Contacts of the helix formed by residues 38 - 64 (chain 8) in PDB entry 1Y69
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 ARG 38 (chain 8).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328 GLY 5.7 0.2 - - - -
338 GLY* 3.6 23.2 - - - +
358 GLU 6.1 0.6 - - - +
368 GLU* 2.8 24.7 + - - +
378 ARG* 1.3 71.0 - - - +
398 LYS* 1.3 61.7 + - - +
408 ASP* 3.0 1.8 + - - -
418 LEU* 3.5 10.5 + - - +
428 THR* 3.1 21.7 + - - -
1108 LEU* 3.6 22.3 - - - +
1118 MET* 3.7 46.4 + - + +
1138 PHE* 5.7 3.4 - - - -
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Residues in contact with LYS 39 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368 GLU 3.9 4.5 + - - +
388 ARG* 1.3 76.3 - - - +
408 ASP* 1.3 68.4 + - - +
418 LEU 3.1 2.5 - - - -
428 THR* 3.0 27.7 + - - +
438 LYS* 3.5 27.6 + - + +
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Residues in contact with ASP 40 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368 GLU 2.9 24.9 - - - +
378 ARG* 3.1 23.5 - - - +
388 ARG 3.0 4.6 + - - -
398 LYS* 1.3 79.5 - - - +
418 LEU* 1.3 66.2 + - - +
438 LYS* 3.0 33.4 - - - +
448 ILE* 4.0 6.4 - - - +
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Residues in contact with LEU 41 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278 ILE* 4.5 24.2 - - + +
288 ARG* 5.7 0.9 - - - -
298 THR* 5.1 8.1 - - - +
328 GLY* 5.6 10.3 - - - -
378 ARG 5.2 2.7 - - - +
388 ARG* 3.5 14.1 + - - +
398 LYS 3.1 0.4 - - - -
408 ASP* 1.3 82.8 - - - +
428 THR* 1.3 67.0 + - - +
438 LYS 3.0 2.2 - - - -
448 ILE* 2.9 31.2 + - + +
458 VAL* 3.7 6.0 + - + -
1108 LEU* 3.3 40.4 - - + -
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Residues in contact with THR 42 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388 ARG 3.1 14.6 + - - -
398 LYS* 3.0 18.3 + - - -
418 LEU* 1.3 79.1 - - - +
438 LYS* 1.3 57.7 + - - +
458 VAL* 2.8 33.5 + - + +
468 ARG* 2.9 39.7 + - + +
1078 GLU* 3.6 27.1 + - - +
1108 LEU* 5.2 3.2 - - - +
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Residues in contact with LYS 43 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19300 C 4.9 2.8 + - - +
19310 G 4.0 18.4 + - - -
398 LYS* 3.8 27.1 - - + +
408 ASP* 3.0 27.8 - - - +
418 LEU 3.0 0.2 - - - -
428 THR* 1.3 77.4 - - - +
448 ILE* 1.3 68.4 + - + +
468 ARG* 3.3 24.7 + - + +
478 GLY* 3.5 5.0 + - - -
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Residues in contact with ILE 44 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278 ILE* 3.2 34.8 - - + -
408 ASP 4.0 5.8 - - - +
418 LEU* 3.0 23.3 - - + +
438 LYS* 1.3 88.8 - - + +
458 VAL* 1.3 61.0 + - - +
478 GLY* 3.3 10.5 + - - -
488 GLU* 3.6 14.4 + - - +
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Residues in contact with VAL 45 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278 ILE* 4.6 5.8 - - + -
418 LEU* 3.9 13.0 - - + +
428 THR* 2.8 19.2 + - + +
448 ILE* 1.3 76.4 - - - +
468 ARG* 1.3 65.4 + - - +
488 GLU* 3.0 14.0 + - - +
498 ALA* 3.2 12.6 + - - +
1038 LEU* 4.0 22.4 - - + +
1068 LYS* 2.8 41.5 - - + +
1078 GLU* 6.1 0.2 - - - +
1108 LEU* 3.5 28.9 - - + -
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Residues in contact with ARG 46 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19290 U 5.4 1.9 - - - +
19300 C 3.4 29.7 + - - +
428 THR* 2.9 38.7 + - + +
438 LYS* 3.4 15.3 - - + +
448 ILE 3.3 0.2 - - - -
458 VAL* 1.3 75.3 - - - +
478 GLY* 1.3 57.2 + - - +
498 ALA* 3.4 7.9 + - - +
508 GLU* 2.8 30.8 + - - +
538 ARG* 5.8 3.8 - - - +
1038 LEU* 6.0 7.2 - - - +
1078 GLU* 5.9 0.2 + - - -
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Residues in contact with GLY 47 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438 LYS 3.5 5.5 + - - -
448 ILE 3.3 7.8 + - - -
458 VAL 3.1 0.8 - - - -
468 ARG* 1.3 79.2 - - - +
488 GLU* 1.3 56.1 + - - +
508 GLU* 3.7 6.9 - - - +
518 GLN* 2.9 32.7 + - - +
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Residues in contact with GLU 48 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208 PHE* 3.6 11.7 - - + +
238 GLN* 3.4 26.6 - - - +
248 ILE* 3.1 51.9 + - + +
278 ILE* 4.8 10.1 - - + -
448 ILE 3.6 13.6 + - - +
458 VAL* 3.0 12.6 + - + +
478 GLY* 1.3 78.1 - - - +
498 ALA* 1.3 56.5 + - - +
518 GLN* 4.1 3.6 - - - +
528 ALA* 3.1 27.5 + - - +
1038 LEU* 6.1 1.3 - - + -
1068 LYS* 4.7 2.2 - - - +
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Residues in contact with ALA 49 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458 VAL 3.2 6.2 + - - +
468 ARG* 3.8 10.5 - - - +
488 GLU* 1.3 74.3 - - - +
508 GLU* 1.3 65.1 + - - +
528 ALA* 3.2 7.5 + - - +
538 ARG* 3.0 50.5 + - - +
998 ILE* 4.7 8.2 - - + +
1038 LEU* 3.8 31.4 - - + +
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Residues in contact with GLU 50 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19280 G 3.6 10.6 + - - +
19290 U 3.1 49.7 - - - +
19460 U 2.9 24.8 - - - +
468 ARG 2.8 17.8 + - - +
478 GLY* 3.7 8.1 - - - +
488 GLU 3.4 0.2 - - - -
498 ALA* 1.3 79.3 - - - +
518 GLN* 1.3 63.5 + - + +
528 ALA 3.3 0.5 + - - -
538 ARG* 3.4 9.4 + - - +
548 VAL* 2.9 25.5 + - + +
578 ARG* 4.8 0.3 + - - -
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Residues in contact with GLN 51 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208 PHE* 5.6 10.8 - - + -
478 GLY 2.9 17.9 + - - +
488 GLU* 4.2 3.8 - - - +
508 GLU* 1.3 79.3 - - + +
528 ALA* 1.3 61.9 + - - +
548 VAL* 3.5 20.4 - - - +
558 ALA* 3.1 21.2 + - + +
588 ASN* 5.0 1.6 + - - -
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Residues in contact with ALA 52 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208 PHE* 4.4 21.5 - - + -
488 GLU 3.1 19.6 + - - +
498 ALA* 3.4 9.6 - - - +
508 GLU 3.1 0.4 - - - -
518 GLN* 1.3 75.8 - - - +
538 ARG* 1.3 66.2 + - + +
558 ALA* 3.2 7.0 + - - +
568 VAL* 3.0 31.1 + - + +
998 ILE* 4.5 24.7 - - + -
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Residues in contact with ARG 53 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19260 U 3.9 30.7 + - - +
19270 U 5.5 4.8 + - - +
19280 G 4.6 4.9 + - - +
19290 U 3.2 30.7 + - - -
468 ARG* 5.8 4.2 - - - +
498 ALA* 3.0 42.3 + - - +
508 GLU* 3.4 18.5 + - - +
528 ALA* 1.3 75.5 - - + +
548 VAL* 1.3 62.5 + - - +
568 VAL* 3.2 8.2 + - - +
578 ARG* 3.0 32.6 + - - +
968 ILE* 5.0 17.8 - - + +
998 ILE* 5.6 4.5 - - + +
1008 GLU* 2.5 34.7 + - - -
1038 LEU* 5.8 0.6 - - - +
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Residues in contact with VAL 54 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19460 U 3.3 57.0 - - + +
508 GLU* 2.9 24.9 - - + +
518 GLN* 3.5 17.3 - - - +
538 ARG* 1.3 74.0 - - - +
558 ALA* 1.3 52.9 + - - +
578 ARG* 2.8 17.1 + - - +
588 ASN* 2.7 47.0 + - - +
618 ARG* 3.2 11.5 + - - +
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Residues in contact with ALA 55 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138 MET* 5.1 0.6 - - - +
168 CYS* 4.9 9.7 - - + -
208 PHE* 4.2 24.5 - - + -
518 GLN* 3.1 20.0 + - - +
528 ALA 3.4 6.7 - - - +
548 VAL* 1.3 79.6 - - - +
568 VAL* 1.3 62.4 + - + +
588 ASN* 3.1 15.5 + - - +
598 VAL* 3.3 23.6 + - - +
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Residues in contact with VAL 56 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138 MET* 3.1 42.2 - - + +
168 CYS* 6.6 0.7 - - + -
178 VAL* 5.5 7.9 - - + -
208 PHE* 5.9 2.9 - - + -
528 ALA* 3.0 21.5 + - + +
538 ARG* 3.7 7.2 - - - +
548 VAL 3.1 0.4 - - - -
558 ALA* 1.3 79.2 - - + +
578 ARG* 1.3 61.1 - - - +
598 VAL 4.4 0.2 - - - -
608 ARG* 3.9 1.7 + - - +
928 THR* 3.7 42.0 + - + +
958 ALA* 3.7 22.2 - - + -
968 ILE* 5.0 8.1 - - + -
998 ILE* 5.7 3.8 - - + -
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Residues in contact with ARG 57 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19190 A 4.9 1.0 + - - -
19250 C 2.7 81.1 + - + +
19260 U 4.3 21.7 + - - +
19280 G 3.7 28.1 + - - -
19460 U 3.5 34.1 + - - +
508 GLU* 4.8 1.2 + - - -
538 ARG* 3.0 17.1 + - - +
548 VAL* 2.8 22.6 + - - +
568 VAL* 1.3 80.0 - - + +
588 ASN* 1.3 55.4 + - - +
598 VAL 3.4 0.2 - - - -
608 ARG* 3.1 7.1 + - - +
618 ARG* 2.7 50.1 + - - +
928 THR* 5.3 4.9 - - + -
968 ILE* 5.7 0.9 - - + -
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Residues in contact with ASN 58 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19460 U 4.5 7.1 - - - +
518 GLN* 5.0 1.6 + - - -
548 VAL* 2.7 43.8 + - - +
558 ALA* 3.1 13.9 - - - +
578 ARG* 1.3 72.3 - - - +
598 VAL* 1.3 66.0 + - + +
618 ARG* 2.3 32.8 + - - +
628 ASP* 2.9 37.8 + - - +
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Residues in contact with VAL 59 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88 ASP* 5.1 0.9 - - - +
98 ALA* 4.2 28.7 - - + +
128 ARG* 5.1 15.7 - - + +
138 MET* 3.2 40.2 - - + +
168 CYS* 6.4 1.6 - - - -
558 ALA 3.3 17.9 - - - +
588 ASN* 1.3 76.1 - - + +
608 ARG* 1.3 57.9 + - - +
628 ASP* 4.3 5.6 - - - -
638 ALA* 3.0 35.7 + - + +
888 VAL* 5.9 0.3 - - - +
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Residues in contact with ARG 60 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19240 C 2.7 56.3 + - - +
19250 C 2.7 58.7 + - - -
138 MET* 4.0 4.2 - - + +
568 VAL 3.9 10.5 + - - +
578 ARG* 3.1 11.3 + - - +
588 ASN 3.0 0.6 - - - -
598 VAL* 1.3 81.6 - - - +
618 ARG* 1.3 66.0 + - - +
628 ASP 3.2 1.0 + - - -
648 ASN* 3.1 28.5 + - + +
858 GLN* 4.4 15.8 + - - +
888 VAL* 4.0 22.0 - - + +
898 GLN* 3.5 25.6 + - - +
928 THR* 4.3 7.4 - - - +
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Residues in contact with ARG 61 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19240 C 2.7 43.0 - - - +
19250 C 3.0 12.7 + - - +
19460 U 2.5 39.9 + - - -
19480 C 3.6 31.4 - - - +
548 VAL* 3.2 15.2 + - - +
578 ARG* 2.7 25.1 + - - +
588 ASN* 2.3 52.6 + - - +
608 ARG* 1.3 82.2 - - - +
628 ASP* 1.3 62.4 + - - +
648 ASN* 4.8 2.2 - - - -
658 ASP* 3.5 19.1 - - - +
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Residues in contact with ASP 62 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588 ASN* 2.9 28.2 + - - +
598 VAL* 4.1 4.3 - - - +
608 ARG 3.2 0.8 + - - -
618 ARG* 1.3 81.4 - - - +
638 ALA* 1.3 65.5 + - - +
648 ASN 3.2 1.7 + - - -
658 ASP* 3.7 7.1 + - - +
668 LYS* 3.2 36.9 + - - +
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Residues in contact with ALA 63 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58 ILE* 4.3 23.8 - - + +
88 ASP* 4.6 9.6 - - - +
98 ALA* 5.3 4.7 - - + -
128 ARG* 6.1 1.3 - - - +
598 VAL* 3.0 26.1 + - + +
628 ASP* 1.3 74.8 - - - +
648 ASN* 1.3 63.3 + - - +
668 LYS* 3.5 26.1 + - + +
678 VAL* 3.6 14.7 + - - +
888 VAL* 5.8 6.7 - - + -
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Residues in contact with ASN 64 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19240 C 5.5 4.6 + - - -
19480 C 4.3 5.9 + - - -
608 ARG* 3.1 22.6 + - + +
618 ARG* 4.9 2.7 - - - -
628 ASP 3.2 0.4 - - - -
638 ALA* 1.3 76.2 - - - +
658 ASP* 1.3 67.7 + - - +
668 LYS 3.1 1.8 - - - -
678 VAL* 3.0 7.3 + - - +
688 LYS* 2.7 45.3 + - - +
818 ASP* 5.3 3.6 - - - +
848 SER* 4.9 11.4 + - - -
858 GLN* 3.7 23.8 + - - +
888 VAL* 6.1 4.9 - - + -
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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