Contacts of the helix formed by residues 433 - 456 (chain C) in PDB entry 6NRB
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 GLU 433 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C VAL* 3.2 29.3 - - + +
124C SER* 2.2 33.3 + - - -
125C ALA* 3.6 9.8 - - + -
128C LYS* 3.1 16.0 + - - -
429C MET* 3.3 22.6 - - + +
432C VAL* 1.3 76.0 - - + +
434C GLN* 1.3 63.6 + - - +
435C TRP 3.0 0.7 - - - -
436C PRO* 3.0 18.5 - - - +
437C TYR* 2.7 46.1 + - - +
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Residues in contact with GLN 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C SER* 3.2 23.6 - - - +
429C MET* 3.8 4.6 - - + -
430C THR* 3.1 22.8 + - - +
431C GLY 2.9 29.9 + - - +
432C VAL 2.8 1.2 + - - -
433C GLU* 1.3 78.1 - - - +
435C TRP* 1.3 89.3 + - + +
437C TYR* 2.9 16.9 + - - +
438C ARG* 2.4 71.1 + - - +
464P ILE* 5.9 0.4 - - - +
465P SER* 4.5 3.0 + - - -
468P TYR* 4.9 8.3 - - - -
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Residues in contact with TRP 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C VAL* 5.5 0.7 - - - +
109C ALA* 5.0 0.3 - - - +
113C LEU* 4.0 24.0 - - + -
116C GLN* 5.8 0.2 - - - -
431C GLY 3.4 6.8 + - - -
432C VAL* 2.8 31.8 + - + +
434C GLN* 1.3 104.1 - - + +
436C PRO* 1.3 59.6 - - + +
438C ARG* 3.2 34.0 - - + +
439C ALA* 2.7 26.4 + - - +
443P GLU* 4.0 25.4 - - + -
461P ASN* 3.2 51.2 + - + +
464P ILE* 5.3 8.7 - - + -
468P TYR* 6.0 0.4 - + - -
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Residues in contact with PRO 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ALA* 4.3 2.9 - - + -
113C LEU* 3.5 21.5 - - + -
118C HIS* 5.1 0.4 - - - +
121C VAL* 4.4 1.1 - - + +
122C VAL* 3.8 26.2 - - + +
125C ALA* 3.4 28.5 - - + -
126C TYR 4.9 0.4 - - - +
432C VAL 3.4 4.0 - - - +
433C GLU* 3.0 20.4 - - - +
435C TRP* 1.3 85.1 - - + +
437C TYR* 1.3 52.9 + - - +
439C ALA* 2.7 10.3 + - + -
440C VAL* 2.4 49.2 + - + +
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Residues in contact with TYR 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ALA* 3.0 33.5 - - + -
128C LYS* 3.1 26.6 - - + +
129C ALA* 3.5 18.8 - - + -
422C LEU* 3.4 28.2 - - + +
425C LYS* 4.2 13.0 - - + -
426C SER* 3.6 15.0 - - - -
429C MET* 3.7 18.9 - - + -
433C GLU* 2.7 46.3 + - - -
434C GLN* 2.9 19.9 + - - +
436C PRO* 1.3 72.8 - - - +
438C ARG* 1.3 54.9 + - - +
440C VAL* 4.3 4.5 - - - +
441C ALA* 2.8 33.8 + - - +
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Residues in contact with ARG 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C THR* 5.2 9.9 - - + +
426C SER* 4.0 14.2 + - - +
427C LYS* 3.8 30.9 - - - +
430C THR* 5.3 0.2 + - - -
434C GLN* 2.4 73.8 + - - +
435C TRP* 3.2 43.7 - - + +
437C TYR* 1.3 69.9 - - - +
439C ALA* 1.3 57.1 + - - -
441C ALA* 4.2 3.9 - - - +
442C GLN* 3.3 30.3 + - - +
468P TYR* 5.1 5.7 - - - -
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Residues in contact with ALA 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C GLU 4.8 4.7 - - - +
105C MET* 5.0 6.1 - - - +
108C VAL* 3.7 35.4 - - + +
109C ALA* 3.8 22.0 - - + +
126C TYR* 6.0 0.2 - - + -
435C TRP 2.7 16.6 + - - +
436C PRO 2.7 9.2 + - - +
438C ARG* 1.3 72.9 - - - +
440C VAL* 1.3 64.1 + - + +
442C GLN* 3.5 7.5 + - - +
443C ALA* 3.2 18.4 + - - +
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Residues in contact with VAL 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C MET* 3.8 25.6 - - + -
126C TYR* 3.4 38.6 - - + -
129C ALA* 3.6 22.2 - - + -
422C LEU* 3.5 18.2 - - + -
436C PRO* 2.4 35.0 + - + +
437C TYR 4.2 0.9 - - - +
439C ALA* 1.3 67.6 - - + +
441C ALA* 1.3 64.8 + - - +
443C ALA* 3.1 19.6 + - + +
444C LEU* 3.2 10.3 + - + +
506C TYR* 4.2 8.3 - - + +
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Residues in contact with ALA 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C ALA* 3.1 39.8 - - + +
422C LEU* 3.6 12.7 - - + +
423C THR* 3.4 12.8 - - - +
437C TYR 2.8 19.8 + - - +
438C ARG 4.2 4.0 - - - +
440C VAL* 1.3 77.6 - - - +
442C GLN* 1.3 61.6 + - + +
444C LEU* 3.1 23.7 - - - +
445C GLU* 3.5 3.6 - - - +
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Residues in contact with GLN 442 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C GLU* 4.3 5.4 - - - +
108C VAL* 4.3 23.1 - - + +
438C ARG* 3.3 19.0 + - - +
439C ALA* 3.5 8.2 + - - +
440C VAL 3.2 0.4 - - - -
441C ALA* 1.3 72.7 - - + +
443C ALA* 1.3 59.4 + - - +
444C LEU 3.0 2.2 - - - -
445C GLU* 2.7 29.4 + - - +
446C VAL* 3.2 9.7 + - - -
449C ARG* 3.8 12.3 + - - +
467C ARG* 5.1 12.2 - - - +
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Residues in contact with ALA 443 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C LEU* 4.1 18.0 - - + +
104C GLU* 3.3 35.9 + - + +
105C MET* 4.3 14.8 - - + -
439C ALA 3.2 13.6 + - - +
440C VAL* 3.1 17.2 + - + +
442C GLN* 1.3 74.7 - - - +
444C LEU* 1.3 62.3 + - + +
446C VAL* 3.1 20.6 - - - +
447C ILE* 4.6 0.3 - - - +
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Residues in contact with LEU 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C LEU* 5.2 6.3 - - + -
133C MET* 4.6 14.8 - - - -
414C SER 4.5 3.6 - - - +
415C GLU* 2.9 63.2 - - - +
418C VAL* 3.5 21.1 - - + -
419C ALA* 3.3 21.8 - - - +
422C LEU* 3.8 11.7 - - + -
440C VAL* 3.6 7.4 - - + +
441C ALA 3.1 10.7 + - - +
442C GLN 3.0 0.2 - - - -
443C ALA* 1.3 79.9 - - + +
445C GLU* 1.3 55.4 + - - +
447C ILE* 3.4 5.2 + - - +
448C PRO* 3.1 15.9 - - - +
502C LYS* 5.2 3.6 - - - +
506C TYR* 4.8 12.6 - - + -
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Residues in contact with GLU 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C GLU* 3.0 35.7 - - - +
416C MET* 3.0 27.7 + - - +
419C ALA* 3.0 10.5 - - + +
441C ALA 3.5 13.5 - - - +
442C GLN* 2.7 16.0 + - - +
444C LEU* 1.3 70.3 - - - +
446C VAL* 1.3 58.0 + - - -
447C ILE 3.1 2.0 - - - -
448C PRO* 3.2 24.4 - - - +
449C ARG* 3.0 45.5 + - - +
463C LEU* 3.7 2.9 - - + +
466C LEU* 3.7 1.6 - - - +
467C ARG* 3.4 25.6 + - - +
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Residues in contact with VAL 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG* 3.5 27.8 - - - +
100C ILE* 4.4 9.6 - - + -
104C GLU* 3.4 36.6 - - + +
442C GLN 3.2 4.8 + - - +
443C ALA 3.1 19.7 - - - +
445C GLU* 1.3 78.8 - - - +
447C ILE* 1.3 62.4 + - + +
449C ARG* 3.0 20.6 - - - +
450C THR* 2.3 40.6 + - - +
453C GLN* 4.5 4.3 - - - +
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Residues in contact with ILE 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU* 4.5 17.9 - - + -
97C SER* 5.2 4.5 - - - +
100C ILE* 4.3 16.8 - - + -
101C LEU* 4.9 8.1 - - + -
411C GLY* 5.0 3.4 - - - -
415C GLU* 4.0 22.0 - - + +
443C ALA 4.6 2.7 - - - +
444C LEU 3.6 9.6 - - - +
445C GLU 3.1 0.4 - - - -
446C VAL* 1.3 86.2 - - + +
448C PRO* 1.3 62.8 - - + +
450C THR* 3.5 15.9 - - + +
451C LEU* 2.4 60.1 + - + +
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Residues in contact with PRO 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C GLY* 3.7 15.0 - - - +
415C GLU* 3.7 5.6 - - + -
444C LEU 3.1 25.8 - - - +
445C GLU* 3.2 26.0 - - - +
447C ILE* 1.3 81.3 - - + +
449C ARG* 1.3 63.3 + - - +
451C LEU* 3.9 0.5 - - - +
452C ILE* 3.0 29.7 + - + +
459C THR* 3.6 3.8 - - - +
463C LEU* 4.0 8.1 - - + -
466C LEU* 3.6 25.6 - - + -
480C VAL* 3.5 16.4 - - + -
487C LEU* 5.8 0.2 - - + -
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Residues in contact with ARG 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C GLU* 5.6 0.4 + - - -
442C GLN* 3.8 15.3 + - - +
445C GLU* 3.0 48.3 + - - +
446C VAL* 3.0 20.5 - - - +
448C PRO* 1.3 74.2 - - - +
450C THR* 1.3 51.2 + - - +
452C ILE 2.7 7.4 + - - -
453C GLN* 2.2 62.6 + - + +
459C THR* 3.2 25.9 + - + +
463C LEU* 3.5 26.0 - - + +
467C ARG* 4.2 15.0 - - - +
121P ILE* 5.7 10.3 - - - +
436P TYR* 5.7 1.2 - - - -
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Residues in contact with THR 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG* 3.0 57.8 + - + +
41C LEU* 4.1 15.3 - - + +
42C GLY 4.8 0.9 - - - +
446C VAL* 2.3 38.3 + - - +
447C ILE* 2.8 22.5 + - + +
449C ARG* 1.3 65.4 - - - +
451C LEU* 1.3 65.9 + - + +
453C GLN* 3.1 11.4 + - - +
454C ASN* 3.0 25.5 + - - +
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Residues in contact with LEU 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLY* 3.7 14.4 - - - -
43C PRO* 3.5 31.6 - - + -
411C GLY* 3.6 20.2 - - - -
412C GLY 4.4 0.7 - - - +
447C ILE* 2.4 43.9 + - + +
450C THR* 1.3 69.1 - - + +
452C ILE* 1.3 60.8 + - - +
454C ASN* 3.4 7.0 - - - +
455C CYS* 3.3 15.5 + - - -
480C VAL* 3.1 45.3 - - + +
482C GLY* 3.7 24.9 - - - +
485C GLY* 5.2 0.2 - - - -
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Residues in contact with ILE 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C PRO* 3.0 21.2 + - + +
449C ARG 2.7 7.3 + - - -
451C LEU* 1.3 68.8 - - - +
453C GLN* 1.3 57.4 + - - +
454C ASN 2.9 9.2 + - - -
455C CYS* 3.0 25.4 + - - -
456C GLY 3.1 12.0 + - - -
457C ALA* 3.3 31.0 - - + +
458C SER 3.8 0.9 - - - +
459C THR* 3.3 32.8 - - - +
462C LEU* 3.6 38.4 - - + -
463C LEU 5.0 0.4 - - - +
480C VAL* 3.8 23.8 - - + -
487C LEU* 5.0 0.9 - - + -
115F HIS* 3.5 3.5 - - - -
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Residues in contact with GLN 453 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG* 3.5 24.0 - - + +
39C THR* 4.9 11.6 - - + +
46C MET* 4.2 5.5 - - - +
446C VAL* 3.8 2.9 - - - +
449C ARG* 2.2 64.0 + - + +
450C THR* 3.1 21.9 + - - +
452C ILE* 1.3 65.1 - - - +
454C ASN* 1.3 59.9 + - - +
459C THR* 4.8 9.0 - - + +
115F HIS* 2.9 27.7 + - + -
----------------------------------------------------------
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Residues in contact with ASN 454 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG 3.6 0.6 + - - +
39C THR* 3.3 29.0 - - - +
41C LEU 2.6 29.2 + - - -
42C GLY* 4.0 5.5 - - - -
44C LYS* 3.5 36.1 - - + +
46C MET* 3.1 23.4 - - + +
450C THR 3.0 17.6 + - - +
451C LEU* 3.4 10.0 + - - +
452C ILE 2.9 1.2 - - - -
453C GLN* 1.3 78.3 - - - +
455C CYS* 1.3 66.3 + - - +
456C GLY 3.0 3.8 + - - -
115F HIS* 3.0 9.0 + - - +
117F ARG* 3.1 6.5 - - - +
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Residues in contact with CYS 455 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LYS* 3.5 32.7 - - + +
451C LEU 3.3 4.1 + - - +
452C ILE* 3.0 32.2 + - - -
454C ASN* 1.3 79.8 - - - +
456C GLY* 1.3 61.1 + - - +
457C ALA* 3.6 17.5 - - - -
482C GLY 4.0 3.6 - - - +
485C GLY* 4.0 19.3 - - - -
117F ARG* 4.0 1.9 - - - +
118F ILE* 3.0 29.1 + - - +
432F ARG* 4.2 10.3 + - - +
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Residues in contact with GLY 456 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452C ILE 3.1 6.1 + - - -
454C ASN 3.0 2.6 + - - -
455C CYS* 1.3 77.3 - - - +
457C ALA* 1.3 65.5 + - - +
114F LEU* 5.3 2.3 - - - +
115F HIS* 3.0 31.4 + - - -
118F ILE* 3.6 22.5 - - - +
457N PHE 5.7 0.3 - - - +
458N ASP* 4.9 7.1 - - - +
461N GLU* 4.8 2.6 - - - +
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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