Contacts of the helix formed by residues 426 - 452 (chain C) in PDB entry 5NC5
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 426 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C GLY 3.5 4.7 - - - +
425C LEU* 1.3 89.3 - - + +
427C PRO* 1.4 76.5 - - + +
428C LYS* 3.0 7.4 + - + +
429C GLU* 3.0 13.5 + - + +
430C ALA 2.9 19.1 + - - -
499C PRO* 5.3 4.0 - - + -
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Residues in contact with PRO 427 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C VAL* 5.0 1.8 - - + -
420C MET* 3.7 23.8 - - - -
425C LEU 3.7 0.4 - - - -
426C PRO* 1.4 85.6 - - + +
428C LYS* 1.3 58.6 + - - +
430C ALA* 3.6 1.6 - - + +
431C THR* 2.7 34.2 + - - -
493C CYS 3.9 14.8 - - - +
494C ALA* 4.1 8.3 - - - +
497C LEU* 3.4 27.6 - - + +
498C LYS 4.2 0.4 - - - -
499C PRO* 4.0 30.1 - - + -
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Residues in contact with LYS 428 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 4.1 15.9 + - + +
7C ASP* 3.3 26.7 + - - +
426C PRO* 3.2 5.0 - - + +
427C PRO* 1.3 81.2 - - - +
429C GLU* 1.3 64.0 + - - +
431C THR* 3.3 3.1 + - - -
432C ARG* 3.1 38.9 + - - +
494C ALA* 4.1 31.5 + - + +
495C THR* 4.8 8.5 - - - -
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Residues in contact with GLU 429 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C LEU* 3.9 24.2 - - + +
426C PRO* 3.0 17.0 + - + +
428C LYS* 1.3 77.0 - - - +
430C ALA* 1.3 65.5 + - - +
432C ARG* 3.4 22.0 + - - +
433C LYS* 3.1 32.6 + - - +
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Residues in contact with ALA 430 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C VAL* 3.9 12.6 - - + +
419C VAL* 4.3 15.3 - - + +
420C MET* 3.4 33.4 - - + -
425C LEU* 4.2 10.9 - - + +
426C PRO 2.9 11.9 + - - +
427C PRO 3.6 3.6 - - - +
429C GLU* 1.3 78.2 - - - +
431C THR* 1.3 57.3 + - - +
433C LYS* 3.4 2.1 + - - +
434C SER* 2.8 33.7 + - - -
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Residues in contact with THR 431 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 3.7 16.8 - - + -
416C VAL* 3.6 18.2 - - + +
427C PRO 2.7 23.0 + - - -
428C LYS 3.6 4.5 - - - -
430C ALA* 1.3 74.7 - - - +
432C ARG* 1.3 56.1 + - - +
434C SER* 3.4 0.2 - - - -
435C MET* 2.8 40.0 + - + +
490C PRO* 3.5 33.7 - - + +
493C CYS* 3.6 21.0 - - + +
494C ALA* 3.7 6.9 + - - -
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Residues in contact with ARG 432 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ASN* 3.6 35.0 + - - +
6C ILE* 4.1 21.9 - - + +
7C ASP* 2.7 42.8 + - - -
428C LYS* 3.1 32.2 + - - +
429C GLU* 3.6 24.7 + - - +
430C ALA 3.4 0.2 - - - -
431C THR* 1.3 79.9 - - - +
433C LYS* 1.3 63.8 + - - +
435C MET* 3.5 3.3 + - - +
436C GLY* 3.5 12.6 + - - -
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Residues in contact with LYS 433 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C VAL* 4.3 11.4 - - + -
423C GLU* 2.9 28.6 + - - +
425C LEU* 4.2 17.0 - - + +
429C GLU* 3.1 26.1 + - - +
430C ALA* 3.8 3.8 - - - +
432C ARG* 1.3 78.7 - - - +
434C SER* 1.3 66.2 + - - +
436C GLY* 3.0 13.5 + - - -
437C GLN* 3.3 39.1 + - + +
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Residues in contact with SER 434 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C VAL* 5.0 0.9 - - - -
415C ASN* 3.0 31.3 + - - +
416C VAL* 3.2 31.8 + - - -
419C VAL* 3.8 4.6 - - - +
430C ALA 2.8 20.4 + - - -
431C THR 3.4 4.3 - - - -
433C LYS* 1.3 77.3 - - - +
435C MET* 1.3 56.4 + - - +
437C GLN* 2.7 32.9 + - - +
438C ILE* 3.3 12.1 + - - +
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Residues in contact with MET 435 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C PRO* 3.9 26.7 - - + -
6C ILE* 4.4 3.1 - - + -
412C VAL* 3.8 27.6 - - + -
431C THR* 2.8 27.1 + - + +
432C ARG* 4.1 4.5 - - - +
433C LYS 3.4 0.2 - - - -
434C SER* 1.3 74.3 - - - +
436C GLY* 1.3 61.9 + - - +
437C GLN 3.4 0.3 + - - -
438C ILE* 4.0 5.1 - - + +
439C GLN* 3.6 33.5 + - + +
442C LEU* 3.6 31.4 - - + -
485C ALA 4.0 2.5 - - - +
486C LEU* 4.0 14.4 - - + -
490C PRO* 3.6 29.4 - - + -
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Residues in contact with GLY 436 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C ARG 3.5 6.5 + - - -
433C LYS 3.0 10.5 + - - -
435C MET* 1.3 78.9 - - - +
437C GLN* 1.3 60.6 + - - +
438C ILE 3.6 0.2 + - - -
439C GLN* 4.4 8.4 + - - +
955C LYS* 4.7 11.4 + - - -
1112C D10 5.3 8.8 - - - +
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Residues in contact with GLN 437 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C ASN* 3.8 7.4 + - - +
418C ARG* 3.3 25.3 + - - -
419C VAL* 4.3 5.8 - - - +
433C LYS* 3.5 45.1 - - + +
434C SER 2.7 16.8 + - - +
436C GLY* 1.3 74.2 - - - +
438C ILE* 1.3 63.1 + - + +
439C GLN 3.8 0.2 - - - -
440C GLY 5.3 0.7 + - - -
947C GLU* 5.5 3.5 - - - +
948C PHE* 4.6 25.3 - - + -
951C ASP* 4.2 13.9 - - - +
955C LYS* 5.8 2.0 + - - +
956C GLU* 5.9 0.8 + - - -
971C ARG* 4.6 1.9 + - - -
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Residues in contact with ILE 438 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C VAL* 4.2 17.3 - - + +
412C VAL* 3.4 43.7 - - + -
415C ASN* 3.7 34.1 - - + +
434C SER* 3.7 13.0 - - - +
435C MET* 4.0 13.0 - - + +
436C GLY 3.5 0.2 - - - -
437C GLN* 1.3 81.8 - - + +
439C GLN* 1.3 68.0 + - - +
440C GLY 3.2 2.9 - - - -
441C ALA* 3.0 10.8 + - + +
442C LEU* 3.0 29.1 + - + +
947C GLU* 6.4 0.2 - - - -
971C ARG* 4.0 15.0 - - - +
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Residues in contact with GLN 439 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C PRO* 3.4 35.0 - - - +
435C MET* 3.6 22.1 + - + +
436C GLY* 4.4 5.8 + - - +
437C GLN 3.8 1.2 - - - -
438C ILE* 1.3 76.7 - - - +
440C GLY* 1.3 65.3 + - - +
442C LEU* 3.2 6.5 + - - +
443C VAL* 3.2 29.3 + - + +
486C LEU* 4.7 20.3 - - + +
1112C D10 3.3 48.2 - - + +
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Residues in contact with GLY 440 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C GLN 5.3 0.8 + - - -
438C ILE 3.2 1.0 - - - -
439C GLN* 1.3 78.4 - - - +
441C ALA* 1.3 62.2 + - - +
443C VAL* 5.2 1.6 - - - -
444C GLY 3.0 12.8 + - - -
891C LEU* 3.9 5.9 - - - +
892C TYR* 2.8 24.6 + - - -
947C GLU* 4.0 18.3 + - - -
1112C D10 5.2 7.9 - - - +
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Residues in contact with ALA 441 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C VAL* 5.4 3.6 - - + -
438C ILE* 3.0 16.2 + - + +
440C GLY* 1.3 75.8 - - - +
442C LEU* 1.3 65.9 + - - +
444C GLY 3.2 0.7 + - - -
445C ILE* 2.8 39.7 + - + +
892C TYR* 4.0 6.3 - - - -
943C ILE* 4.2 8.9 - - + +
944C LEU* 4.4 15.3 - - + -
947C GLU* 3.8 18.7 - - + +
971C ARG* 4.6 9.2 - - - +
----------------------------------------------------------
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Residues in contact with LEU 442 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C ASP* 2.8 68.5 - - + +
411C VAL* 3.9 20.0 - - + -
412C VAL* 3.9 9.0 - - + -
435C MET* 3.6 20.9 - - + -
438C ILE* 3.0 21.0 + - + +
439C GLN* 3.2 8.2 + - - +
441C ALA* 1.3 75.6 - - - +
443C VAL* 1.3 63.4 + - + +
445C ILE* 4.4 0.4 - - + -
446C ALA* 3.3 14.6 + - - +
482C VAL* 3.9 7.6 - - + +
485C ALA* 4.7 2.7 - - + -
486C LEU* 3.4 30.7 - - + -
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Residues in contact with VAL 443 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C GLN* 3.2 17.7 + - + +
440C GLY* 5.2 0.2 - - - -
442C LEU* 1.3 74.6 - - + +
444C GLY* 1.3 63.2 + - - +
446C ALA* 3.3 3.1 + - + +
447C MET* 2.8 34.4 + - + +
482C VAL* 4.3 17.3 - - + -
486C LEU* 5.0 9.6 - - + -
891C LEU* 3.8 27.1 - - + -
1112C D10 4.1 40.8 - - + -
----------------------------------------------------------
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Residues in contact with GLY 444 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C GLY 3.0 13.8 + - - -
441C ALA 3.6 1.8 - - - -
443C VAL* 1.3 78.2 - - - +
445C ILE* 1.3 61.1 + - - +
447C MET* 3.3 2.8 + - - +
448C VAL* 3.1 30.8 + - - +
888C LEU* 5.0 1.8 - - - -
891C LEU* 3.4 20.7 - - - +
892C TYR* 3.7 8.3 - - - -
943C ILE* 4.1 9.9 - - - -
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Residues in contact with ILE 445 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C ASP* 4.8 13.7 - - + +
408C ASP* 3.5 24.9 - - - +
411C VAL* 4.6 9.4 - - + -
441C ALA* 2.8 30.2 + - + +
442C LEU* 4.4 1.3 - - + -
444C GLY* 1.3 72.7 - - - +
446C ALA* 1.3 67.4 + - - +
448C VAL* 3.2 9.3 - - - +
449C LEU* 3.2 33.1 + - + +
478C MET* 5.1 3.4 - - + -
940C LYS* 4.1 34.1 - - + +
943C ILE* 4.6 8.7 - - + +
944C LEU* 3.9 27.8 - - + -
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Residues in contact with ALA 446 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C ASP* 4.0 3.6 - - - +
442C LEU 3.3 15.2 + - - +
443C VAL* 3.7 3.6 - - - +
445C ILE* 1.3 83.6 - - - +
447C MET* 1.3 56.7 + - - +
449C LEU* 3.7 0.9 + - - -
450C SER* 2.8 34.2 + - - +
478C MET* 4.1 25.2 - - + +
479C ALA* 5.6 0.7 - - - -
482C VAL* 3.9 27.4 - - + -
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Residues in contact with MET 447 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1121B D12 3.7 36.1 - - + -
443C VAL* 2.8 33.8 + - + +
444C GLY 3.6 4.3 - - - +
445C ILE 3.2 0.2 - - - -
446C ALA* 1.3 70.5 - - - +
448C VAL* 1.3 64.1 + - + +
450C SER* 3.0 4.3 + - - -
451C ALA* 2.7 34.6 + - + +
887C CYS* 3.5 47.6 - - + +
888C LEU* 4.5 4.3 - - - -
891C LEU* 4.3 12.8 - - + -
1112C D10 5.0 3.8 - - + -
----------------------------------------------------------
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Residues in contact with VAL 448 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C GLY 3.1 13.0 + - - +
445C ILE* 3.2 14.8 - - - +
447C MET* 1.3 77.5 - - + +
449C LEU* 1.3 68.3 + - + +
451C ALA* 4.7 1.6 - - - -
452C VAL* 3.2 28.6 + - - +
884C VAL* 3.9 20.9 - - + +
888C LEU* 3.8 24.5 - - + -
936C GLY* 3.8 21.3 - - - +
939C ALA* 4.1 9.4 - - + -
940C LYS* 4.1 7.6 - - - +
943C ILE* 3.6 23.6 - - + -
----------------------------------------------------------
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Residues in contact with LEU 449 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C LEU* 4.3 29.4 - - + +
407C ASP* 5.2 1.8 - - - +
445C ILE* 3.2 31.5 + - + +
448C VAL* 1.3 79.3 - - + +
450C SER* 1.3 57.5 + - - +
452C VAL* 4.2 2.5 - - - -
453C PHE* 2.9 33.6 - - + -
474C ILE* 4.2 6.2 - - + +
478C MET* 3.8 29.4 - - + -
933C THR* 4.6 1.6 - - + +
936C GLY* 3.4 37.0 - - - +
937C LEU* 3.8 15.5 - - + +
940C LYS* 4.8 7.6 - - + -
----------------------------------------------------------
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Residues in contact with SER 450 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C ALA* 2.8 21.9 + - - +
447C MET* 3.0 6.7 + - - -
449C LEU* 1.3 74.0 - - - +
451C ALA* 1.3 62.1 + - - +
452C VAL 3.2 0.2 - - - -
453C PHE* 3.0 21.5 + - - +
454C VAL* 3.1 17.3 + - - +
475C VAL* 3.7 27.4 + - - +
478C MET* 3.5 17.7 - - - +
479C ALA* 4.7 2.6 + - - +
----------------------------------------------------------
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Residues in contact with ALA 451 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C MET* 2.7 22.6 + - + +
448C VAL* 4.3 2.0 - - - +
450C SER* 1.3 73.1 - - - +
452C VAL* 1.3 56.6 + - - +
453C PHE 3.2 0.2 - - - -
454C VAL* 4.0 9.9 - - - -
455C PRO* 3.1 25.5 - - - +
880C SER 4.7 0.2 - - - +
883C VAL* 3.7 26.0 - - + +
884C VAL* 4.2 11.6 - - + +
887C CYS* 4.1 18.2 - - + -
1107C D12 5.6 2.2 - - + -
----------------------------------------------------------
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Residues in contact with VAL 452 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C VAL 3.2 18.8 + - - +
449C LEU 3.9 1.1 - - - +
451C ALA* 1.3 77.1 - - - +
453C PHE* 1.3 84.8 + - + +
454C VAL 3.5 0.2 - - - -
455C PRO* 4.3 1.7 - - - +
456C MET* 4.8 1.0 - - - +
880C SER* 3.1 35.0 + - - -
884C VAL* 3.6 14.1 - - + +
932C LEU* 3.5 37.5 - - - +
935C ILE* 3.7 24.0 - - + -
936C GLY* 4.1 9.9 - - - +
----------------------------------------------------------
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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