307E THR* 3.2 9.6 + - - +
309E LEU* 1.3 80.2 - - - +
311E TYR* 1.3 89.2 + - + +
313E VAL* 4.4 3.8 - - - +
314E TYR* 5.2 1.0 + - - -
462E GLU 3.0 8.9 + - - -
463E ILE* 3.1 37.8 + - - +
465E ARG 2.7 29.0 + - - -
466E ASP* 4.5 4.2 - - - +
467E MET* 4.2 16.4 - - + +
687F HIS* 2.6 44.1 + - + +
690F LEU* 4.4 7.8 - - + +
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Residues in contact with TYR 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E THR* 3.3 32.5 + - + -
310E LYS* 1.3 102.2 - - + +
312E GLY* 1.3 63.1 + - - +
314E TYR 4.5 2.4 + - - -
315E GLU* 3.5 21.3 + - - +
388E ARG* 3.3 35.0 - - + +
389E PRO* 3.9 31.9 + - + +
437E VAL* 5.2 0.5 - - - +
466E ASP 3.9 9.2 + - - -
467E MET* 3.8 48.5 + - + +
468E TYR* 3.4 30.7 - + - -
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Residues in contact with GLY 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308E LEU 3.1 16.5 + - - -
311E TYR* 1.3 76.7 - - - +
313E VAL* 1.3 65.8 + - - +
314E TYR 3.3 2.7 - - - -
315E GLU* 3.0 5.1 + - - +
316E ALA* 3.0 24.1 + - - +
382E ILE* 3.9 12.7 - - - +
383E ILE* 4.9 7.9 - - - -
388E ARG* 3.9 15.8 - - - +
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Residues in contact with VAL 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284E VAL* 3.4 38.1 - - + +
287E LEU* 3.3 35.4 - - + +
309E LEU* 2.9 29.2 + - + +
310E LYS 4.4 1.8 - - - +
311E TYR 3.6 0.2 - - - -
312E GLY* 1.3 74.3 - - - +
314E TYR* 1.3 80.9 + - + +
316E ALA 3.4 0.5 + - - -
317E ILE* 3.0 32.8 + - + +
383E ILE* 5.2 1.9 - - - +
463E ILE* 4.0 22.2 - - + -
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Residues in contact with TYR 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280E SER* 4.2 5.2 - - - -
284E VAL* 5.6 0.2 - - + -
310E LYS 5.2 0.7 - - - +
311E TYR 4.5 2.7 + - - +
312E GLY 3.3 1.0 - - - -
313E VAL* 1.3 90.6 - - + +
315E GLU* 1.3 65.0 + - - +
317E ILE* 3.7 14.0 - - + +
318E PHE* 3.0 51.9 + + + -
437E VAL* 3.8 27.4 - - + -
440E HIS* 4.9 0.7 - + - -
460E LEU* 3.5 21.3 - - + +
463E ILE* 3.6 29.2 - - + -
464E TYR* 3.3 36.9 - + - -
467E MET* 5.2 5.2 - - + -
501E 544 2.5 43.3 + - + -
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Residues in contact with GLU 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311E TYR 3.5 9.1 + - - +
312E GLY 3.0 7.2 + - - +
314E TYR* 1.3 78.1 - - - +
316E ALA* 1.3 63.8 + - - +
318E PHE 3.6 0.2 + - - -
319E ALA* 3.1 23.7 + - - +
382E ILE* 3.5 17.5 - - + +
388E ARG* 2.7 46.2 + - - -
430E MET* 4.5 8.2 - - - +
433E LEU* 3.6 31.3 - - + +
434E ARG* 3.7 23.6 + - - +
437E VAL* 3.5 23.1 - - + +
467E MET* 5.9 0.3 - - - +
468E TYR* 5.2 1.9 + - - -
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Residues in contact with ALA 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287E LEU* 3.8 16.6 - - + -
312E GLY 3.0 15.1 + - - +
313E VAL 3.7 4.5 - - - +
315E GLU* 1.3 78.2 - - - +
317E ILE* 1.3 56.9 + - - +
319E ALA* 3.2 5.9 + - - +
320E MET* 2.8 38.6 + - + +
379E VAL* 3.9 27.4 - - + -
382E ILE* 4.1 12.9 - - + +
383E ILE* 5.1 2.7 - - + -
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Residues in contact with ILE 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279E THR* 5.9 0.7 - - + -
280E SER* 4.3 9.4 - - - -
283E THR* 3.6 36.6 - - + +
284E VAL* 4.1 21.1 - - + -
287E LEU* 4.2 2.2 - - + -
313E VAL* 3.0 23.4 + - + +
314E TYR* 3.7 28.7 - - + +
315E GLU 3.3 0.4 - - - -
316E ALA* 1.3 74.8 - - - +
318E PHE* 1.3 63.5 + - + +
320E MET* 3.1 7.5 + - - +
321E LEU* 2.6 56.2 + - + +
501E 544 4.8 12.1 - - + -
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Residues in contact with PHE 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314E TYR* 3.0 40.9 + + + +
317E ILE* 1.3 77.6 - - + +
319E ALA* 1.3 61.8 + - - +
321E LEU* 3.7 16.6 - - + +
322E SER* 3.3 22.9 + - - -
325E MET* 5.6 0.7 - - - +
358E LYS* 3.7 29.6 - - + -
361E PHE* 4.5 2.6 - - + -
433E LEU* 4.0 7.9 - - + -
436E LEU* 3.8 27.4 - - + -
437E VAL* 4.0 20.2 - - + -
440E HIS* 3.8 40.8 - + + -
501E 544 4.2 23.8 - + + -
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Residues in contact with ALA 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315E GLU 3.1 19.4 + - - +
316E ALA* 3.5 7.4 - - - +
318E PHE* 1.3 80.1 - - - +
320E MET* 1.3 62.7 + - + +
322E SER* 3.3 16.8 + - - -
323E SER* 4.2 2.1 + - - -
361E PHE* 4.4 6.5 - - - -
365E PHE* 4.3 13.1 - - + -
375E ILE* 5.5 5.0 - - + +
378E PHE* 3.9 20.2 - - + -
379E VAL* 5.3 2.2 - - + -
382E ILE* 4.5 0.4 - - + -
433E LEU* 3.7 22.3 - - + +
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Residues in contact with MET 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E TYR* 4.0 20.2 - - - +
218E PHE* 4.0 23.8 - - + -
283E THR* 4.0 21.3 - - + -
287E LEU* 3.6 28.7 - - + -
316E ALA* 2.8 31.1 + - + +
317E ILE* 3.8 2.9 - - - +
319E ALA* 1.3 74.7 - - - +
321E LEU* 1.3 66.1 + - - +
323E SER* 2.9 28.6 + - - -
324E VAL* 4.3 2.3 + - - +
375E ILE* 4.3 12.8 - - + -
379E VAL* 4.1 16.4 - - + -
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Residues in contact with LEU 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279E THR* 4.9 9.0 - - + -
317E ILE* 2.6 28.4 + - + +
318E PHE* 3.7 28.3 - - + +
319E ALA 3.3 0.2 - - - -
320E MET* 1.3 73.6 - - - +
322E SER* 1.3 61.0 + - - +
324E VAL* 3.0 30.3 + - + +
325E MET* 3.2 25.7 - - - +
330E MET* 5.2 4.3 - - - -
355E MET* 5.3 4.5 - - - -
358E LYS* 5.6 1.6 - - + -
501E 544 3.8 52.7 - - + +
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Residues in contact with SER 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318E PHE 3.3 13.0 + - - -
319E ALA 3.3 12.6 + - - -
320E MET 3.1 0.2 - - - -
321E LEU* 1.3 78.3 - - - +
323E SER* 1.3 62.5 + - - +
325E MET* 2.9 24.9 + - - +
358E LYS 5.0 0.2 + - - -
361E PHE* 3.7 12.5 - - - -
362E ALA* 3.4 26.3 - - - +
365E PHE* 4.3 9.2 - - - -
366E ASN* 3.1 31.3 + - - -
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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