Contacts of the helix formed by residues 76 - 103 (chain D) in PDB entry 5W97
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 76 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D THR* 1.3 76.8 - - - +
77D GLU* 1.3 64.0 + - - +
78D TRP* 3.1 12.9 + - - -
79D LYS* 3.2 49.0 + - + +
80D THR* 3.8 1.6 + - - -
8K ASP* 5.3 0.4 + - - -
10K HIS* 3.5 29.2 - - + +
11K ASP* 2.7 34.2 + - - +
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Residues in contact with GLU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASP* 4.1 2.6 - - - +
408A THR* 2.4 46.6 + - + +
411A LYS* 2.9 36.8 + - - -
75D THR* 3.4 14.1 + - - +
76D ASN* 1.3 75.3 - - - +
78D TRP* 1.3 63.0 + - - +
80D THR* 2.9 5.9 + - - -
81D VAL* 2.9 22.0 + - + +
201D TGL 3.7 13.9 - - - +
10K HIS* 3.5 30.6 - - + +
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Residues in contact with TRP 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D THR 3.9 18.8 + - - -
76D ASN* 3.1 7.2 + - - +
77D GLU* 1.3 76.9 - - - +
79D LYS* 1.3 84.0 + - + +
81D VAL* 3.2 2.0 + - - +
82D VAL* 2.8 54.2 + - + +
201D TGL 3.3 36.1 + - + +
18K LEU* 3.9 29.6 - - + -
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Residues in contact with LYS 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ASN* 3.3 41.7 + - + +
78D TRP* 1.3 108.7 - - + +
80D THR* 1.3 61.4 + - - +
83D GLY* 2.9 27.7 + - - -
10K HIS 5.2 1.6 + - - -
11K ASP* 6.3 0.2 - - - +
14K GLY 3.6 22.2 - - - +
15K ASN* 2.8 34.7 + - - +
18K LEU* 3.7 23.9 - - + +
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Residues in contact with THR 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A THR* 4.1 9.9 - - + -
412A ILE* 4.9 0.2 - - - -
606A PGV 3.6 30.3 - - + -
77D GLU 2.9 8.3 + - - -
79D LYS* 1.3 77.0 - - - +
81D VAL* 1.3 58.5 + - - +
84D ALA* 2.8 34.5 + - - +
9K PHE* 3.9 13.3 - - + -
10K HIS* 2.9 32.5 + - + +
14K GLY* 3.7 16.7 + - - -
17K VAL* 3.7 15.3 - - + +
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Residues in contact with VAL 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A THR* 4.1 9.9 - - + +
411A LYS* 3.9 45.1 - - + +
412A ILE* 3.8 12.6 - - - +
415A ALA* 4.7 3.6 - - + -
77D GLU* 2.9 34.5 + - + +
78D TRP* 3.6 9.4 - - - +
79D LYS 3.2 0.2 - - - -
80D THR* 1.3 76.7 - - - +
82D VAL* 1.3 59.5 + - - +
85D ALA* 2.9 27.5 + - - +
201D TGL 3.9 28.5 - - + -
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Residues in contact with VAL 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ALA* 6.1 0.7 - - - -
78D TRP* 2.8 38.2 + - + +
81D VAL* 1.3 68.7 - - - +
83D GLY* 1.3 67.2 + - - +
85D ALA* 3.2 6.4 + - - +
86D MET* 2.9 55.0 + - + +
201D TGL 4.6 39.3 - - + -
18K LEU* 3.9 12.3 - - + -
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Residues in contact with GLY 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D LYS 2.9 18.7 + - - -
80D THR 3.9 0.2 - - - -
82D VAL* 1.3 77.1 - - - +
84D ALA* 1.3 57.4 + - - +
86D MET* 3.5 3.5 + - - -
87D PHE* 3.0 22.9 + - - +
17K VAL* 3.6 23.5 - - - +
18K LEU* 3.7 13.1 - - - +
21K GLY* 3.5 12.4 - - - -
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Residues in contact with ALA 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ILE* 3.4 29.8 - - + -
606A PGV 3.8 24.7 - - + -
80D THR 2.8 22.6 + - - +
83D GLY* 1.3 70.7 - - - +
85D ALA* 1.3 65.8 + - - +
87D PHE* 3.1 8.5 + - - +
88D PHE* 3.1 32.0 + - + -
17K VAL* 3.7 3.7 - - - +
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Residues in contact with ALA 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ILE* 4.1 5.5 - - - +
415A ALA* 3.9 26.5 - - + -
416A ILE* 4.0 18.7 - - + +
81D VAL 2.9 18.6 + - - +
82D VAL* 3.2 6.5 + - - +
84D ALA* 1.3 76.7 - - - +
86D MET* 1.3 58.3 + - + +
88D PHE* 3.1 4.2 + - - +
89D ILE* 2.9 39.3 + - + +
201D TGL 5.4 5.6 - - + -
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Residues in contact with MET 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D VAL* 2.9 44.6 + - + +
83D GLY 3.8 3.8 - - - +
85D ALA* 1.3 72.6 - - - +
87D PHE* 1.3 65.8 + - - +
89D ILE* 4.4 6.7 - - - -
90D GLY* 2.9 17.8 + - - -
201D TGL 4.8 28.3 - - + -
18K LEU* 4.4 9.0 - - + -
21K GLY 3.7 15.5 - - - +
22K ALA* 3.8 28.3 - - + +
25K CYS* 3.2 24.5 - - + +
26K VAL* 6.1 3.1 - - - -
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Residues in contact with PHE 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A PGV 3.9 59.5 - - + -
83D GLY 3.0 14.8 + - - +
84D ALA* 3.1 12.1 + - - +
86D MET* 1.3 77.2 - - - +
88D PHE* 1.3 81.1 + + - +
90D GLY* 3.2 2.3 + - - -
91D PHE* 2.8 34.5 + + + +
20K SER* 5.5 2.2 - - - -
21K GLY* 4.1 13.9 + - - -
24K PHE* 3.5 41.6 - + + -
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Residues in contact with PHE 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A TRP* 3.7 30.1 - + - -
412A ILE* 4.3 10.3 - - + -
416A ILE* 3.7 22.0 - - + -
463A THR* 3.7 13.0 - - + +
467A LEU* 4.1 6.5 - - + -
606A PGV 4.5 14.4 - - + -
84D ALA* 3.1 27.5 + - + -
85D ALA 3.8 0.9 - - - +
87D PHE* 1.3 95.6 - + - +
89D ILE* 1.3 61.3 + - - +
91D PHE* 3.4 9.0 + + - +
92D THR* 2.9 29.6 + - - -
19M LEU* 3.5 26.9 - - + -
23M PHE* 3.7 36.3 - + - -
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Residues in contact with ILE 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ALA 5.6 0.2 - - - -
416A ILE* 4.5 13.5 - - + -
419A VAL* 4.1 30.7 - - + -
460A ILE* 4.2 33.4 - - + -
85D ALA* 2.9 27.4 + - + +
86D MET* 3.9 6.1 - - - +
88D PHE* 1.3 75.2 - - - +
90D GLY* 1.3 57.6 + - - +
92D THR* 2.9 29.8 + - - -
93D ALA 3.3 0.2 + - - -
201D TGL 4.4 25.4 - - + -
25K CYS* 4.1 10.5 - - - -
29K TRP* 3.1 26.0 + - + +
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Residues in contact with GLY 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D MET 2.9 15.3 + - - -
87D PHE 3.5 4.3 - - - -
89D ILE* 1.3 75.1 - - - +
91D PHE* 1.3 61.8 + - - +
93D ALA* 3.0 19.6 + - - +
94D LEU 3.7 2.8 + - - -
24K PHE* 3.5 15.7 - - - -
25K CYS* 3.9 17.2 - - - -
28K VAL* 3.9 8.9 - - - +
29K TRP* 4.0 7.9 - - - -
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Residues in contact with PHE 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A THR* 4.3 7.6 - - + -
466A MET* 4.4 3.6 - - + -
606A PGV 4.6 24.2 - - + -
87D PHE* 2.8 28.4 + + + +
88D PHE* 3.4 17.9 - + + +
89D ILE 3.2 0.2 - - - -
90D GLY* 1.3 74.0 - - - +
92D THR* 1.3 65.2 + - - +
94D LEU* 3.1 35.5 + - + +
95D LEU* 3.6 37.3 + - + +
24K PHE* 3.4 12.4 - + + -
23M PHE* 3.5 40.4 - + - -
27M LEU* 4.3 7.6 - - + -
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Residues in contact with THR 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ILE* 5.8 0.2 - - - +
459A PHE* 3.4 44.4 - - + +
460A ILE* 3.5 18.3 - - + +
463A THR* 2.8 23.0 + - - +
88D PHE 2.9 13.9 + - - -
89D ILE* 2.9 16.1 + - - -
91D PHE* 1.3 79.3 - - - +
93D ALA* 1.3 60.7 + - - +
95D LEU* 2.9 19.3 + - + +
96D LEU* 3.2 15.4 + - + +
29K TRP* 4.9 0.9 - - + -
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Residues in contact with ALA 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ILE 3.3 2.2 + - - -
90D GLY 3.0 13.6 + - - +
92D THR* 1.3 77.4 - - - +
94D LEU* 1.3 56.8 + - - +
96D LEU* 3.4 12.7 + - - +
97D ILE* 3.0 30.1 + - - +
28K VAL* 3.5 24.5 - - + +
29K TRP* 3.5 32.9 - - + +
32K MET* 4.2 6.4 - - + +
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Residues in contact with LEU 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D GLY 4.3 3.4 - - - +
91D PHE* 3.1 29.9 + - + +
93D ALA* 1.3 74.8 - - - +
95D LEU* 1.3 65.4 + - + +
97D ILE* 3.6 13.7 - - + +
98D TRP* 2.9 29.5 + - - +
24K PHE* 4.5 15.5 - - + -
28K VAL* 3.5 29.8 - - + -
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Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A PHE* 3.8 27.5 - - + +
462A LEU* 4.6 7.6 - - + -
463A THR* 4.4 11.9 - - - +
466A MET* 5.1 1.8 - - + -
91D PHE* 4.0 33.2 - - + +
92D THR* 2.9 13.7 + - + +
94D LEU* 1.3 80.1 - - + +
96D LEU* 1.3 58.1 + - - +
98D TRP* 3.4 10.0 - - + +
99D GLU* 2.9 26.3 + - - +
27M LEU* 3.9 33.0 - - + -
101M DMU 3.9 25.1 - - + +
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Residues in contact with LEU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A SER 4.9 0.2 - - - +
456A MET* 3.7 48.0 - - + +
459A PHE* 3.8 26.0 - - + -
92D THR* 3.2 16.5 + - + +
93D ALA* 3.6 9.2 - - - +
95D LEU* 1.3 74.9 - - - +
97D ILE* 1.3 63.5 + - - +
99D GLU* 3.2 23.8 + - - +
100D LYS* 3.1 23.7 + - - +
29K TRP* 4.1 18.6 - - + -
32K MET* 4.0 18.2 - - - -
36K ILE* 4.6 0.7 - - - +
38K ILE* 5.8 1.3 - - + +
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Residues in contact with ILE 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ALA 3.0 20.5 + - - +
94D LEU* 3.3 16.8 + - + +
96D LEU* 1.3 70.0 - - - +
98D TRP* 1.3 69.4 + - - +
99D GLU 3.2 0.2 + - - -
100D LYS* 3.3 3.8 + - - +
101D HIS* 3.1 25.6 + - + +
28K VAL* 4.1 19.7 - - + -
31K TYR* 3.9 28.5 - - + -
32K MET* 3.9 10.5 - - + -
36K ILE* 3.9 33.2 - - + +
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Residues in contact with TRP 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LEU 2.9 13.4 + - - +
95D LEU* 3.4 11.2 - - + +
97D ILE* 1.3 80.2 - - - +
99D GLU* 1.3 69.6 + - + +
101D HIS* 4.7 0.9 - - - -
102D TYR* 3.0 56.4 + + + +
103D VAL* 3.3 30.3 - - + -
31M GLY* 3.7 28.5 - - - -
34M LEU* 4.6 5.4 - - + -
35M TYR* 4.4 6.3 - - + -
101M DMU 3.2 86.9 + - + +
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Residues in contact with GLU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA* 4.0 15.9 - - - +
455A SER* 6.1 0.7 - - - -
459A PHE* 3.7 29.1 - - + -
95D LEU 2.9 14.8 + - - +
96D LEU* 3.4 27.2 - - - +
97D ILE 3.1 0.8 - - - -
98D TRP* 1.3 86.3 - - + +
100D LYS* 1.3 62.6 + - - +
103D VAL* 3.0 40.5 + - + +
104D TYR* 3.2 45.1 + - + -
34M LEU* 5.5 5.6 - - + +
101M DMU 5.6 0.6 - - + +
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Residues in contact with LYS 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLN* 4.2 14.5 + - - +
96D LEU 3.1 15.8 + - - +
97D ILE 3.3 4.0 + - - +
99D GLU* 1.3 75.5 - - - +
101D HIS* 1.3 63.5 + - - +
104D TYR* 3.3 42.4 + - + +
105D GLY 5.1 5.5 + - - -
106D PRO* 6.2 0.6 - - - +
107D ILE* 5.5 4.3 - - - +
36K ILE* 3.9 30.1 + - + +
37K GLY* 3.7 26.5 + - - -
38K ILE* 3.7 27.8 - - + +
39K GLU 5.0 0.9 - - - +
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Residues in contact with HIS 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ILE* 3.1 19.2 + - + +
98D TRP* 3.9 2.5 - - - +
100D LYS* 1.3 84.2 - - - +
102D TYR* 1.3 98.2 + + + +
103D VAL 4.0 0.2 + - - -
104D TYR 4.5 3.8 - - - +
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Residues in contact with TYR 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D TRP* 3.0 56.7 + + + +
101D HIS* 1.3 106.7 - + + +
103D VAL* 1.3 59.7 + - - +
104D TYR 5.2 0.2 - - - -
35M TYR* 3.6 52.5 - + + +
101M DMU 4.3 21.9 + - - -
----------------------------------------------------------
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Residues in contact with VAL 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA* 6.2 0.4 - - + -
47A LEU* 3.9 31.1 - - + +
98D TRP* 3.3 37.2 - - + -
99D GLU* 3.0 26.2 + - + +
102D TYR* 1.3 80.9 - - - +
104D TYR* 1.3 68.7 + - + +
105D GLY 3.5 2.8 + - - -
34M LEU* 4.0 40.6 - - + +
37M LEU* 4.9 3.1 - - + +
----------------------------------------------------------
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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