Contacts of the helix formed by residues 408 - 434 (chain A) in PDB entry 1JIH
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 SER 408 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A CYS* 4.3 0.2 - - - -
407A ASN* 1.3 79.6 - - - +
409A ILE* 1.3 61.4 + - - +
410A VAL* 2.8 32.1 - - - +
411A ASP* 3.1 11.0 + - - +
412A CYS* 3.0 29.5 + - - -
494A TYR* 3.3 24.5 - - - -
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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
----------------------------------------------------------
408A SER* 1.3 73.3 - - - +
410A VAL* 1.3 72.5 + - + +
412A CYS* 3.1 4.9 + - + +
413A ILE* 3.0 32.9 + - + +
481A VAL* 3.4 46.4 - - + +
482A THR* 3.9 17.7 - - + +
485A ASP* 4.2 12.1 - - + +
494A TYR* 3.4 18.3 + - - +
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Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A SER* 2.8 28.5 - - - +
409A ILE* 1.3 84.6 - - + +
411A ASP* 1.3 65.4 + - - +
413A ILE* 3.3 10.1 + - - +
414A SER* 2.9 38.2 + - - +
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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
----------------------------------------------------------
97A LYS* 2.6 30.2 + - - +
404A LYS 4.4 0.9 - - - +
405A SER 3.9 2.5 - - - +
406A CYS* 3.6 18.8 - - - -
407A ASN* 2.8 26.6 + - - +
408A SER* 3.1 21.2 + - - +
410A VAL* 1.3 86.9 - - - +
412A CYS* 1.3 65.4 + - - +
414A SER* 3.2 7.5 + - - -
415A TRP* 3.0 27.7 + - - -
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Residues in contact with CYS 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A CYS* 3.6 18.8 - - - -
408A SER 3.0 18.7 + - - -
409A ILE* 3.1 7.6 + - - +
411A ASP* 1.3 74.7 - - - +
413A ILE* 1.3 63.0 + - - +
415A TRP* 3.2 4.3 + - - +
416A LEU* 3.0 27.8 + - - +
447A LEU* 5.5 1.3 - - - -
481A VAL* 3.4 32.3 - - + -
493A TYR* 5.6 1.1 - - - -
494A TYR* 3.5 27.1 - - - -
496A LEU* 3.8 11.9 - - - -
499A LEU* 3.9 6.3 - - + +
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Residues in contact with ILE 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ILE* 3.0 27.8 + - + +
410A VAL* 3.6 9.6 - - - +
412A CYS* 1.3 76.6 - - - +
414A SER* 1.3 64.2 + - - +
416A LEU* 3.0 8.7 + - - +
417A GLU* 3.0 39.3 + - + +
478A ILE* 3.7 50.5 - - + -
481A VAL* 4.1 10.5 - - + -
482A THR* 5.0 1.3 - - - +
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Residues in contact with SER 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LYS* 4.1 13.4 - - - -
98A GLY* 3.1 42.2 + - - -
410A VAL* 2.9 25.7 + - - +
411A ASP* 3.2 12.8 + - - -
413A ILE* 1.3 77.0 - - - +
415A TRP* 1.3 61.4 + - - +
417A GLU* 3.5 16.5 + - - +
418A VAL* 3.6 3.6 + - - +
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Residues in contact with TRP 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE 5.7 0.2 - - - -
97A LYS* 3.8 22.4 - - + +
122A GLU 3.3 22.7 - - - -
123A ASP* 3.8 21.1 - - - -
124A HIS 3.9 2.2 - - - -
125A LYS* 4.4 16.4 - - + -
399A LYS* 3.7 33.0 - - + -
401A LEU* 3.6 21.1 - - + +
405A SER* 3.3 19.7 + - - -
406A CYS* 4.0 17.9 - - + -
411A ASP 3.0 23.5 + - - -
412A CYS 3.6 6.3 - - - +
414A SER* 1.3 73.5 - - - +
416A LEU* 1.3 61.3 + - - +
417A GLU 3.2 0.4 - - - -
418A VAL* 3.0 18.5 + - + +
419A PHE* 2.9 48.8 + + + -
499A LEU* 3.9 15.0 - - + -
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Residues in contact with LEU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A CYS 3.0 18.1 + - - +
413A ILE* 3.0 10.5 + - - +
415A TRP* 1.3 73.1 - - - +
417A GLU* 1.3 60.6 + - + +
419A PHE* 3.7 23.0 - - + +
420A CYS* 2.8 34.2 + - - +
445A ILE* 3.8 19.7 - - + -
474A LEU* 5.8 4.3 - - + +
477A GLY* 3.6 34.8 - - - +
478A ILE* 4.0 9.2 - - + +
481A VAL* 3.8 18.8 - - + -
499A LEU* 4.1 15.9 - - + -
500A SER 5.4 0.4 - - - +
501A MET* 4.2 14.6 - - + +
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Residues in contact with GLU 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLY* 3.0 29.7 - - - +
99A GLU* 4.4 9.8 - - - +
100A ASP* 4.2 9.9 - - + +
413A ILE* 3.0 34.9 + - + +
414A SER* 3.6 11.0 + - - +
415A TRP 3.2 0.2 - - - -
416A LEU* 1.3 76.6 - - + +
418A VAL* 1.3 61.8 + - - +
420A CYS* 3.9 5.1 - - - +
421A ALA* 3.1 24.1 + - - +
474A LEU* 5.9 7.2 - - + -
478A ILE* 6.0 2.2 - - + -
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Residues in contact with VAL 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 3.5 27.3 - - + -
96A LYS 3.4 22.4 - - - +
97A LYS* 4.1 3.4 - - - -
98A GLY 3.9 2.7 - - - +
99A GLU 3.3 21.1 - - - +
125A LYS* 4.0 27.4 - - + -
414A SER 3.6 13.0 + - - +
415A TRP* 3.0 17.2 + - + +
417A GLU* 1.3 75.7 - - - +
419A PHE* 1.3 66.1 + - + +
421A ALA* 3.2 5.6 + - - +
422A GLU* 3.0 21.4 + - + +
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Residues in contact with PHE 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LYS* 3.8 19.3 - - + -
397A SER* 3.4 34.0 + - - +
398A ASN 4.0 2.5 - - - -
399A LYS* 3.6 27.8 - - + -
415A TRP* 2.9 33.3 + + + -
416A LEU* 3.7 21.3 - - + +
418A VAL* 1.3 76.7 - - + +
420A CYS* 1.3 63.9 + - - +
422A GLU* 3.1 3.7 + - - +
423A LEU* 3.0 28.9 + - - +
499A LEU* 3.4 50.9 - - + -
501A MET* 4.2 15.9 - - + -
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Residues in contact with CYS 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LEU 2.8 21.3 + - - +
417A GLU* 3.9 5.6 - - - +
419A PHE* 1.3 75.2 - - - +
421A ALA* 1.3 52.5 + - - +
423A LEU* 3.6 3.5 + - - +
424A THR* 2.6 38.7 + - - -
470A SER* 3.1 40.4 - - - -
473A LEU* 3.5 25.1 - - - -
474A LEU* 3.8 11.2 - - + +
501A MET* 4.3 14.5 - - + -
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Residues in contact with ALA 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 3.7 16.1 - - + -
100A ASP* 3.5 31.6 - - + +
417A GLU 3.1 19.1 + - - +
418A VAL 3.2 4.9 + - - +
420A CYS* 1.3 76.7 - - - +
422A GLU* 1.3 64.1 + - - +
424A THR* 3.4 6.7 + - - +
425A SER* 3.0 22.9 + - - -
470A SER* 5.5 3.6 + - - -
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Residues in contact with GLU 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 4.1 20.6 - - + -
125A LYS* 2.7 36.1 + - - +
126A VAL 4.8 5.3 - - - +
127A SER* 6.2 1.1 - - - -
132A ARG* 5.6 2.2 + - - +
396A MET 4.0 0.2 - - - +
397A SER* 2.8 22.0 + - - +
418A VAL* 3.0 13.2 + - + +
419A PHE 3.1 7.8 + - - +
421A ALA* 1.3 76.5 - - - +
423A LEU* 1.3 63.7 + - - +
425A SER* 2.7 24.6 + - - +
426A ARG* 3.0 45.8 + - + +
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A MET* 3.8 38.3 - - + +
396A MET 4.0 6.1 - - - -
397A SER* 3.9 5.8 - - - -
419A PHE 3.0 15.7 + - - +
420A CYS 4.1 2.7 - - - +
422A GLU* 1.3 76.8 - - - +
424A THR* 1.3 55.7 - - - +
426A ARG* 3.3 23.3 + - - +
427A ILE* 2.9 35.7 + - - +
473A LEU* 4.7 7.0 - - + -
501A MET* 3.6 47.6 - - + +
503A ILE* 4.1 23.3 - - + -
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Residues in contact with THR 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A CYS* 2.6 24.9 + - - -
421A ALA* 3.5 8.3 - - - +
423A LEU* 1.3 74.6 - - - +
425A SER* 1.3 64.9 + - - +
427A ILE* 3.2 9.7 + - - +
428A GLN* 3.0 47.6 + - + +
467A ASN* 4.8 8.3 - - - +
469A GLN* 4.7 5.7 - - + +
470A SER* 3.8 35.1 + - - +
473A LEU* 4.9 2.9 - - - +
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Residues in contact with SER 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 5.3 3.9 - - - -
102A TRP* 6.0 1.1 - - - -
129A GLU* 3.0 36.6 + - - +
132A ARG* 5.2 0.9 + - - -
421A ALA 3.0 12.1 + - - -
422A GLU* 2.7 22.2 + - - +
424A THR* 1.3 77.3 - - - +
426A ARG* 1.3 60.7 + - - +
428A GLN* 3.2 14.6 + - - +
429A ASP* 3.0 33.1 + - - +
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Residues in contact with ARG 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ARG* 3.6 38.9 - - - +
394A SER 5.3 0.4 + - - -
395A MET* 3.7 40.0 - - - +
396A MET 2.8 30.3 + - - +
422A GLU* 3.0 41.0 + - + +
423A LEU* 3.7 14.0 - - - +
425A SER* 1.3 84.8 + - - +
427A ILE* 1.3 60.4 + - - +
429A ASP* 3.6 8.8 + - - +
430A LEU* 3.3 27.2 + - - +
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Residues in contact with ILE 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A MET* 3.4 24.0 - - + -
423A LEU* 2.9 22.0 + - + +
424A THR* 3.6 7.6 - - - +
425A SER 3.2 0.2 - - - -
426A ARG* 1.3 73.4 - - - +
428A GLN* 1.3 62.6 + - + +
429A ASP 3.1 0.2 - - - -
430A LEU* 3.2 5.8 + - - +
431A GLU* 2.9 46.1 + - + +
438A VAL* 3.6 24.9 - - + +
440A PRO* 4.2 22.4 - - + -
467A ASN* 5.1 5.8 - - - +
469A GLN* 5.0 12.1 - - + -
473A LEU* 5.2 2.7 - - + -
503A ILE* 3.7 24.2 - - + -
506A PHE* 4.6 2.2 - - + -
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Residues in contact with GLN 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ARG* 6.0 2.2 - - - +
136A ARG* 5.1 1.2 + - - +
424A THR* 3.0 35.3 + - + +
425A SER* 3.2 11.2 + - - +
427A ILE* 1.3 77.1 - - + +
429A ASP* 1.3 59.9 + - - +
431A GLU* 3.4 19.7 + - - +
432A GLN* 3.0 29.1 + - - +
467A ASN* 4.1 17.2 - - - +
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Residues in contact with ASP 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU* 2.9 21.4 - - - +
132A ARG* 2.8 40.4 - - - +
136A ARG* 3.0 34.2 + - - +
425A SER 3.0 15.2 + - - +
426A ARG 3.7 6.7 - - - +
427A ILE 3.1 0.2 - - - -
428A GLN* 1.3 77.0 - - - +
430A LEU* 1.3 60.1 + - + +
432A GLN* 3.9 0.2 - - - +
433A GLU* 2.8 52.9 + - - +
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Residues in contact with LEU 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ARG* 6.2 1.3 - - - +
392A VAL* 3.8 30.1 - - + +
395A MET* 3.8 25.8 - - + -
426A ARG 3.3 10.2 + - - +
427A ILE* 3.2 9.0 + - - +
429A ASP* 1.3 79.3 - - + +
431A GLU* 1.3 62.4 + - - +
433A GLU* 4.2 14.4 - - - +
434A TYR* 3.3 38.6 + - + +
436A LYS* 4.5 1.7 - - - +
438A VAL* 4.6 16.9 - - + +
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Residues in contact with GLU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ILE* 2.9 28.9 + - + +
428A GLN* 3.5 23.2 + - - +
430A LEU* 1.3 76.7 - - - +
432A GLN* 1.3 53.4 + - - +
435A ASN* 2.6 37.6 + - - -
436A LYS 2.9 23.3 + - - +
437A ILE* 3.5 16.8 - - + +
438A VAL* 3.0 30.9 + - + +
467A ASN* 3.3 30.5 + - - -
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Residues in contact with GLN 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ARG* 3.9 31.0 - - - +
140A LYS* 4.3 11.1 - - - -
428A GLN 3.0 16.7 + - - +
429A ASP 3.9 2.0 - - - +
431A GLU* 1.3 72.3 - - - +
433A GLU* 1.3 68.0 + - - +
434A TYR 2.8 4.0 + - - -
435A ASN* 2.9 15.4 + - - +
10B ILE* 4.5 7.4 - - - +
199B TYR* 3.0 30.8 + - - -
201B ILE* 4.8 18.2 - - - +
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Residues in contact with GLU 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ARG* 4.6 8.5 - - - +
136A ARG* 3.5 27.8 - - + +
139A LEU* 3.9 27.7 - - + +
143A LYS* 4.4 11.1 + - - -
151A ARG* 3.6 29.5 + - - +
429A ASP* 2.8 50.5 + - - +
430A LEU* 4.2 8.1 - - - +
432A GLN* 1.3 72.0 - - - +
434A TYR* 1.3 86.3 + - + +
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Residues in contact with TYR 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ARG* 3.8 39.7 + - + +
388A SER* 4.6 23.1 - - - -
389A ARG* 4.2 25.4 + - + +
430A LEU* 3.3 29.7 + - + +
432A GLN 3.0 0.4 - - - -
433A GLU* 1.3 108.8 - - + +
435A ASN* 1.3 72.7 + - - +
436A LYS* 3.4 10.3 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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