Contacts of the helix formed by residues 22 - 54 (chain L) in PDB entry 1F33
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 SER 22 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L ASP 3.6 3.2 + - - -
21L VAL* 1.3 74.1 - - - +
23L ASP* 1.3 56.0 + - - +
24L SER* 3.6 11.4 - - - -
25L GLU* 3.0 32.7 + - - +
26L LYS* 2.7 32.4 + - - +
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Residues in contact with ASP 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L THR 4.2 11.7 + - - +
14L LEU* 3.7 28.0 - - + +
21L VAL 3.4 3.9 + - - +
22L SER* 1.3 72.6 - - - +
24L SER* 1.3 62.6 + - - +
26L LYS* 3.6 7.7 + - - +
27L LYS* 3.0 27.3 + - + +
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Residues in contact with SER 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L SER* 2.9 11.8 - - - -
23L ASP* 1.3 80.4 - - - +
25L GLU* 1.3 63.8 + - - +
27L LYS* 4.0 3.3 - - - +
28L ALA* 3.0 22.6 + - - +
140L LYS* 4.2 12.4 + - - -
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Residues in contact with GLU 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L VAL* 3.7 17.4 - - + +
22L SER* 3.0 18.7 + - - +
24L SER* 1.3 78.5 - - - +
26L LYS* 1.3 58.4 + - - +
28L ALA* 4.1 6.5 - - - -
29L THR* 2.6 44.6 + - - +
140L LYS* 3.1 44.1 - - + +
141L ASP* 3.4 16.1 + - - +
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Residues in contact with LYS 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14L LEU* 3.9 19.2 - - + +
15L LEU 5.1 2.0 + - - -
17L THR* 3.3 24.0 + - - +
19L ASN* 2.8 30.5 + - - -
20L ASP* 4.9 0.2 - - - +
21L VAL* 2.9 36.6 + - + +
22L SER 2.7 21.3 + - - +
23L ASP* 3.6 10.4 + - - +
25L GLU* 1.3 71.1 - - - +
27L LYS* 1.3 58.6 + - - +
29L THR* 3.7 2.6 - - - -
30L VAL* 2.8 36.5 + - - +
87L LEU* 3.1 36.3 - - + +
88L GLY* 5.4 0.2 - - - -
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Residues in contact with LYS 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L THR* 2.7 35.0 + - - +
13L ASN* 3.5 33.9 + - - +
14L LEU* 3.5 22.2 - - + -
23L ASP* 3.0 17.7 + - + +
24L SER* 4.0 2.5 - - - +
26L LYS* 1.3 75.6 - - - +
28L ALA* 1.3 64.6 + - - +
30L VAL* 3.4 4.1 + - - +
31L GLU* 3.0 25.4 + - - +
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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 SER 3.0 18.5 + - - +
25L GLU* 3.6 4.0 - - - +
27L LYS* 1.3 76.5 - - - +
29L THR* 1.3 57.6 + - - +
31L GLU* 3.3 8.8 + - - +
32L LEU* 3.0 27.0 + - - +
140L LYS* 3.9 30.1 - - + +
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Residues in contact with THR 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L VAL* 5.7 0.2 - - - +
25L GLU* 2.6 30.4 + - - +
28L ALA* 1.3 70.8 - - - +
30L VAL* 1.3 60.5 + - - +
32L LEU* 3.0 9.1 + - + +
33L LEU* 2.8 37.9 + - + +
87L LEU* 3.3 25.0 - - + +
140L LYS* 5.2 4.2 + - - +
141L ASP* 3.8 18.7 + - + +
144L THR* 3.1 35.7 - - + +
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Residues in contact with VAL 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14L LEU* 4.6 4.5 - - + -
26L LYS 2.8 31.7 + - - +
27L LYS* 3.8 6.1 - - - +
29L THR* 1.3 73.4 - - - +
31L GLU* 1.3 57.1 + - - +
33L LEU* 3.9 1.2 - - - +
34L ASN* 3.0 46.4 + - - +
84L ALA* 3.6 32.3 - - + +
87L LEU* 4.1 10.1 - - + +
89L GLY* 3.6 28.3 - - - +
90L VAL 4.2 2.9 - - - +
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Residues in contact with GLU 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L LYS 3.0 18.2 + - - +
28L ALA* 3.5 8.3 - - - +
30L VAL* 1.3 77.7 - - - +
32L LEU* 1.3 64.6 + - - +
34L ASN* 3.6 4.6 + - - +
35L ARG* 3.2 27.4 + - - +
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Residues in contact with LEU 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L ALA 3.0 12.6 + - - +
29L THR* 3.0 12.2 + - + +
31L GLU* 1.3 76.6 - - - +
33L LEU* 1.3 64.1 + - - +
35L ARG* 3.3 36.6 - - - +
36L GLN* 3.3 21.1 + - + +
135L ALA* 3.9 31.4 - - + +
138L GLU* 3.6 19.7 - - + +
139L ALA* 4.0 23.6 - - + +
144L THR* 5.1 4.9 - - + -
148L LEU* 4.2 11.2 - - + -
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Residues in contact with LEU 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29L THR* 2.8 29.4 + - + +
30L VAL 3.9 3.1 - - - +
32L LEU* 1.3 72.7 - - - +
34L ASN* 1.3 57.8 + - - +
35L ARG 3.0 1.8 - - - -
36L GLN* 2.7 27.6 + - - +
37L VAL* 2.8 16.4 + - - +
80L MET* 3.6 34.0 - - + +
83L ARG* 3.5 21.5 - - + -
84L ALA* 3.4 37.2 - - + +
144L THR* 3.5 25.4 - - + -
147L ILE* 5.2 2.7 - - + -
148L LEU* 4.6 10.3 - - + -
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Residues in contact with ASN 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L VAL* 3.0 38.1 + - - +
31L GLU* 4.1 5.1 - - - +
33L LEU* 1.3 76.0 - - - +
35L ARG* 1.3 61.2 + - - +
37L VAL* 3.6 9.0 - - - +
38L ILE* 3.1 33.0 + - + +
81L ALA* 6.0 0.2 - - - -
84L ALA* 4.5 4.8 - - - +
90L VAL 3.0 21.7 + - - -
91L ALA* 3.3 6.0 - - - +
92L LEU* 2.6 51.0 + - + +
101L LYS* 5.8 1.1 - - - +
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Residues in contact with ARG 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L GLU* 3.2 18.2 + - - +
32L LEU* 3.3 38.2 - - - +
33L LEU 3.0 0.2 - - - -
34L ASN* 1.3 78.4 - - - +
36L GLN* 1.3 70.8 + - - +
38L ILE* 3.7 9.3 + - - +
39L GLN* 3.4 22.8 + - - +
103L PRO* 5.7 1.4 - - - +
131L ASP* 2.8 41.4 + - - -
135L ALA* 4.4 4.0 - - - +
138L GLU* 3.8 14.6 + - - -
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Residues in contact with GLN 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L LEU* 3.5 16.8 - - + +
33L LEU* 2.7 8.7 + - - +
35L ARG* 1.3 84.7 + - - +
37L VAL* 1.3 55.3 + - - +
39L GLN* 2.9 26.5 + - - +
40L PHE* 2.7 58.9 + - - -
80L MET* 3.6 18.6 - - + -
131L ASP* 3.6 10.9 - - - +
132L VAL* 3.6 21.0 - - - +
135L ALA* 3.6 19.8 - - - +
148L LEU* 4.0 17.7 - - + -
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Residues in contact with VAL 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L LEU 2.8 23.2 + - - +
34L ASN* 3.4 15.2 + - - +
36L GLN* 1.3 72.9 - - - +
38L ILE* 1.3 57.4 + - - +
40L PHE* 3.2 2.2 + - - +
41L ILE* 2.8 52.7 + - + +
77L LEU* 4.1 13.0 - - + +
80L MET* 4.0 14.5 - - + +
81L ALA* 3.8 36.6 - - + +
84L ALA* 6.1 0.4 - - + -
91L ALA* 5.9 0.4 - - + -
92L LEU 3.6 21.5 - - - +
93L GLY* 4.8 0.4 - - - -
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Residues in contact with ILE 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L ASN 3.1 20.8 + - - +
35L ARG* 3.8 8.5 - - - +
37L VAL* 1.3 76.1 - - - +
39L GLN* 1.3 63.4 + - - +
41L ILE 3.5 0.2 + - - -
42L ASP* 3.1 23.9 + - - +
92L LEU* 4.0 16.8 - - + +
97L VAL* 3.6 7.9 - - + -
98L ILE* 3.5 36.9 - - + +
101L LYS* 3.4 46.0 - - + +
102L THR* 4.0 24.2 - - - +
103L PRO* 5.0 1.1 - - + -
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Residues in contact with GLN 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L ARG* 3.4 10.7 + - - +
36L GLN* 2.9 33.2 + - - +
38L ILE* 1.3 80.7 - - - +
40L PHE* 1.3 57.1 + - + +
42L ASP* 3.4 5.1 + - - +
43L LEU* 3.0 28.6 + - - +
103L PRO* 3.4 38.0 - - + +
104L LEU* 4.1 3.4 - - + +
127L ILE* 4.3 6.9 - - - +
128L VAL* 3.4 37.9 - - + +
131L ASP* 3.0 35.8 + - - +
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Residues in contact with PHE 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36L GLN* 2.7 52.0 + - - +
37L VAL 3.7 3.1 - - - +
39L GLN* 1.3 72.2 - - - +
41L ILE* 1.3 66.3 + - - +
43L LEU* 3.1 6.7 + - - +
44L SER* 2.9 25.5 + - - -
73L LEU* 3.8 29.8 - - + +
76L HIS* 4.0 15.9 - + + -
77L LEU* 4.0 16.3 - - + +
80L MET* 3.6 23.1 - - + -
128L VAL* 3.6 17.5 - - + -
132L VAL* 4.3 8.1 - - + -
151L ALA* 3.9 13.5 - - + -
155L LEU* 3.2 34.8 - - + -
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Residues in contact with ILE 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L VAL* 2.8 35.7 + - + +
38L ILE 3.9 3.8 - - - +
40L PHE* 1.3 72.4 - - - +
42L ASP* 1.3 61.2 + - - +
44L SER* 2.7 21.5 + - - +
45L LEU* 3.1 23.4 + - + +
77L LEU* 3.2 30.7 - - + -
93L GLY* 3.6 36.1 - - - +
98L ILE* 3.9 19.5 - - + -
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Residues in contact with ASP 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L ILE 3.1 17.7 + - - +
39L GLN 3.8 3.6 - - - +
41L ILE* 1.3 75.8 - - - +
43L LEU* 1.3 59.2 + - - +
45L LEU* 3.2 13.1 + - - +
46L ILE* 2.9 44.3 + - - +
98L ILE* 3.7 16.8 - - + +
102L THR* 2.7 35.6 + - - +
104L LEU* 3.4 20.4 - - + +
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Residues in contact with LEU 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L GLN 3.0 17.8 + - - +
40L PHE* 3.1 6.7 + - + +
42L ASP* 1.3 76.1 - - - +
44L SER* 1.3 53.2 + - - +
46L ILE* 3.3 8.2 + - + +
47L THR* 2.7 36.8 + - - -
73L LEU* 4.1 10.8 - - + -
104L LEU* 3.9 10.7 - - + +
124L ARG* 3.8 28.9 - - + +
125L TYR* 3.5 46.4 - - + -
128L VAL* 4.0 12.1 - - + -
155L LEU* 3.8 28.7 - - + -
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Residues in contact with SER 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L PHE 2.9 13.8 + - - -
41L ILE* 2.7 24.1 + - - +
43L LEU* 1.3 75.8 - - - +
45L LEU* 1.3 66.9 + - - +
47L THR* 3.2 5.6 + - - -
48L LYS* 3.2 21.0 + - - +
70L ARG* 4.1 20.5 + - - +
73L LEU* 3.8 26.4 - - - +
74L ILE* 4.6 13.9 - - - +
77L LEU* 4.7 2.3 - - - +
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Residues in contact with LEU 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L ILE* 3.1 27.0 + - + +
42L ASP* 3.2 19.9 + - - +
44L SER* 1.3 83.9 + - - +
46L ILE* 1.3 64.1 + - + +
48L LYS* 3.3 8.9 + - - +
49L GLN* 3.1 22.3 + - - +
52L TRP* 5.3 1.6 - - - -
98L ILE* 5.2 7.4 - - + -
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Residues in contact with ILE 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42L ASP* 2.9 33.8 + - - +
43L LEU* 3.5 6.7 - - + +
45L LEU* 1.3 75.1 - - + +
47L THR* 1.3 66.2 + - - +
49L GLN* 3.0 17.5 + - + +
50L ALA* 3.0 13.3 + - - +
104L LEU* 3.7 29.6 - - + -
105L LYS 4.7 2.2 - - - +
106L SER* 6.2 0.2 - - - -
107L TYR* 3.4 40.4 - - + +
121L LEU* 3.9 11.0 - - + -
124L ARG* 4.1 24.9 - - + +
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Residues in contact with THR 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L LEU 2.7 23.3 + - - -
44L SER* 3.2 11.6 + - - -
46L ILE* 1.3 76.0 - - - +
48L LYS* 1.3 58.2 + - + +
50L ALA* 3.5 2.3 + - - +
51L HIS* 2.9 28.8 + - + +
66L LEU* 3.3 45.3 - - + +
70L ARG* 4.5 9.6 - - + +
73L LEU* 3.8 3.0 - - - +
121L LEU* 4.2 9.9 - - - -
125L TYR* 2.6 32.6 + - - +
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Residues in contact with LYS 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44L SER 3.2 10.6 + - - +
45L LEU* 3.6 9.4 - - + +
46L ILE 3.2 0.6 - - - -
47L THR* 1.3 78.7 - - + +
49L GLN* 1.3 59.4 + - - +
51L HIS* 3.1 34.1 + - + +
52L TRP* 2.8 71.5 + - + +
67L ASP* 2.8 24.5 + - - +
70L ARG* 2.9 52.8 - - + +
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Residues in contact with GLN 49 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45L LEU 3.1 13.9 + - - +
46L ILE* 3.0 14.5 + - - +
48L LYS* 1.3 78.1 - - - +
50L ALA* 1.3 63.1 + - - +
52L TRP* 4.0 14.8 - - + -
53L ASN* 2.9 55.2 + - - +
107L TYR* 4.2 21.3 - - + -
108L PRO 4.5 3.8 + - - -
109L LEU* 4.0 32.2 - - + +
117L HIS* 4.6 1.6 - - - -
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Residues in contact with ALA 50 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46L ILE 3.0 3.3 + - - +
47L THR 3.8 2.5 - - - +
49L GLN* 1.3 79.4 - - - +
51L HIS* 1.3 64.7 + - - +
53L ASN 3.3 1.7 + - - -
54L MET* 3.2 32.0 + - + +
107L TYR* 3.4 24.1 - - + +
117L HIS* 3.4 17.9 - - + +
121L LEU* 3.6 35.2 - - + -
----------------------------------------------------------
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Residues in contact with HIS 51 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47L THR* 2.9 20.8 + - + +
48L LYS* 3.1 37.4 + - + +
50L ALA* 1.3 78.0 - - - +
52L TRP* 1.3 87.8 + + - +
54L MET* 3.5 10.1 + - - +
59L PHE* 4.6 1.2 - - - -
63L HIS* 2.7 80.4 + + - -
64L GLU* 5.0 0.4 - - - -
66L LEU* 4.0 17.0 - - + +
67L ASP* 3.8 21.1 + - + -
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Residues in contact with TRP 52 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160H TRP* 3.8 27.4 + + + -
45L LEU 5.3 0.9 - - - -
48L LYS* 2.8 59.7 + - + +
49L GLN* 4.0 17.7 - - + -
51L HIS* 1.3 95.5 + + - +
53L ASN* 1.3 73.4 + - - +
54L MET 3.7 2.8 + - - +
63L HIS* 4.7 4.5 - + - -
70L ARG* 5.5 2.5 - - - -
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Residues in contact with ASN 53 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49L GLN* 2.9 46.0 + - - +
50L ALA 3.3 5.2 + - - -
52L TRP* 1.3 89.3 - - - +
54L MET* 1.3 60.4 + - - +
55L ARG* 4.7 2.8 - - - +
111L ILE 4.6 1.3 - - - +
112L HIS* 3.1 39.2 + - + +
117L HIS* 3.4 15.7 + - + +
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Residues in contact with MET 54 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160H TRP* 5.2 1.4 + - - -
164H SER* 4.4 0.9 + - - -
50L ALA* 3.2 18.3 + - + +
51L HIS 3.5 11.0 - - - +
52L TRP 3.6 3.3 - - - +
53L ASN* 1.3 78.8 - - - +
55L ARG* 1.3 69.0 + - - +
59L PHE* 3.4 32.3 - - + +
62L VAL* 3.5 27.4 - - + -
63L HIS* 4.2 12.3 - - - -
66L LEU* 3.4 30.7 - - + -
112L HIS 3.2 5.4 - - - +
114L VAL* 4.4 16.8 - - + +
117L HIS* 3.7 29.6 - - + -
118L LEU* 5.0 0.9 - - + -
121L LEU* 4.6 2.0 - - + -
----------------------------------------------------------
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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