Contacts of the helix formed by residues 400 - 423 (chain A) in PDB entry 3DCU
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 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A LEU* 5.9 0.4 - - + -
312A ASP* 5.7 3.1 - - + -
315A ASP* 3.1 14.9 + - - +
398A ILE* 4.1 3.6 - - - -
399A LYS* 1.3 74.4 - - + +
401A ARG* 1.3 64.8 + - - +
402A GLU* 3.1 4.5 - - + +
403A ALA* 3.0 31.7 + - + +
404A VAL* 3.4 8.8 + - - +
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Residues in contact with ARG 401 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A PRO* 3.0 39.8 + - + +
394A ASP* 3.7 13.5 + - - +
395A ARG 2.7 31.9 + - - -
396A GLN* 3.9 6.3 - - - +
397A TYR 4.9 2.4 - - - +
398A ILE* 3.3 36.6 + - + +
399A LYS 3.2 4.5 + - - +
400A ASP* 1.3 72.9 - - - +
402A GLU* 1.3 60.9 + - - +
404A VAL* 3.3 2.5 + - - -
405A GLU* 3.2 18.9 + - - +
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Residues in contact with GLU 402 (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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400A ASP* 3.1 2.6 - - + +
401A ARG* 1.3 77.0 - - - +
403A ALA* 1.3 64.2 + - - +
405A GLU* 3.2 8.8 + - - +
406A LYS* 3.1 22.7 + - - +
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Residues in contact with ALA 403 (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 LEU* 3.7 22.4 - - + +
400A ASP* 3.0 25.4 + - + +
402A GLU* 1.3 80.1 - - - +
404A VAL* 1.3 60.8 + - - +
406A LYS* 3.6 12.2 - - - +
407A LEU* 3.2 21.0 - - - +
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Residues in contact with VAL 404 (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 LEU* 4.7 8.1 - - + -
315A ASP* 5.3 3.6 - - + +
319A LEU* 4.2 24.5 - - + -
391A LEU* 2.9 41.7 - - + +
392A SER 3.6 2.2 - - - +
393A PRO* 3.4 27.4 - - + -
398A ILE* 4.4 9.9 - - + -
400A ASP 3.7 13.0 - - - +
401A ARG* 3.3 6.0 + - - +
402A GLU 3.1 0.4 - - - -
403A ALA* 1.3 76.1 - - - +
405A GLU* 1.3 56.3 + - - +
407A LEU* 2.8 30.1 + - - +
408A GLN* 2.9 10.6 + - - +
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Residues in contact with GLU 405 (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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393A PRO* 3.3 17.6 - - + +
401A ARG 3.2 10.8 + - - +
402A GLU* 3.2 11.9 + - - +
404A VAL* 1.3 76.6 - - - +
406A LYS* 1.3 58.8 + - - +
408A GLN* 3.0 4.9 + - - -
409A GLU* 2.8 35.4 + - - +
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Residues in contact with LYS 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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402A GLU 3.1 10.2 + - - +
403A ALA* 3.6 14.1 - - - +
404A VAL 3.1 0.2 - - - -
405A GLU* 1.3 78.5 - - - +
407A LEU* 1.3 60.3 + - + +
409A GLU* 4.7 2.9 - - - +
410A PRO* 3.2 22.3 - - - +
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Residues in contact with LEU 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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306A PRO 3.6 23.7 - - - +
307A GLY* 3.9 17.5 - - - +
311A LEU* 3.2 42.2 - - + -
391A LEU* 4.0 24.0 - - + +
403A ALA 3.2 17.7 - - - +
404A VAL* 2.8 9.0 + - - +
406A LYS* 1.3 83.0 - - + +
408A GLN* 1.3 60.8 + - - +
409A GLU 3.6 0.2 - - - -
410A PRO* 3.5 12.2 - - - +
411A LEU* 3.9 15.8 - - - +
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Residues in contact with GLN 408 (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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388A ILE* 2.9 43.7 + - + +
391A LEU* 3.2 31.4 + - + +
392A SER* 3.4 13.7 + - - +
393A PRO* 3.4 14.7 - - - +
394A ASP* 5.6 0.2 + - - -
404A VAL 2.9 8.7 + - - +
405A GLU* 3.0 6.0 + - - +
407A LEU* 1.3 78.1 - - - +
409A GLU* 1.3 67.5 + - - +
411A LEU* 3.1 16.5 + - - +
412A LEU* 3.2 31.1 + - + +
437A LEU* 5.6 2.0 - - - +
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Residues in contact with GLU 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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405A GLU* 2.8 19.1 + - + +
406A LYS* 4.7 3.1 - - - +
408A GLN* 1.3 71.8 - - - +
410A PRO* 1.3 70.8 - - + +
412A LEU* 3.1 23.0 + - - +
413A ASP* 3.1 24.0 + - - +
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Residues in contact with PRO 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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249A GLN* 4.6 1.6 + - - +
252A LEU* 4.1 15.5 - - + -
406A LYS 3.2 21.8 - - - +
407A LEU* 3.5 8.7 - - - +
408A GLN 3.5 3.8 - - - -
409A GLU* 1.3 96.5 - - + +
411A LEU* 1.3 58.4 + - + +
413A ASP* 3.8 9.7 + - - +
414A VAL* 2.9 30.3 + - - +
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Residues in contact with LEU 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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252A LEU* 3.6 23.1 - - + -
256A ILE* 3.1 29.4 - - + -
305A LEU* 5.7 0.7 - - + -
306A PRO* 6.1 1.6 - - + -
384A LEU* 4.5 10.3 - - + +
387A ALA* 3.8 25.8 - - + -
388A ILE* 3.9 15.9 - - + +
391A LEU* 3.6 30.5 - - + -
407A LEU 3.9 11.7 - - - +
408A GLN* 3.1 7.5 + - - +
410A PRO* 1.3 75.5 - - + +
412A LEU* 1.3 68.2 + - - +
413A ASP 3.2 0.2 - - - -
414A VAL* 3.0 6.4 + - + +
415A LEU* 2.8 23.6 + - - +
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Residues in contact with LEU 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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388A ILE* 3.8 31.2 - - + -
408A GLN* 3.2 34.5 + - + +
409A GLU* 3.1 15.6 + - - +
411A LEU* 1.3 77.8 - - - +
413A ASP* 1.3 55.4 + - - +
415A LEU* 3.0 6.2 + - - +
416A GLN 2.7 30.7 + - - -
430A PHE* 3.4 17.2 - - + -
434A LEU* 4.1 24.7 - - + -
437A LEU* 5.2 2.2 - - + -
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Residues in contact with ASP 413 (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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249A GLN* 4.1 13.9 + - - +
409A GLU* 3.1 23.5 - - - +
410A PRO* 3.9 9.1 - - - +
411A LEU 3.2 0.4 - - - -
412A LEU* 1.3 76.9 - - - +
414A VAL* 1.3 56.6 + - - +
416A GLN* 3.5 18.3 + - - +
417A LYS* 2.5 38.6 + - - +
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Residues in contact with VAL 414 (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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245A LEU* 4.6 11.4 - - + -
249A GLN* 4.1 23.3 - - + +
252A LEU* 3.5 23.8 - - + -
253A LEU* 4.1 24.2 - - + -
384A LEU* 4.0 17.3 - - + -
410A PRO 2.9 24.2 + - - +
411A LEU* 3.0 8.2 + - - +
413A ASP* 1.3 76.7 - - - +
415A LEU* 1.3 60.9 + - - +
417A LYS* 3.4 6.4 + - - +
418A LEU* 2.8 38.6 + - + +
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Residues in contact with LEU 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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381A GLU* 4.5 16.2 - - + +
384A LEU* 3.7 27.1 - - + +
385A LEU* 4.7 7.9 - - + -
388A ILE* 3.8 22.7 - - + -
411A LEU 2.8 11.4 + - - +
412A LEU* 3.1 9.0 - - - +
414A VAL* 1.3 77.6 - - - +
416A GLN* 1.3 62.7 + - - +
418A LEU* 3.2 10.0 + - + +
419A CYS* 3.0 22.6 + - - -
430A PHE* 3.5 24.0 - - + -
433A LEU* 3.6 31.2 - - + -
434A LEU* 4.4 11.2 - - + -
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Residues in contact with GLN 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 LEU 2.7 12.7 + - - +
413A ASP* 3.0 20.1 + - - +
415A LEU* 1.3 71.7 - - - +
417A LYS* 1.3 68.1 + - - +
419A CYS* 2.8 14.3 + - + +
420A LYS* 2.9 44.4 + - + +
430A PHE* 3.4 46.4 - - + -
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Residues in contact with LYS 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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244A GLU 5.3 5.2 - - - +
245A LEU* 4.0 23.1 - - + -
249A GLN* 4.3 6.3 - - - +
413A ASP 2.5 20.1 + - - +
414A VAL* 3.6 6.3 - - - +
416A GLN* 1.3 74.5 - - - +
418A LEU* 1.3 62.2 + - + +
420A LYS* 3.2 11.2 + - - +
421A ILE* 3.1 30.9 + - + +
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Residues in contact with LEU 418 (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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245A LEU* 3.9 28.9 - - + -
253A LEU* 4.6 11.2 - - + -
380A GLU* 4.3 23.6 - - + +
381A GLU* 6.1 3.6 - - + +
384A LEU* 4.0 22.0 - - + -
414A VAL* 2.8 26.7 + - + +
415A LEU* 3.4 10.1 - - + +
416A GLN 3.1 0.4 - - - -
417A LYS* 1.3 75.2 - - - +
419A CYS* 1.3 66.2 + - - +
421A ILE* 3.5 13.6 - - + +
422A HIS* 2.9 45.4 + - + +
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Residues in contact with CYS 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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381A GLU* 4.7 2.9 - - - -
415A LEU* 3.0 19.1 + - - -
416A GLN* 2.8 15.5 + - + +
418A LEU* 1.3 71.1 - - - +
420A LYS* 1.3 57.7 + - + +
423A GLN* 2.9 41.2 + - - +
426A ASN 5.9 0.2 - - - -
427A PRO 6.1 0.2 - - - +
429A HIS* 3.6 23.1 - - + -
430A PHE* 3.6 46.2 - - + +
433A LEU* 3.9 11.2 - - - -
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Residues in contact with LYS 420 (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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416A GLN* 2.9 45.0 + - + +
417A LYS* 3.5 11.9 - - - +
419A CYS* 1.3 76.9 - - + +
421A ILE* 1.3 64.4 + - + +
423A GLN 4.8 2.2 - - - -
424A PRO* 3.7 19.9 - - - +
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Residues in contact with ILE 421 (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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244A GLU* 4.1 18.4 - - - +
245A LEU* 4.0 32.5 - - + +
417A LYS* 3.1 20.0 - - + +
418A LEU* 3.0 13.6 + - + +
420A LYS* 1.3 77.0 - - + +
422A HIS* 1.3 81.3 + - + +
423A GLN 3.2 3.1 - - - -
424A PRO* 3.0 22.0 - - - +
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Residues in contact with HIS 422 (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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378A THR* 6.4 2.7 - - + -
380A GLU* 5.3 7.9 + - - -
418A LEU* 2.9 38.9 + - + +
421A ILE* 1.3 90.8 - - + +
423A GLN* 1.3 74.6 + - + +
424A PRO* 3.4 4.3 - - - +
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Residues in contact with GLN 423 (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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375A LEU 5.5 0.5 - - - +
376A LYS 5.6 1.7 - - - +
381A GLU* 5.3 1.6 - - - +
419A CYS* 2.9 24.0 + - - +
420A LYS* 4.6 1.4 - - - +
422A HIS* 1.3 92.3 + - + +
424A PRO* 1.3 62.9 - - - +
425A GLU* 3.2 6.3 - - - +
426A ASN* 2.9 40.5 - - - +
427A PRO* 4.7 1.4 - - - +
429A HIS* 3.7 42.6 + - + +
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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