Contacts of the helix formed by residues 395 - 420 (chain A) in PDB entry 1K89
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 ALA 395 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LEU* 3.5 28.6 - - + +
204A VAL* 3.8 18.9 - - + +
394A THR* 1.3 73.4 - - - +
396A GLU* 1.3 70.3 + - - +
398A VAL* 3.5 1.0 + - - +
399A ASP* 3.0 32.7 + - - +
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Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A THR* 3.6 12.4 - - - +
395A ALA* 1.3 92.6 + - - +
397A GLU* 1.3 57.9 + - - +
399A ASP* 4.0 4.0 - - - +
400A SER* 2.9 33.5 + - - -
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Residues in contact with GLU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A TRP* 3.3 26.4 - - + +
394A THR* 2.7 55.2 + - - +
396A GLU* 1.3 78.5 - - + +
398A VAL* 1.3 63.5 + - - +
400A SER* 3.3 4.6 + - - -
401A LYS* 3.1 32.5 + - + +
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A SER* 3.8 16.6 - - - +
203A LEU* 3.8 18.4 - - + +
204A VAL* 3.9 15.3 - - + -
379A VAL* 4.1 14.1 - - + -
382A PHE* 3.8 23.9 - - + -
386A GLN* 4.2 2.0 - - - +
393A TRP* 4.1 28.7 - - + +
394A THR 3.1 14.1 + - - +
395A ALA* 3.9 5.6 - - - +
397A GLU* 1.3 74.7 - - - +
399A ASP* 1.3 59.7 + - - +
401A LYS* 3.2 4.8 + - - +
402A LEU* 2.8 28.6 + - + +
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Residues in contact with ASP 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 4.5 9.0 - - + +
211A TYR* 3.6 21.2 - - - -
215A TYR* 2.7 29.7 + - - -
248A LYS* 4.5 4.8 + - - -
395A ALA 3.0 19.5 + - - +
396A GLU* 4.0 4.7 - - - +
398A VAL* 1.3 78.3 - - - +
400A SER* 1.3 58.3 + - - +
402A LEU* 3.3 9.2 + - - +
403A HIS* 2.9 30.8 + - - +
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Residues in contact with SER 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A GLU 2.9 19.1 + - - -
397A GLU* 3.9 4.4 + - - -
399A ASP* 1.3 80.8 + - - +
401A LYS* 1.3 55.0 + - - +
403A HIS* 3.5 5.6 + - - +
404A GLN* 2.5 53.6 + - - +
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Residues in contact with LYS 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A PHE* 3.5 25.1 - - + -
393A TRP* 3.9 36.4 - - + -
397A GLU* 3.1 16.9 + - + +
398A VAL 3.7 4.0 - - - +
400A SER* 1.3 79.8 + - - +
402A LEU* 1.3 68.5 + - - +
404A GLN* 3.2 14.3 + - - +
405A VAL* 3.0 30.8 + - + +
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Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 4.5 11.4 - - + -
208A ALA* 4.1 24.0 - - - +
211A TYR* 4.3 9.6 - - + -
212A GLY* 4.3 1.8 - - - -
215A TYR* 4.0 21.3 - - + -
375A GLY* 3.8 26.0 - - - +
378A LEU* 4.0 11.0 - - + -
379A VAL* 4.6 6.3 - - + -
382A PHE* 3.9 11.5 - - + -
398A VAL 2.8 14.3 + - - +
399A ASP* 3.3 13.7 - - - +
401A LYS* 1.3 78.3 - - - +
403A HIS* 1.3 64.7 + - - +
405A VAL* 3.9 1.0 - - - +
406A MET* 2.9 44.8 + - + +
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Residues in contact with HIS 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A TYR* 3.3 49.7 + + + +
218A GLU* 2.9 32.8 + - - -
252A LEU* 6.0 1.6 - - + -
399A ASP* 2.9 19.2 + - - +
400A SER* 3.7 7.4 - - - +
401A LYS 3.2 0.2 - - - -
402A LEU* 1.3 80.2 - - - +
404A GLN* 1.3 63.3 + - - +
406A MET* 3.5 1.6 + - - +
407A THR* 3.2 27.5 + - - -
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Residues in contact with GLN 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A SER* 2.5 46.9 + - - +
401A LYS* 3.4 19.6 - - - +
403A HIS* 1.3 76.2 - - - +
405A VAL* 1.3 63.6 + - + +
407A THR* 3.4 7.2 + - - -
408A ASP* 3.1 30.7 + - - +
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Residues in contact with VAL 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A THR 3.4 23.6 - - - +
118A THR* 4.6 11.9 - - + +
119A LEU* 6.2 1.6 - - + -
378A LEU* 3.2 35.7 - - + -
382A PHE* 5.0 4.9 - - + -
401A LYS* 3.0 19.6 + - + +
404A GLN* 1.3 78.6 - - + +
406A MET* 1.3 65.4 + - - +
408A ASP* 2.9 10.7 + - + +
409A ILE* 2.8 32.3 + - + +
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Residues in contact with MET 406 (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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212A GLY* 3.6 25.1 - - - +
215A TYR* 3.8 20.6 - - + -
216A TYR* 4.2 22.1 - - + +
371A ALA 3.4 26.0 - - - +
372A VAL 3.7 12.8 - - - +
374A ALA 4.3 0.2 - - - +
375A GLY* 3.8 22.0 - - - +
378A LEU* 3.9 14.6 - - - -
402A LEU* 2.9 33.5 + - + +
403A HIS 4.0 0.2 - - - +
404A GLN 3.4 0.2 - - - -
405A VAL* 1.3 76.1 - - - +
407A THR* 1.3 61.8 + - - +
409A ILE* 3.3 14.8 + - + +
410A HIS* 3.2 21.1 + - - +
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Residues in contact with THR 407 (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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215A TYR 4.4 7.3 + - - -
218A GLU* 4.9 2.8 + - - +
219A ALA* 4.1 18.6 - - + +
403A HIS* 3.2 24.7 + - - -
404A GLN* 3.5 11.1 - - - +
405A VAL 3.1 0.2 - - - -
406A MET* 1.3 78.0 - - - +
408A ASP* 1.3 63.5 + - - +
410A HIS* 3.2 4.0 + - - +
411A ASP* 2.9 44.7 + - - +
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Residues in contact with ASP 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 5.6 8.1 - - + -
404A GLN* 3.1 20.4 + - - +
405A VAL* 2.9 14.3 + - + +
407A THR* 1.3 86.8 - - - +
409A ILE* 1.3 57.0 + - + +
411A ASP* 4.3 8.8 - - - +
412A GLY* 2.8 28.8 + - - -
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Residues in contact with ILE 409 (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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116A LEU* 3.6 36.7 - - + +
117A THR* 4.3 4.5 - - - -
118A THR* 5.7 1.1 - - + -
216A TYR* 4.1 6.1 - - + -
371A ALA* 3.8 34.1 - - + +
374A ALA* 3.8 28.0 - - + -
378A LEU* 4.8 0.4 - - + -
405A VAL* 2.8 32.4 + - + +
406A MET* 3.5 20.2 - - - +
407A THR 3.3 0.2 - - - -
408A ASP* 1.3 71.4 - - + +
410A HIS* 1.3 59.2 + - - +
412A GLY* 4.2 0.4 - - - -
413A SER* 2.5 36.1 + - - +
433A VAL* 6.1 1.0 - - - +
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Residues in contact with HIS 410 (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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216A TYR* 3.7 22.9 - + + -
219A ALA* 3.6 32.0 - - + +
220A VAL* 3.4 27.1 - - + +
223A HIS* 3.9 14.8 - + + -
406A MET 3.2 6.3 + - - +
407A THR 3.5 6.7 - - - +
409A ILE* 1.3 82.8 - - - +
411A ASP* 1.3 74.0 + - - +
413A SER* 3.1 5.4 + - - -
414A ALA* 3.0 29.5 + - + +
424A TYR* 2.6 37.0 + + - -
426A LEU* 3.9 12.8 - - + +
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Residues in contact with ASP 411 (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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219A ALA* 4.4 3.8 - - - +
222A LYS* 5.8 2.4 + - - -
407A THR* 2.9 36.2 + - - +
408A ASP* 3.9 10.6 - - - +
410A HIS* 1.3 93.4 + - - +
412A GLY* 1.3 66.3 + - - +
414A ALA* 3.4 4.1 + - - +
415A ALA* 3.0 24.4 + - - +
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Residues in contact with GLY 412 (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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408A ASP 2.8 20.1 + - - -
409A ILE 4.2 0.2 - - - -
411A ASP* 1.3 74.4 - - - +
413A SER* 1.3 59.0 + - - +
415A ALA* 3.3 5.6 + - - +
416A ALA* 2.9 30.5 + - - +
433A VAL* 3.5 13.4 - - - +
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Residues in contact with SER 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 4.8 3.5 - - - +
216A TYR* 5.1 2.0 - - - -
371A ALA* 4.9 1.9 - - - +
409A ILE* 2.5 29.0 + - - +
410A HIS* 3.1 6.8 + - - -
412A GLY* 1.3 77.4 - - - +
414A ALA* 1.3 62.4 + - - +
416A ALA* 3.3 0.9 + - - +
417A ALA* 3.0 20.3 + - - +
426A LEU* 4.2 15.5 - - - -
429A GLY* 3.4 24.3 + - - -
430A ALA* 4.0 17.0 - - - +
433A VAL* 4.0 12.5 - - - +
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Residues in contact with ALA 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A HIS* 4.6 7.9 - - + +
410A HIS* 3.0 20.9 + - + +
411A ASP* 3.9 5.4 - - - +
413A SER* 1.3 77.0 - - - +
415A ALA* 1.3 64.6 + - - +
417A ALA* 3.2 5.7 + - - +
418A GLU* 2.9 26.9 + - - +
423A GLY 4.5 1.2 - - - +
424A TYR* 4.0 31.9 - - + -
426A LEU* 4.1 6.5 - - + +
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Residues in contact with ALA 415 (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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411A ASP 3.0 18.3 + - - +
412A GLY* 3.7 6.7 - - - +
413A SER 3.2 0.2 - - - -
414A ALA* 1.3 78.5 - - - +
416A ALA* 1.3 63.6 + - - +
418A GLU* 3.4 8.3 + - - +
419A ARG* 3.0 24.1 + - - +
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Residues in contact with ALA 416 (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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412A GLY 2.9 17.6 + - - +
413A SER 3.7 2.9 - - - +
414A ALA 3.2 0.2 - - - -
415A ALA* 1.3 74.8 - - - +
417A ALA* 1.3 68.3 + - - +
419A ARG* 3.2 14.1 + - - +
420A TYR* 3.3 21.9 + - + -
429A GLY 4.4 2.2 - - - +
432A ILE* 3.9 20.6 - - + +
433A VAL* 3.5 21.5 - - + -
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Residues in contact with ALA 417 (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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413A SER 3.0 14.5 + - - +
414A ALA* 3.7 4.0 - - - +
416A ALA* 1.3 74.7 - - - +
418A GLU* 1.3 63.3 + - - +
420A TYR* 3.1 7.1 + - - -
422A LEU* 2.8 38.0 + - + +
423A GLY 3.3 18.2 - - - +
425A ASN* 3.4 32.8 - - + +
429A GLY* 4.1 7.5 - - - +
432A ILE* 5.0 1.1 - - - -
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Residues in contact with GLU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ALA 2.9 18.3 + - - +
415A ALA* 3.6 7.6 - - - +
417A ALA* 1.3 77.4 - - - +
419A ARG* 1.3 61.1 + - - +
421A GLY* 2.8 22.7 + - - -
423A GLY* 3.5 18.7 + - - +
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Residues in contact with ARG 419 (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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39A HIS* 5.5 4.0 + - - -
415A ALA 3.0 18.0 + - - +
416A ALA* 3.2 4.0 + - - +
418A GLU* 1.3 80.7 + - - +
420A TYR* 1.3 103.6 + - + +
421A GLY 3.0 2.4 + - - -
436A GLN* 6.4 0.2 - - - -
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Residues in contact with TYR 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PRO* 3.9 46.2 - - + +
35A VAL* 3.7 34.7 - - + +
38A ALA* 4.4 10.6 - - + +
39A HIS* 4.4 10.2 + - - -
416A ALA* 3.3 18.8 + - + +
417A ALA 3.1 6.2 + - - +
419A ARG* 1.3 117.3 + - + +
421A GLY* 1.3 62.5 + - - +
422A LEU* 3.4 17.4 + - + +
432A ILE* 4.3 15.0 - - + -
436A GLN* 4.6 6.1 + - + +
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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