Contacts of the helix formed by residues 13 - 37 (chain L) in PDB entry 4IL6
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 ASN 13 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A TYR* 3.3 29.4 + - - +
621B LHG 3.0 12.6 + - - -
410D LHG 3.0 29.0 + - - -
11L GLU* 4.6 1.3 + - - +
12L LEU* 1.3 75.6 - - - +
14L ARG* 1.3 65.3 + - - +
15L THR* 3.5 4.4 + - - -
16L SER* 2.7 38.1 + - - -
17L LEU* 3.1 18.2 + - - +
26M TYR* 3.9 3.1 - - - -
29M THR* 5.0 5.8 - - + -
30M GLU* 5.7 1.3 - - - -
25T GLU* 6.5 0.4 - - + -
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Residues in contact with ARG 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L ASN* 1.3 74.0 - - - +
15L THR* 1.3 63.7 + - - +
17L LEU* 3.1 6.9 + - + +
18L TYR* 2.9 46.5 + - + -
26M TYR* 3.1 39.6 + - + +
30M GLU* 4.4 11.4 + - - +
23T PHE 2.8 37.6 + - - -
24T ARG 3.1 14.0 + - - -
25T GLU* 3.9 33.7 + - + +
26T PRO* 4.9 1.4 - - - +
623b SQD 3.0 55.8 + - + -
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Residues in contact with THR 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D LHG 3.6 65.5 + - - -
13L ASN* 3.3 7.9 + - - -
14L ARG* 1.3 76.7 - - - +
16L SER* 1.3 57.2 + - - +
18L TYR* 3.2 12.4 + - - +
19L LEU* 2.8 42.5 + - + +
24T ARG* 6.0 0.7 - - - +
25T GLU* 4.6 16.3 + - - +
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Residues in contact with SER 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B LHG 3.4 63.1 - - - +
410D LHG 3.7 2.3 + - - -
12L LEU* 3.6 18.4 - - - +
13L ASN* 2.7 29.4 + - - -
15L THR* 1.3 72.3 - - - +
17L LEU* 1.3 60.3 + - - +
19L LEU* 4.3 0.2 - - - -
20L GLY* 2.8 28.4 + - - -
22M LEU* 5.2 0.3 - - - +
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Residues in contact with LEU 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L LEU* 4.1 8.1 - - + +
13L ASN 3.1 12.2 + - - +
14L ARG* 3.1 10.3 + - + +
16L SER* 1.3 75.9 - - - +
18L TYR* 1.3 61.5 + - + +
20L GLY* 3.2 1.2 + - - -
21L LEU* 2.8 56.8 + - + +
22M LEU* 3.8 37.8 - - + +
23M ILE* 4.0 12.6 - - + +
26M TYR* 3.6 39.3 - - + -
623b SQD 4.5 20.4 - - + -
101l UNL 5.5 2.7 - - + -
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Residues in contact with TYR 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D LHG 3.4 26.8 - - + +
14L ARG* 2.9 37.5 + - + -
15L THR* 3.2 7.4 + - - +
17L LEU* 1.3 81.5 - - + +
19L LEU* 1.3 57.2 + - - +
21L LEU* 3.5 0.4 + - + -
22L LEU* 3.0 29.8 + - - +
16T LEU* 3.6 24.5 - - + +
19T PHE* 3.2 31.7 + - + +
20T ALA* 3.7 14.1 - - + -
23T PHE* 2.8 28.7 + - - +
24T ARG* 4.2 6.7 - - + -
25T GLU 5.1 0.2 - - - -
623b SQD 3.4 42.3 - - + +
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Residues in contact with LEU 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B LHG 3.8 50.9 - - + +
266D TRP* 3.6 28.5 - - + -
270D PHE* 5.0 0.4 - - + -
410D LHG 3.8 52.9 - - + +
15L THR* 2.8 40.6 + - + +
16L SER 3.8 2.9 - - - +
18L TYR* 1.3 73.0 - - - +
20L GLY* 1.3 58.2 + - - +
22L LEU* 3.5 3.8 + - - +
23L LEU* 3.0 28.4 + - - +
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Residues in contact with GLY 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B LHG 3.5 21.9 - - - +
16L SER 2.8 20.2 + - - -
17L LEU 3.7 0.2 - - - -
19L LEU* 1.3 72.1 - - - +
21L LEU* 1.3 58.8 + - - +
23L LEU* 3.3 4.2 + - - +
24L ILE* 3.0 33.3 + - - +
22M LEU* 3.5 18.2 - - - -
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Residues in contact with LEU 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L LEU* 2.8 44.1 + - + +
18L TYR 4.0 2.9 - - - +
20L GLY* 1.3 75.0 - - - +
22L LEU* 1.3 58.5 + - - +
24L ILE* 3.4 4.2 + - - +
25L LEU* 2.9 39.9 + - + +
19M SER* 3.7 43.7 - - - +
22M LEU* 3.8 3.3 - - + +
23M ILE* 4.8 8.3 - - + -
16T LEU* 4.0 17.0 - - + -
623b SQD 3.7 43.7 - - + -
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Residues in contact with LEU 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B LHG 3.8 28.0 - - + -
410D LHG 4.0 52.3 - - + -
18L TYR 3.0 18.3 + - - +
19L LEU* 3.6 5.6 - - - +
21L LEU* 1.3 74.5 - - - +
23L LEU* 1.3 64.5 + - - +
25L LEU* 4.0 1.3 - - - -
26L VAL* 2.9 46.8 + - + +
13T ILE* 4.5 6.1 - - + -
16T LEU* 3.5 19.7 - - + +
17T PHE* 4.2 20.4 - - + -
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Residues in contact with LEU 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B CLA 4.5 4.9 - - + -
621B LHG 3.9 54.9 - - + +
273D PHE* 5.8 1.1 - - + -
407D PL9 3.7 31.0 - - + -
409D LHG 3.7 39.0 - - + -
19L LEU 3.0 14.9 + - - +
20L GLY* 3.5 7.2 - - - +
22L LEU* 1.3 76.9 - - - +
24L ILE* 1.3 58.3 + - + +
26L VAL* 3.8 0.9 - - - +
27L LEU* 2.8 49.0 + - + +
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Residues in contact with ILE 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B LHG 4.4 10.3 - - + -
409D LHG 4.2 24.7 - - + -
20L GLY 3.0 24.4 + - - +
21L LEU 3.8 3.8 - - - +
22L LEU 3.3 0.2 - - - -
23L LEU* 1.3 80.9 - - + +
25L LEU* 1.3 59.8 + - + +
27L LEU* 3.3 6.8 + - + +
28L ALA* 2.9 27.5 + - - +
14M PHE* 3.9 5.5 - - + +
15M VAL* 3.6 23.8 - - + +
18M PRO* 3.7 34.8 - - + -
19M SER* 3.5 24.0 - - - +
22M LEU* 4.5 8.3 - - + -
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Residues in contact with LEU 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L LEU* 2.9 27.4 + - + +
22L LEU* 4.1 2.0 - - - +
24L ILE* 1.3 74.8 - - + +
26L VAL* 1.3 52.3 + - - +
28L ALA* 3.2 3.7 + - - +
29L LEU* 2.8 30.7 + - - +
15M VAL* 4.0 27.4 - - + -
19M SER* 5.2 1.3 - - - +
8T PHE* 6.0 0.7 - - + -
9T ILE* 3.3 23.6 - - + +
12T CYS* 3.9 46.4 - - + +
13T ILE* 3.6 20.0 - - + +
16T LEU* 4.3 9.6 - - + -
623b SQD 4.3 21.3 - - + -
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Residues in contact with VAL 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B LHG 3.8 25.1 - - + -
407D PL9 3.7 40.5 - - + +
410D LHG 4.2 16.4 - - + -
22L LEU* 2.9 41.3 + - + +
23L LEU 4.1 0.2 - - - +
25L LEU* 1.3 74.5 - - - +
27L LEU* 1.3 58.6 + - - +
29L LEU* 3.3 7.0 + - + +
30L LEU* 3.0 28.1 + - - +
13T ILE* 4.1 15.0 - - + -
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Residues in contact with LEU 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B CLA 4.2 17.3 - - + -
199D MET* 3.8 29.6 - - - -
407D PL9 4.0 16.2 - - + -
409D LHG 4.2 22.7 - - + -
23L LEU* 2.8 45.8 + - + +
24L ILE* 3.6 6.1 - - - +
26L VAL* 1.3 76.9 - - - +
28L ALA* 1.3 57.1 + - - +
30L LEU* 3.4 4.2 + - + -
31L PHE* 2.9 47.5 + - + +
14M PHE* 3.7 19.5 - - + -
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Residues in contact with ALA 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L ILE 2.9 15.0 + - - +
25L LEU* 3.4 5.8 - - - +
27L LEU* 1.3 74.5 - - - +
29L LEU* 1.3 62.3 + - - +
30L LEU 3.1 0.2 - - - -
31L PHE* 4.5 1.3 - - - +
32L SER* 2.9 34.8 + - - +
35L PHE* 6.0 1.3 - - - -
11M THR* 4.8 4.7 - - + -
14M PHE* 3.8 14.1 - - + -
15M VAL* 3.4 33.0 - - + -
9T ILE* 3.9 10.8 - - + -
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Residues in contact with LEU 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 3.7 43.2 - - + +
407D PL9 3.8 39.9 - - + -
410D LHG 3.8 14.4 - - + -
25L LEU 2.8 19.1 + - - +
26L VAL* 3.6 7.9 - - - +
28L ALA* 1.3 73.7 - - - +
30L LEU* 1.3 60.1 + - - +
32L SER* 3.4 11.3 + - - +
33L SER* 4.9 0.3 + - - -
6T TYR* 3.9 20.0 - - - +
9T ILE* 3.8 17.4 - - + +
10T PHE* 4.4 6.1 - - + +
13T ILE* 3.8 20.0 - - + -
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Residues in contact with LEU 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 5.6 0.7 - - - -
78A ILE* 4.2 10.7 - - + +
195D PRO* 4.0 11.2 - - + +
198D MET* 3.7 31.2 - - + -
199D MET* 3.7 31.4 - - + -
403D CLA 3.9 7.0 - - - -
407D PL9 3.9 33.6 - - + +
26L VAL 3.0 16.4 + - - +
27L LEU* 3.7 5.8 - - + +
28L ALA 3.1 0.2 - - - -
29L LEU* 1.3 78.8 - - - +
31L PHE* 1.3 81.8 + - + +
32L SER 3.6 0.3 + - - -
33L SER 4.2 3.1 + - - -
34L TYR* 3.3 23.2 - - - -
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Residues in contact with PHE 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B PHE* 4.0 23.1 - + - -
607B CLA 3.7 39.9 - - + -
195D PRO* 3.8 25.6 - - + -
196D PHE* 4.2 7.9 - + - -
199D MET* 3.8 30.5 - - + -
27L LEU* 2.9 35.2 + - + +
28L ALA* 4.8 1.1 - - - +
30L LEU* 1.3 91.7 - - + +
32L SER* 1.3 65.0 + - - +
33L SER 3.3 0.9 - - - -
34L TYR* 3.0 18.3 + + - +
35L PHE* 3.0 43.0 + + + -
14M PHE* 5.1 3.6 - + + -
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Residues in contact with SER 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L ALA* 2.9 21.9 + - - +
29L LEU* 3.4 12.3 + - - -
30L LEU 3.4 0.2 - - - -
31L PHE* 1.3 76.9 - - - +
33L SER* 1.3 57.2 + - - +
35L PHE* 3.1 6.8 + - - +
36L PHE* 2.9 38.7 + - - -
11M THR* 3.7 30.3 - - - -
5T THR* 4.9 0.2 - - - -
6T TYR* 3.3 24.6 - - - -
9T ILE* 4.3 3.2 - - - +
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Residues in contact with SER 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASN* 3.4 21.5 + - - +
77A ILE* 3.2 36.9 + - - +
78A ILE* 3.6 20.2 + - - +
298D PHE* 3.7 8.5 - - - -
30L LEU 4.2 2.8 + - - -
31L PHE 3.3 0.6 - - - -
32L SER* 1.3 79.3 + - - +
34L TYR* 1.3 54.6 + - - +
36L PHE* 3.6 1.7 + - - +
37L ASN* 2.8 30.8 + - - +
6T TYR* 3.4 13.2 + - - -
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Residues in contact with TYR 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 3.4 23.5 - - + +
325B PHE* 3.7 56.8 - + + +
622B LMG 5.5 0.9 - - - +
193D LEU* 2.5 32.4 + - + -
195D PRO* 3.8 23.3 - - + -
198D MET* 3.3 19.8 - - - +
295D SER* 4.2 7.6 - - - -
297D ASP 5.8 1.3 - - - -
298D PHE* 3.6 23.6 - + - -
30L LEU* 3.3 26.2 - - + -
31L PHE* 3.0 11.7 + + - +
33L SER* 1.3 75.0 - - - +
35L PHE* 1.3 67.4 + - - +
37L ASN* 3.4 18.3 + - - +
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Residues in contact with PHE 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B PHE* 4.4 7.9 - + - -
607B CLA 3.9 17.7 - - + -
622B LMG 3.7 51.4 - - + +
28L ALA* 6.0 0.9 - - - -
31L PHE* 3.0 43.1 + + + -
32L SER* 3.5 9.4 - - - +
34L TYR* 1.3 81.3 - - - +
36L PHE* 1.3 60.3 + - - +
37L ASN* 4.4 1.0 - - - +
4M ASN* 3.5 18.2 + - - +
7M GLY* 3.6 16.7 - - - +
10M ALA* 4.2 8.5 - - + -
11M THR* 3.7 30.7 - - + +
14M PHE* 4.1 32.3 - + + -
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Residues in contact with PHE 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L SER* 2.9 23.9 + - - +
33L SER 4.0 0.9 - - - +
35L PHE* 1.3 75.8 - - - +
37L ASN* 1.3 70.1 + - - +
3M VAL* 3.4 23.3 - - + +
4M ASN 2.7 30.4 + - - +
7M GLY* 3.9 8.1 - - - -
8M LEU* 3.4 35.9 - - + -
11M THR* 4.2 7.9 - - - -
1T FME 4.4 9.2 - - + -
2T GLU* 3.9 28.3 - - + -
5T THR* 3.7 41.1 - - + -
6T TYR* 3.4 28.7 - + - +
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Residues in contact with ASN 37 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASN* 4.9 3.1 + - - -
325B PHE* 3.0 33.1 + - - +
326B ARG* 4.4 1.6 - - - +
297D ASP* 3.5 8.5 + - - +
298D PHE* 3.4 22.1 - - - +
299D ILE* 3.1 49.1 + - - +
300D SER* 2.6 48.8 + - - -
33L SER 2.8 23.4 + - - +
34L TYR* 3.4 14.3 + - - +
35L PHE 3.3 3.0 - - - +
36L PHE* 1.3 81.4 - - - +
2M GLU 4.7 2.3 - - - +
3M VAL* 4.2 2.6 - - - +
4M ASN* 4.8 8.5 + - + +
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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