Contacts of the helix formed by residues 398 - 419 (chain A) in PDB entry 3U78
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 PHE 398 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A TRP* 4.0 12.5 - + + -
261A PHE* 3.4 32.8 - + + -
262A PRO* 3.3 43.1 - - + -
264A PRO* 6.0 2.0 - - + +
396A PHE* 3.2 7.6 - - + -
397A PRO* 1.3 102.8 - - + +
399A PHE* 1.3 64.9 + - - +
400A GLU 3.1 2.2 - - - -
401A ALA* 3.2 18.5 + - + +
402A ILE* 3.3 13.3 + - - +
453A PHE* 4.7 14.4 - + - -
454A GLU* 3.1 24.2 - - - +
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Residues in contact with PHE 399 (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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250A TRP* 5.1 2.5 - + - -
286A GLY* 3.5 28.5 - - - -
370A LEU* 4.1 26.9 - - + -
378A GLN* 4.0 12.8 - - + -
379A LEU* 3.9 13.9 - - + -
382A TYR* 3.3 62.6 - + + -
393A LEU* 5.6 0.7 - - + -
396A PHE* 3.3 30.1 + + + +
397A PRO 3.4 2.7 + - - +
398A PHE* 1.3 75.9 - - - +
400A GLU* 1.3 67.9 + - - +
402A ILE* 2.9 20.6 - - - +
403A CYS* 3.1 30.9 + - - -
442A TRP* 4.1 2.0 - + - -
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Residues in contact with GLU 400 (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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382A TYR* 2.5 38.8 + - + +
386A LYS* 5.0 0.9 + - - -
398A PHE 3.1 1.4 - - - -
399A PHE* 1.3 78.2 - - - +
401A ALA* 1.3 63.8 + - - +
403A CYS* 3.1 12.5 + - - +
404A TRP* 3.0 22.9 + - - +
442A TRP* 3.5 38.5 - - + -
451A HIS* 3.0 44.4 + - - +
454A GLU* 3.6 28.4 + - + +
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Residues in contact with ALA 401 (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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255A TRP* 4.8 3.6 - - + -
261A PHE* 3.7 28.9 - - + -
398A PHE* 3.2 19.6 + - + +
400A GLU* 1.3 78.7 - - - +
402A ILE* 1.3 62.9 + - - +
404A TRP* 3.0 16.8 + - - +
405A PHE* 3.1 17.5 + - + -
454A GLU* 3.5 27.4 + - - +
456A PRO* 4.0 2.6 - - + +
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Residues in contact with ILE 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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250A TRP* 3.6 56.3 - - + +
251A VAL 5.1 0.4 - - - +
254A TYR* 4.0 11.2 - - + +
255A TRP* 3.6 35.4 - - + -
370A LEU* 4.3 4.0 - - + -
396A PHE* 4.2 12.6 - - + -
398A PHE 3.3 2.4 + - - +
399A PHE* 2.9 31.4 - - + +
401A ALA* 1.3 77.6 - - - +
403A CYS* 1.3 50.6 + - - +
405A PHE* 3.0 21.7 + - + +
406A VAL* 2.8 39.9 + - + +
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Residues in contact with CYS 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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250A TRP* 3.9 17.5 - - - -
379A LEU* 4.2 9.6 - - - -
399A PHE* 3.5 41.5 - - - -
400A GLU 3.1 12.2 + - - +
402A ILE* 1.3 83.0 - - - +
404A TRP* 1.3 61.0 + - - +
406A VAL* 3.5 7.7 + - - +
407A ALA* 3.0 23.4 + - - +
435A LEU* 3.7 20.4 - - + +
439A LEU* 4.7 2.6 - - + +
442A TRP* 4.1 16.2 - - + -
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Residues in contact with TRP 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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400A GLU* 3.0 34.0 + - - +
401A ALA 3.0 7.8 + - - +
403A CYS* 1.3 73.0 - - - +
405A PHE* 1.3 69.0 + - - +
407A ALA* 3.1 13.7 + - - +
408A LYS* 3.1 14.0 + - - +
439A LEU* 3.5 50.0 - - + -
442A TRP* 4.2 18.7 - + + -
443A MET* 4.1 19.1 - - + -
451A HIS* 5.4 0.6 + - + -
454A GLU* 4.0 5.2 + - - +
455A ILE* 3.9 27.5 - - + +
456A PRO* 3.8 27.1 - - + -
459A VAL* 3.6 15.0 - - + -
461A PRO* 3.8 34.1 - - + -
464A LEU* 3.6 21.1 - - + +
465A ILE* 4.4 1.3 - - + -
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Residues in contact with PHE 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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254A TYR* 3.6 18.2 - - - +
255A TRP* 4.7 9.2 - + - -
256A PRO* 3.3 38.6 - - + -
259A SER* 3.7 22.7 - - - -
261A PHE* 4.6 6.7 - + - -
401A ALA* 3.1 14.8 + - + -
402A ILE* 3.0 20.3 + - + +
404A TRP* 1.3 79.6 - - - +
406A VAL* 1.3 58.6 + - - +
408A LYS* 3.3 18.8 - - + +
409A ASN* 2.7 28.6 + - - +
456A PRO* 3.3 37.7 - - + -
458A ASN* 5.4 7.4 - - + -
459A VAL* 4.4 7.9 - - + -
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Residues in contact with VAL 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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250A TRP* 3.4 48.5 - - + -
254A TYR* 3.7 20.2 - - + -
372A ASN* 3.9 6.5 - - - +
402A ILE* 2.8 23.1 + - + +
403A CYS* 3.7 7.9 - - - +
404A TRP 3.1 0.2 - - - -
405A PHE* 1.3 75.2 - - - +
407A ALA* 1.3 59.0 + - - +
409A ASN* 3.4 5.6 + - - +
410A LEU* 2.8 51.8 + - + +
435A LEU* 4.0 6.3 - - + -
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Residues in contact with ALA 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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403A CYS 3.0 14.3 + - - +
404A TRP 3.1 4.7 + - - +
406A VAL* 1.3 74.2 - - - +
408A LYS* 1.3 61.4 + - - +
410A LEU* 4.4 2.0 - - - +
411A LEU* 2.9 30.7 + - - +
435A LEU* 3.5 24.0 - - + -
439A LEU* 3.9 24.2 - - + -
464A LEU* 4.0 8.0 - - + +
468A LEU* 4.1 14.6 - - + +
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Residues in contact with LYS 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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404A TRP 3.1 8.4 + - - +
405A PHE* 3.3 18.9 - - + +
407A ALA* 1.3 78.6 - - - +
409A ASN* 1.3 66.4 + - - +
411A LEU* 3.4 4.0 - - - +
412A GLU* 3.0 22.9 + - - +
458A ASN* 3.9 26.6 + - - +
459A VAL* 4.1 33.1 - - + +
460A ARG* 5.3 1.3 - - - +
464A LEU* 4.3 20.5 - - + +
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Residues in contact with ASN 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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254A TYR* 3.6 46.0 + - + +
405A PHE* 2.7 28.5 + - - +
406A VAL 3.4 4.0 + - - +
408A LYS* 1.3 81.7 - - - +
410A LEU* 1.3 66.2 + - + +
412A GLU* 3.2 9.0 + - - +
413A THR* 3.2 24.1 + - - -
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Residues in contact with LEU 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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254A TYR* 4.8 4.7 - - + +
372A ASN* 3.9 25.4 - - - +
375A ILE* 3.6 25.1 - - + -
406A VAL* 2.8 40.9 + - + +
407A ALA* 4.3 3.8 - - - +
409A ASN* 1.3 74.7 - - + +
411A LEU* 1.3 62.7 + - - +
413A THR* 3.3 9.9 + - - +
414A LEU* 3.1 27.8 + - - +
428A LEU* 3.9 22.5 - - + +
432A VAL* 4.0 22.9 - - + +
435A LEU* 3.9 11.2 - - + -
468A LEU* 6.2 0.4 - - + -
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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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407A ALA 2.9 21.1 + - - +
408A LYS* 3.4 4.7 - - + +
410A LEU* 1.3 76.1 - - - +
412A GLU* 1.3 57.4 + - - +
414A LEU* 3.0 7.5 + - - -
415A LYS* 2.8 49.3 + - - +
464A LEU* 3.9 19.5 - - + -
467A GLU* 3.6 35.7 - - + +
468A LEU* 3.9 18.2 - - + +
471A VAL* 3.9 27.4 - - + -
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Residues in contact with GLU 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 LYS 3.0 13.1 + - - +
409A ASN* 3.2 12.3 + - - +
411A LEU* 1.3 76.4 - - - +
413A THR* 1.3 61.7 + - - +
415A LYS* 3.4 24.2 + - - +
416A GLU* 2.7 53.0 + - - +
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Residues in contact with THR 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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409A ASN 3.2 12.5 + - - -
410A LEU* 3.7 12.7 - - - +
411A LEU 3.2 0.2 - - - -
412A GLU* 1.3 78.0 - - - +
414A LEU* 1.3 58.4 + - - +
416A GLU* 3.3 12.7 + - - +
417A LEU* 3.0 37.1 + - + +
428A LEU* 4.0 22.2 - - + -
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Residues in contact with LEU 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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410A LEU 3.1 14.3 + - - +
411A LEU* 3.0 9.9 + - - +
413A THR* 1.3 74.4 - - - +
415A LYS* 1.3 59.2 + - - +
417A LEU* 4.0 4.0 - - + +
418A ARG* 3.0 30.3 + - - +
424A PRO* 3.6 29.5 - - + +
428A LEU* 3.6 33.2 - - + +
429A VAL* 5.2 2.9 - - + -
432A VAL* 3.6 33.7 - - + -
471A VAL* 3.6 34.4 - - + +
472A ILE* 5.7 0.4 - - + -
475A ILE* 4.8 7.9 - - + -
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Residues in contact with LYS 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 LEU* 2.8 37.9 + - + +
412A GLU* 3.5 28.0 - - - +
413A THR 3.2 0.2 - - - -
414A LEU* 1.3 77.8 - - - +
416A GLU* 1.3 57.0 + - + +
418A ARG* 3.4 4.5 + - - +
419A GLU* 3.0 58.4 + - + +
467A GLU* 4.0 19.0 + - - +
471A VAL* 5.0 10.2 - - + +
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Residues in contact with GLU 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 GLU* 2.7 46.7 + - - +
413A THR* 3.6 11.2 + - - +
414A LEU 3.3 0.2 - - - -
415A LYS* 1.3 74.6 - - + +
417A LEU* 1.3 66.8 + - + +
419A GLU* 3.7 8.0 + - - +
420A ASP* 3.5 21.5 + - - +
422A PHE* 5.2 0.3 - - - -
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Residues in contact with LEU 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 THR* 3.0 33.5 + - + +
414A LEU* 4.0 8.1 - - + +
415A LYS 3.3 0.2 - - - -
416A GLU* 1.3 78.9 - - + +
418A ARG* 1.3 61.6 + - - +
420A ASP 3.3 5.4 + - - -
422A PHE* 3.0 62.4 + - + +
423A GLN 4.8 1.8 - - - +
424A PRO* 3.8 36.8 - - + -
425A GLN 5.2 0.7 - - - +
428A LEU* 4.7 3.4 - - + -
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Residues in contact with ARG 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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414A LEU 3.0 18.6 + - - +
415A LYS* 4.0 4.9 - - - +
417A LEU* 1.3 72.0 - - - +
419A GLU* 1.3 58.7 + - + +
420A ASP 2.9 10.8 + - - -
421A GLY* 3.1 12.9 + - - +
422A PHE 4.6 4.5 - - - -
424A PRO* 6.1 0.2 - - - +
471A VAL* 5.9 5.2 - - + -
475A ILE* 6.3 4.3 - - + -
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Residues in contact with GLU 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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415A LYS* 3.0 45.9 + - + +
416A GLU* 4.1 7.5 - - - +
417A LEU 3.3 0.4 - - - -
418A ARG* 1.3 75.9 - - + +
420A ASP* 1.3 62.5 + - - +
421A GLY 3.6 0.4 - - - -
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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