Contacts of the helix formed by residues 431 - 457 (chain A) in PDB entry 5DSG
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 PRO 431 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A SER 4.6 4.2 - - - +
429A CYS 3.6 9.6 - - - +
430A ILE* 1.3 88.9 - - + +
432A ASP* 1.3 66.4 + - - +
433A THR* 3.2 7.2 - - - +
434A VAL* 3.2 37.9 + - + +
435A TRP* 3.2 10.9 + - - -
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Residues in contact with ASP 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ILE 5.2 0.2 - - - +
431A PRO* 1.3 74.2 - - - +
433A THR* 1.3 58.3 + - - +
435A TRP* 3.3 16.4 + - - +
436A SER* 2.9 34.9 + - - +
1205A P6G 5.5 4.9 - - - +
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Residues in contact with THR 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PRO* 3.2 6.5 - - - +
432A ASP* 1.3 78.1 - - - +
434A VAL* 1.3 60.8 + - + +
436A SER* 3.2 7.3 + - - -
437A ILE* 2.9 50.9 + - + +
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Residues in contact with VAL 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A MET* 3.5 30.1 - - + +
430A ILE* 3.8 13.9 - - + -
431A PRO* 3.2 31.9 + - + +
433A THR* 1.3 75.4 - - + +
435A TRP* 1.3 65.4 + - - +
437A ILE* 3.3 11.1 + - + +
438A GLY 2.9 19.8 + - - -
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Residues in contact with TRP 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A TYR* 3.7 34.8 - + - -
419A MET* 3.4 46.0 - - + -
420A VAL* 3.8 9.6 - - + -
423A ASN* 3.5 31.3 - - + +
427A GLN 4.9 0.8 + - - -
430A ILE* 3.1 34.6 + - + +
431A PRO 3.2 25.6 + - - -
432A ASP* 3.4 18.4 - - - +
434A VAL* 1.3 78.7 - - - +
436A SER* 1.3 57.2 + - - +
438A GLY* 3.3 1.6 + - - -
439A TYR* 2.9 30.1 + - - +
1205A P6G 3.6 50.2 + - - +
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Residues in contact with SER 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 3.1 26.9 + - - -
93A ILE* 5.1 11.5 - - - +
432A ASP* 2.9 20.4 + - - +
433A THR* 3.5 7.3 - - - -
435A TRP* 1.3 72.3 - - - +
437A ILE* 1.3 61.1 + - - +
440A TRP* 2.9 31.2 + - - +
1205A P6G 4.3 6.3 - - - -
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Residues in contact with ILE 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A MET* 6.1 0.9 - - + -
433A THR* 2.9 38.5 + - + +
434A VAL* 3.6 10.8 - - + +
436A SER* 1.3 76.0 - - - +
438A GLY* 1.3 58.6 + - - +
440A TRP* 3.5 6.5 + - - +
441A LEU* 2.9 32.3 + - + +
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Residues in contact with GLY 438 (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 THR 4.8 0.3 - - - +
415A PRO* 5.3 0.4 - - - -
416A TYR* 4.0 13.5 - - - +
419A MET* 3.9 19.0 - - - +
434A VAL 2.9 14.7 + - - -
435A TRP 3.7 2.5 - - - -
437A ILE* 1.3 75.3 - - - +
439A TYR* 1.3 65.2 + - - +
441A LEU* 2.9 20.9 + - - +
442A CYS* 3.0 17.2 + - - -
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Residues in contact with TYR 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 3.7 32.3 - + - +
108A TRP* 4.4 3.9 - + - -
109A LEU* 4.8 1.6 - - - +
112A ASP* 2.8 18.8 + - - +
113A TYR* 3.7 21.4 - - - -
416A TYR* 3.6 22.6 - + + -
435A TRP 2.9 17.9 + - - +
438A GLY* 1.3 75.3 - - - +
440A TRP* 1.3 62.8 + - - +
442A CYS* 3.4 6.5 + - - +
443A TYR* 3.2 27.2 + + - -
1201A 0HK 3.4 49.1 - - + -
1205A P6G 3.7 42.5 - - - -
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Residues in contact with TRP 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 5.7 1.2 - - - +
39A THR* 3.5 46.1 - - + +
42A LEU* 3.9 27.8 - - + +
86A MET* 3.5 55.6 - - + -
89A TYR* 3.6 21.3 - + + -
90A THR* 3.6 8.7 - - + -
93A ILE* 5.0 5.6 - - + -
436A SER 2.9 17.9 + - - +
437A ILE* 3.9 6.1 - - - +
439A TYR* 1.3 75.2 - - - +
441A LEU* 1.3 62.1 + - - +
443A TYR* 3.0 43.7 + + + +
444A VAL* 3.6 12.6 - - + +
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Residues in contact with LEU 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A LEU 4.8 1.8 - - - +
412A THR* 3.5 31.6 - - + +
415A PRO* 3.8 31.9 - - + -
437A ILE* 2.9 25.7 + - + +
438A GLY* 2.9 10.7 + - - +
440A TRP* 1.3 77.6 - - - +
442A CYS* 1.3 61.0 + - - +
444A VAL* 3.2 32.6 + - + +
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Residues in contact with CYS 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 6.0 1.4 - - - +
412A THR 3.9 1.6 - - - -
413A TRP* 2.9 55.3 + - + +
416A TYR* 3.7 23.3 - - - -
438A GLY 3.0 17.2 + - - -
439A TYR 3.5 10.1 - - - +
440A TRP 3.2 0.2 - - - -
441A LEU* 1.3 77.8 - - - +
443A TYR* 1.3 61.8 + - - +
444A VAL 3.5 0.2 + - - -
445A ASN* 3.8 5.9 + - - +
446A SER* 5.3 1.0 + - - -
1201A 0HK 3.6 38.8 - - + -
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Residues in contact with TYR 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 3.6 19.6 - - + +
85A SER* 3.6 23.5 - - - -
86A MET* 3.6 26.3 - - + +
89A TYR* 3.9 26.7 - + + -
108A TRP* 3.8 7.4 - - - -
112A ASP* 2.3 30.1 + - - -
439A TYR* 3.2 16.3 - + - -
440A TRP* 3.0 42.6 + + + +
442A CYS* 1.3 75.1 - - - +
444A VAL* 1.3 63.9 + - + +
445A ASN 3.0 5.1 + - - -
446A SER* 3.0 23.1 + - - -
1201A 0HK 3.6 27.6 - - - -
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Residues in contact with VAL 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 5.1 16.4 - - + -
86A MET* 4.7 2.2 - - + -
412A THR* 4.4 6.3 - - + -
440A TRP* 3.6 25.6 - - + +
441A LEU* 3.2 31.8 + - + +
443A TYR* 1.3 76.3 - - + +
445A ASN* 1.3 57.7 + - - +
447A THR* 2.9 31.5 + - + +
448A ILE* 2.9 28.1 + - + +
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Residues in contact with ASN 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 6.0 1.0 - - - +
78A ASP* 4.6 3.1 - - - +
119A SER* 6.0 1.9 - - - -
123A LEU* 5.6 1.4 - - - +
405A ILE* 3.9 2.6 + - - +
408A ALA* 3.4 13.1 - - - +
409A PHE* 3.1 44.2 - - - +
412A THR* 3.3 24.8 - - - +
413A TRP* 3.9 8.6 + - - +
442A CYS 3.8 11.6 + - - +
443A TYR 3.0 0.2 + - - -
444A VAL* 1.3 77.8 - - - +
446A SER* 1.3 58.2 + - - +
448A ILE* 3.0 4.9 + - - +
449A ASN* 2.9 53.2 + - - -
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Residues in contact with SER 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR* 3.8 7.2 - - - -
50A ASN* 3.2 22.7 + - - -
78A ASP* 2.9 48.7 + - - +
81A ILE* 3.4 27.0 - - - +
86A MET* 5.0 0.2 - - - -
442A CYS 5.3 0.5 + - - -
443A TYR* 3.0 13.7 + - - -
445A ASN* 1.3 79.6 + - - +
447A THR* 1.3 57.1 + - - +
450A PRO* 3.3 11.4 - - - +
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Residues in contact with THR 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.8 20.5 + - + +
45A VAL* 3.7 29.1 - - + +
46A THR* 2.3 35.3 + - - +
86A MET* 3.4 14.6 - - - +
444A VAL* 2.9 18.8 + - + +
446A SER* 1.3 76.7 - - - +
448A ILE* 1.3 65.1 + - + +
450A PRO* 3.3 11.1 - - - +
451A ALA* 4.2 7.1 + - - +
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Residues in contact with ILE 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ALA* 3.7 20.9 - - + -
412A THR* 3.7 29.2 - - + -
444A VAL* 2.9 27.5 + - + +
445A ASN* 3.0 6.3 + - - +
447A THR* 1.3 78.7 - - + +
449A ASN* 1.3 65.9 + - - +
451A ALA* 3.0 12.6 + - + +
452A CYS* 3.0 36.5 + - - -
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Residues in contact with ASN 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASN* 5.1 0.2 - - - +
74A LEU* 4.2 8.6 - - - +
78A ASP* 2.6 35.4 + - - +
405A ILE* 3.3 43.9 - - + +
408A ALA* 4.4 1.7 - - - +
445A ASN* 2.9 37.9 + - - +
446A SER 4.3 0.2 - - - +
448A ILE* 1.3 75.4 - - - +
450A PRO* 1.4 69.1 - - + +
452A CYS* 3.0 6.8 + - - +
453A TYR* 2.9 34.4 + - + +
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Residues in contact with PRO 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL 5.6 0.7 - - - +
46A THR 4.8 0.7 - - - +
49A GLY* 3.8 16.2 - - - +
50A ASN* 3.6 36.1 - - - +
53A VAL* 3.8 13.2 - - + -
446A SER 3.3 15.7 - - - +
447A THR* 3.3 12.8 - - - +
449A ASN* 1.4 92.2 - - + +
451A ALA* 1.3 55.5 + - - +
453A TYR* 3.1 15.8 + - + +
454A ALA* 2.9 27.5 + - - +
464A PHE* 4.0 6.1 - - + -
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Residues in contact with ALA 451 (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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447A THR 4.2 5.1 + - - +
448A ILE* 3.0 16.0 + - + +
450A PRO* 1.3 79.5 - - - +
452A CYS* 1.3 58.5 + - - +
454A ALA* 3.2 7.3 + - - +
455A LEU* 2.9 32.7 + - - +
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Residues in contact with CYS 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A THR* 4.3 3.4 - - - +
404A ALA* 4.0 34.3 - - + -
405A ILE* 3.6 17.5 - - + -
408A ALA* 4.6 1.6 - - - -
448A ILE* 3.0 38.7 + - - -
449A ASN* 3.2 8.1 - - - +
451A ALA* 1.3 76.4 - - - +
453A TYR* 1.3 59.8 + - - +
455A LEU* 4.5 3.6 - - - +
456A CYS* 2.9 37.6 + - - +
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Residues in contact with TYR 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASN* 5.5 1.6 - - - -
53A VAL* 3.6 30.3 - - + -
71A LEU* 3.2 62.2 + - + +
74A LEU* 4.1 13.9 - - - +
75A ALA* 5.1 4.2 + - + -
78A ASP* 5.7 0.8 + - - -
401A THR* 3.6 24.0 - - + -
405A ILE* 4.3 8.7 - - + +
449A ASN* 2.9 34.4 + - + -
450A PRO* 3.1 16.6 + - + +
452A CYS* 1.3 77.5 - - - +
454A ALA* 1.3 60.2 + - - +
457A ASN* 3.3 29.4 + - - +
460A PHE* 3.6 30.5 - + + +
464A PHE* 4.6 2.0 - - + -
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Residues in contact with ALA 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A PRO 2.9 11.8 + - - +
451A ALA* 3.8 8.1 - - - +
453A TYR* 1.3 75.5 - - - +
455A LEU* 1.3 59.3 + - - +
457A ASN 3.6 8.8 - - - +
461A LYS* 3.5 34.5 + - + +
464A PHE* 3.6 29.2 - - + -
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Residues in contact with LEU 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ARG* 5.3 0.3 + - - -
451A ALA 2.9 17.4 + - - +
452A CYS* 4.2 3.8 - - - +
454A ALA* 1.3 78.9 - - - +
456A CYS* 1.3 66.9 + - - +
457A ASN 3.3 3.9 + - - +
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Residues in contact with CYS 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A LYS* 4.0 12.8 - - - +
400A ARG* 3.5 39.2 + - - +
401A THR* 3.6 24.0 + - - +
404A ALA* 3.6 29.2 - - - -
452A CYS* 2.9 22.3 + - - +
455A LEU* 1.3 80.5 - - - +
457A ASN* 1.3 59.1 + - - +
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Residues in contact with ASN 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 5.2 2.4 - - - +
397A LYS* 4.6 16.9 - - - +
398A VAL* 5.2 3.4 - - - +
401A THR* 4.0 14.9 + - + +
453A TYR* 3.3 23.0 + - - +
454A ALA 3.6 14.0 - - - +
455A LEU 3.3 2.2 - - - -
456A CYS* 1.3 82.6 - - - +
458A ALA* 1.3 76.5 + - - +
459A THR* 2.8 24.6 + - - -
460A PHE* 3.5 30.0 - - + -
461A LYS* 3.6 6.6 + - - +
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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
------------------------------------------------------------
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