Contacts of the helix formed by residues 5 - 36 (chain A) in PDB entry 1KF9
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 5 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A PHE* 3.5 26.2 - - + +
2A PRO* 3.7 9.2 - - + -
3A THR* 3.8 8.0 - - + -
4A ILE* 1.3 97.7 - - - +
6A LEU* 1.3 66.5 + - - +
7A SER* 3.3 9.6 - - - +
8A ARG* 3.7 28.0 - - + +
9A LEU* 3.7 9.0 + - - +
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Residues in contact with LEU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 1.3 75.9 - - - +
7A SER* 1.3 65.6 + - - +
8A ARG 3.1 1.6 - - - -
9A LEU* 3.4 6.3 + - + +
10A ALA* 3.1 24.8 + - - +
124A LEU* 4.5 17.1 - - + +
127A ARG* 3.1 50.5 - - + +
128A LEU* 5.0 13.9 - - + -
184A SER* 6.2 3.8 - - - -
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Residues in contact with SER 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 3.3 7.9 - - - +
6A LEU* 1.3 78.5 - - - +
8A ARG* 1.3 68.2 + - - +
10A ALA* 3.6 4.0 - - - -
11A ASP* 2.7 39.2 + - - +
184A SER 5.5 9.1 + - - -
188A SER 5.1 9.2 + - - -
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Residues in contact with ARG 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 3.8 18.2 - - + -
5A PRO* 3.7 27.8 + - + +
7A SER* 1.3 84.3 - - - +
9A LEU* 1.3 62.2 - - + +
11A ASP* 3.0 6.2 + - - +
12A ASN* 3.0 32.8 + - - +
626C ASP* 5.8 2.2 - - - +
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 3.0 33.0 - - + -
5A PRO 3.7 9.1 + - - +
6A LEU* 3.4 8.0 + - + +
7A SER 3.3 0.4 - - - -
8A ARG* 1.3 73.8 - - - +
10A ALA* 1.3 58.0 + - - +
12A ASN* 5.6 1.8 - - - +
13A ALA* 2.8 32.7 + - - +
120A GLY 4.9 2.0 - - - +
123A THR* 3.3 33.9 - - + -
124A LEU* 3.6 36.5 - - + +
127A ARG* 4.5 16.2 - - + +
603C ILE 5.6 0.2 - - - +
604C TRP* 3.8 28.7 - - + +
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU 3.1 14.4 + - - +
7A SER* 3.8 4.5 - - - +
9A LEU* 1.3 75.7 - - - +
11A ASP* 1.3 69.4 + - - +
13A ALA* 3.9 5.9 - - - +
14A TRP* 3.2 22.7 + - - +
124A LEU* 4.3 12.8 - - + +
177A LEU* 5.1 0.9 - - - +
180A VAL* 5.2 5.2 - - + +
181A GLN* 3.7 33.1 - - + +
184A SER 6.4 1.1 - - - -
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Residues in contact with ASP 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A SER* 2.7 35.2 + - - +
8A ARG* 3.4 6.4 + - - +
10A ALA* 1.3 75.0 - - - +
12A ASN* 1.3 67.5 + - - +
14A TRP* 3.8 2.6 - - - +
15A LEU* 3.1 33.1 + - + +
181A GLN* 2.9 23.2 - - - +
188A SER 5.8 0.3 - - - +
718C ASN* 5.8 2.1 + - - -
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Residues in contact with ASN 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 6.1 0.6 - - - +
8A ARG* 3.0 22.7 + - - +
9A LEU* 5.2 1.4 - - - +
11A ASP* 1.3 80.6 - - - +
13A ALA* 1.3 66.5 + - - +
15A LEU* 3.4 5.7 + - - +
16A ARG* 3.0 22.0 + - - +
543C ARG* 3.4 18.4 + - - +
603C ILE* 4.3 16.4 + - - +
604C TRP* 3.4 19.2 - - + -
626C ASP* 3.6 19.4 + - - +
669C TRP* 3.1 32.9 - - + -
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU 2.8 23.0 + - - +
10A ALA* 3.9 4.9 - - - +
11A ASP 3.4 0.2 - - - -
12A ASN* 1.3 72.8 - - - +
14A TRP* 1.3 58.2 + - - +
16A ARG* 3.3 3.9 - - - +
17A ALA* 3.0 23.6 + - - +
117A LEU* 3.6 16.4 - - + +
120A GLY 5.2 6.7 - - - -
121A ILE* 5.2 0.9 - - + -
124A LEU* 4.2 17.9 - - + -
177A LEU* 4.3 17.5 - - + -
604C TRP* 3.8 12.7 - - + -
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Residues in contact with TRP 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA 3.2 9.7 + - - +
11A ASP 4.2 2.2 - - - -
13A ALA* 1.3 76.2 - - - +
15A LEU* 1.3 90.0 + - + +
17A ALA* 2.7 9.6 + - - +
18A ASP* 2.5 58.2 + - + +
174A SER* 3.4 38.3 + - - -
177A LEU* 4.4 12.5 - - + +
178A ARG* 3.6 37.3 - - + +
181A GLN* 3.2 31.9 - - - +
371B VAL* 3.9 30.1 - - + +
393B LEU* 4.4 15.0 - - + -
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 3.1 22.9 + - + +
12A ASN* 3.4 13.0 + - - +
14A TRP* 1.3 107.1 - - + +
16A ARG* 1.3 62.6 + - - +
18A ASP* 3.1 8.6 + - + +
19A ARG* 3.0 22.9 + - - +
543C ARG* 5.5 1.3 - - - +
668C GLY 5.4 4.7 - - - +
669C TRP* 3.7 24.2 - - + -
671C VAL* 6.2 3.4 - - + -
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Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASN 3.0 8.1 + - - +
13A ALA* 3.3 10.5 - - - +
15A LEU* 1.3 76.3 - - - +
17A ALA* 1.3 61.3 + - - +
19A ARG* 3.1 15.6 + - - +
20A LEU* 3.2 17.1 + - + +
112A ASP 5.4 0.4 + - - -
113A LEU* 3.0 49.5 - - - +
116A ASP* 3.0 25.6 + - - +
117A LEU* 4.2 20.2 - - + -
544C GLU* 6.2 1.6 - - - +
604C TRP* 4.5 10.1 - - + -
667C LYS* 4.7 6.3 + - - +
668C GLY 6.1 0.4 - - - -
669C TRP* 2.9 73.0 - - + +
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Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA 3.0 12.6 + - - +
14A TRP* 2.7 12.3 + - - +
16A ARG* 1.3 72.9 - - - +
18A ASP* 1.3 57.7 + - - +
20A LEU* 3.7 4.9 + - - +
21A ASN* 3.1 25.6 + - - +
117A LEU* 3.9 10.9 - - + +
170A MET* 4.2 3.9 - - - +
173A VAL* 3.5 31.2 - - + -
174A SER* 3.7 17.0 - - - -
177A LEU* 3.7 6.7 - - + -
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Residues in contact with ASP 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TRP* 2.5 47.5 + - + +
15A LEU* 3.3 14.4 - - + +
16A ARG 3.0 0.2 - - - -
17A ALA* 1.3 74.8 - - - +
19A ARG* 1.3 61.2 + - - +
21A ASN* 3.2 4.2 - - - +
22A GLN* 3.0 22.2 + - - +
174A SER* 3.9 10.1 + - - -
371B VAL* 5.1 0.9 - - - +
393B LEU* 5.5 0.9 - - - +
417B ARG* 2.7 46.5 + - - +
418B ASN* 3.4 9.0 + - - -
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Residues in contact with ARG 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU 3.0 10.9 + - - +
16A ARG* 3.1 10.3 + - - +
18A ASP* 1.3 72.0 + - - +
20A LEU* 1.3 53.8 - - - +
21A ASN 2.9 4.5 - - - -
22A GLN* 2.5 40.0 + - - +
23A LEU* 2.7 50.2 + - + +
103A TYR* 3.7 18.0 + - - +
113A LEU* 4.3 7.2 - - + -
417B ARG* 5.2 6.9 - - - +
665C ILE* 3.2 22.6 + - - +
666C GLN* 3.6 11.6 + - - +
667C LYS 3.1 22.0 - - - +
668C GLY* 3.1 33.0 - - - +
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 3.2 11.6 + - + +
17A ALA 3.8 4.0 - - - +
19A ARG* 1.3 78.3 - - - +
21A ASN* 1.3 57.3 + - - +
23A LEU* 3.8 6.6 - - + +
24A ALA* 2.8 32.2 + - - +
110A VAL* 3.7 31.6 - - + +
113A LEU* 3.6 30.5 - - + +
114A LEU* 3.9 31.0 - - + +
117A LEU* 3.8 28.3 - - + -
166A PHE* 4.2 7.7 - - + -
170A MET* 3.4 17.5 - - - +
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Residues in contact with ASN 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA 3.1 15.7 + - - +
18A ASP* 3.2 13.6 - - - +
19A ARG 2.9 0.2 - - - -
20A LEU* 1.3 78.1 - - - +
22A GLN* 1.3 64.6 + - - +
25A PHE* 2.9 23.7 + - - +
167A ASN* 3.5 19.8 - - - +
170A MET* 4.1 6.7 - - - +
171A SER* 3.8 29.8 + - - +
174A SER* 4.0 14.4 + - - -
417B ARG 4.1 3.8 - - - +
418B ASN* 2.9 28.0 + - - +
----------------------------------------------------------
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Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASP 3.0 7.8 + - - +
19A ARG* 2.5 62.0 + - - +
21A ASN* 1.3 76.2 - - - +
23A LEU* 1.3 85.8 + - - +
26A ASP* 2.5 45.7 + - - +
102A VAL* 5.1 0.8 - - - +
103A TYR* 3.5 33.3 + - - +
417B ARG* 4.2 15.5 - - - +
418B ASN* 2.9 22.8 - - - +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG* 2.7 48.9 + - + +
20A LEU* 3.8 9.2 - - + +
22A GLN* 1.3 91.0 - - - +
24A ALA* 1.3 54.9 + - - +
26A ASP* 4.4 0.3 - - - +
27A THR* 2.5 36.6 + - - +
97A PHE* 5.4 2.0 - - - -
102A VAL* 4.5 4.3 - - + -
103A TYR 4.1 3.6 - - - +
104A GLY* 3.5 28.5 - - - +
105A ALA* 3.8 11.2 - - + -
109A ASN* 4.2 8.5 - - - +
110A VAL* 4.2 23.1 - - + -
113A LEU* 3.8 18.8 - - + -
666C GLN 4.7 0.4 - - - +
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU 2.8 24.5 + - - +
21A ASN 3.9 1.8 - - - +
23A LEU* 1.3 72.1 - - - +
25A PHE* 1.3 61.5 + - - +
27A THR* 3.7 4.1 + - - -
28A TYR* 3.2 22.0 + - - +
163A LEU* 4.3 4.9 - - - +
166A PHE* 3.7 23.7 - - + -
167A ASN* 3.7 18.8 - - - +
170A MET* 3.6 22.0 - - + -
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Residues in contact with PHE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN 2.9 22.7 + - - +
22A GLN 3.7 1.3 - - - +
24A ALA* 1.3 71.4 - - - +
26A ASP* 1.3 65.9 + - - +
28A TYR* 2.7 36.9 + + - +
29A GLN* 2.8 61.7 + - + +
167A ASN* 3.4 29.1 - - - +
415B LYS* 4.5 9.2 - - - -
418B ASN* 3.2 37.7 - - + +
419B SER* 4.2 12.1 - - - -
420B GLY 4.7 6.1 - - - -
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Residues in contact with ASP 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN* 2.5 48.7 + - - +
25A PHE* 1.3 86.0 - - - +
27A THR* 1.3 56.4 + - - +
29A GLN* 3.7 13.9 - - - +
30A GLU* 2.8 30.7 + - - +
102A VAL* 3.6 23.6 - - + +
103A TYR* 2.3 33.4 + - + +
418B ASN* 4.0 2.8 - - - +
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Residues in contact with THR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 2.5 22.5 + - - +
24A ALA 3.7 3.8 + - - -
26A ASP* 1.3 77.3 - - - +
28A TYR* 1.3 57.8 + - - +
30A GLU* 3.6 3.3 - - - +
31A PHE* 2.9 31.2 + - - +
96A VAL* 5.3 4.7 - - - +
97A PHE* 3.5 27.9 - - + -
100A SER* 3.3 26.7 - - - +
102A VAL* 3.5 22.9 - - + -
105A ALA* 3.8 12.3 - - + -
163A LEU* 3.9 8.8 - - - +
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Residues in contact with TYR 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA 3.2 15.4 + - - +
25A PHE* 2.7 25.1 + + - +
27A THR* 1.3 77.9 + - - +
29A GLN* 1.3 68.6 + - + -
31A PHE* 3.7 1.9 - - - +
32A GLU* 3.3 42.5 + - - +
42A HIS* 3.7 11.1 + - - -
44A PHE* 3.5 19.7 - + - -
160A TYR* 3.5 26.7 - + - -
163A LEU* 3.7 23.1 - - + +
164A TYR* 3.6 40.1 - + + -
167A ASN* 4.5 14.1 - - + -
327B GLU* 5.1 1.5 + - - -
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Residues in contact with GLN 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 2.8 59.1 + - + +
26A ASP* 3.7 14.6 - - - +
28A TYR* 1.3 80.3 - - + +
30A GLU* 1.3 56.7 + - - +
32A GLU* 3.3 9.6 + - - +
33A GLU* 2.7 58.1 + - - +
415B LYS* 5.9 0.4 - - - +
420B GLY 4.9 6.3 + - - -
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASP 2.8 18.9 + - - +
27A THR* 3.6 5.8 - - - +
29A GLN* 1.3 79.5 - - - +
31A PHE* 1.3 68.4 + - - +
33A GLU* 3.0 14.3 + - - +
34A ALA* 3.0 20.2 + - + +
35A TYR* 5.8 2.5 - - + -
100A SER* 2.6 35.9 + - - -
101A LEU* 3.4 21.9 + - - +
102A VAL* 3.5 15.5 + - + +
----------------------------------------------------------
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Residues in contact with PHE 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR 2.9 22.2 + - - +
28A TYR 3.7 3.8 - - - +
30A GLU* 1.3 73.8 - - - +
32A GLU* 1.3 56.5 + - - +
35A TYR* 2.7 67.6 + + + +
36A ILE* 4.4 9.0 - - + -
96A VAL* 3.8 17.9 - - + -
156A LEU* 3.5 15.3 - - + -
159A ASN* 3.3 38.6 - - + -
160A TYR* 3.6 37.7 - + + -
163A LEU* 3.5 19.3 - - + -
----------------------------------------------------------
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 3.3 32.2 + - - +
29A GLN* 3.3 9.0 + - - +
30A GLU 3.2 0.2 - - - -
31A PHE* 1.3 74.2 - - - +
33A GLU* 1.3 60.1 + - - +
34A ALA 2.8 14.7 + - - -
35A TYR 3.3 0.2 + - - -
36A ILE* 3.1 46.0 + - + +
41A ILE* 3.4 30.4 - - + +
42A HIS* 4.9 0.9 + - - -
160A TYR* 2.7 40.0 + - + +
----------------------------------------------------------
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Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLN* 2.7 49.4 + - - +
30A GLU* 3.6 6.3 - - - +
32A GLU* 1.3 76.1 + - - +
34A ALA* 1.3 57.0 + - - +
1614F ASN 5.0 2.6 - - - +
1615F GLY* 3.1 26.5 - - - +
----------------------------------------------------------
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 3.0 17.4 + - + +
31A PHE 3.7 2.0 - - - +
32A GLU 2.8 2.6 + - - -
33A GLU* 1.3 82.4 - - - +
35A TYR* 1.3 82.9 + - + +
36A ILE 5.5 0.2 - - - -
1615F GLY 3.7 15.1 - - - +
1616F GLY* 4.1 14.2 - - - +
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Residues in contact with TYR 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 5.8 2.5 - - + -
31A PHE* 2.7 67.0 + + + +
32A GLU 3.3 0.2 + - - -
34A ALA* 1.3 94.6 - - + +
36A ILE* 1.3 65.5 + - + +
37A PRO* 3.4 11.3 - - - +
99A ASN* 5.5 3.5 + - - +
156A LEU* 4.7 22.8 - - + +
1617F THR* 5.9 1.4 + - - -
----------------------------------------------------------
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Residues in contact with ILE 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 4.4 7.0 - - + -
32A GLU* 3.1 36.1 + - + +
35A TYR* 1.3 77.0 - - - +
37A PRO* 1.4 71.1 - - + +
38A LYS* 3.6 2.4 + - - -
40A GLN* 3.5 27.8 - - + +
41A ILE* 3.8 6.3 - - + +
156A LEU* 3.8 28.9 - - + -
157A LEU* 5.1 4.3 - - + -
160A TYR* 3.3 54.1 - - + +
----------------------------------------------------------
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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