Contacts of the helix formed by residues 77 - 106 (chain F) in PDB entry 3A68
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 LEU 77 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F PHE* 3.5 39.3 + - + +
75F VAL* 3.2 2.2 + - + +
76F ALA* 1.3 79.0 - - - +
78F ARG* 1.3 59.8 + - - +
80F LEU* 3.4 4.7 + - + +
81F ALA* 3.0 26.5 + - - +
128F ASP* 3.9 9.9 - - - +
129F ALA* 4.1 14.6 - - + -
197F VAL* 4.2 5.8 - - + -
198F TRP* 4.5 8.3 - - + -
201F ASP* 3.3 32.5 - - + +
190V ARG* 3.7 52.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F PHE 5.2 0.2 - - - -
76F ALA* 3.6 8.4 + - - -
77F LEU* 1.3 72.0 - - - +
79F GLY* 1.3 60.4 + - - +
81F ALA* 3.7 8.2 - - + +
82F LYS* 3.0 29.5 + - - +
198F TRP* 4.8 0.2 - - - +
201F ASP* 3.1 5.9 + - - +
202F GLN* 3.0 23.8 + - - +
205F LEU* 3.8 29.1 - - + +
183V GLU* 4.9 22.0 - - - +
184V TYR* 6.2 0.2 - - - -
187V GLN* 3.0 36.6 + - - +
203V MET* 3.7 15.8 - - - +
207V GLU* 3.3 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 79 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F ARG* 1.3 75.5 - - - +
80F LEU* 1.3 59.7 + - - +
82F LYS* 3.4 3.3 + - - +
83F PHE* 2.9 28.8 + - - +
201F ASP* 2.9 30.2 + - - -
204F LEU* 3.8 11.4 - - - +
205F LEU* 3.6 20.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F PHE* 3.7 40.2 - - + -
77F LEU* 3.8 7.0 - - + +
79F GLY* 1.3 69.6 - - - +
81F ALA* 1.3 66.2 + - - +
83F PHE* 3.2 2.1 + - - +
84F PHE* 3.0 42.3 + - + -
129F ALA* 3.8 31.0 - - + +
133F MET* 4.3 9.2 - - + -
197F VAL* 5.7 0.4 - - + +
200F PHE* 4.1 18.2 - - + -
201F ASP* 2.7 36.0 + - + +
204F LEU* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F PHE* 3.3 29.6 - - + +
70F PHE* 3.8 28.1 - - - +
71F ASP* 3.9 10.8 - - + +
77F LEU 3.0 17.4 + - - +
78F ARG* 3.7 8.3 - - + +
79F GLY 3.3 0.2 - - - -
80F LEU* 1.3 76.2 - - - +
82F LYS* 1.3 58.6 + - - +
84F PHE* 3.3 1.0 + - - -
85F LYS 2.9 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F PHE* 5.8 0.2 - - - -
78F ARG 3.0 17.1 + - - +
79F GLY 3.6 4.3 - - - +
81F ALA* 1.3 74.7 - - - +
83F PHE* 1.3 65.6 + - - +
85F LYS* 3.3 8.3 + - + +
86F GLU* 3.0 54.8 + - + +
204F LEU 4.3 6.0 + - - -
205F LEU* 3.1 44.5 + - + +
207F GLU 5.4 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F TYR* 5.6 2.5 - + - -
79F GLY 2.9 18.0 + - - +
80F LEU 3.2 3.1 + - - +
82F LYS* 1.3 76.9 - - - +
84F PHE* 1.3 84.7 + + - +
86F GLU* 3.4 6.9 + - + +
87F SER* 2.8 49.3 + - - -
133F MET* 3.7 28.7 - - + -
136F ALA* 5.4 0.2 - - + -
180F ARG* 3.5 42.8 - - - -
181F ILE* 4.3 21.8 - - + -
184F TYR* 3.8 17.3 - + - -
204F LEU* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F TYR* 3.6 44.9 - + - +
66F MET* 3.7 31.0 - - + -
67F PHE* 3.6 9.2 - - - +
70F PHE* 3.7 32.5 - + - -
80F LEU* 3.0 35.6 + - + +
83F PHE* 1.3 95.5 - + - +
85F LYS* 1.3 60.3 + - - +
87F SER* 3.6 3.2 - - - -
88F SER* 2.8 30.3 + - - -
132F ALA* 4.2 11.4 - - + -
133F MET* 4.2 20.2 - - + -
136F ALA* 4.1 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 85 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ARG* 4.6 1.9 + - - -
96B GLU* 3.2 40.3 + - - +
100B GLU* 2.6 25.9 + - - -
216B CA 4.5 3.4 - - - -
64F HIS* 4.9 0.4 - - - +
67F PHE* 3.5 36.3 - - + +
81F ALA 2.9 17.7 + - - +
82F LYS* 3.7 8.3 - - + +
84F PHE* 1.3 77.2 - - - +
86F GLU* 1.3 62.6 + - + +
88F SER* 3.4 7.5 + - - -
89F GLU* 3.3 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F LYS* 3.0 54.5 + - + +
83F PHE* 3.9 6.0 - - + +
85F LYS* 1.3 75.7 - - + +
87F SER* 1.3 65.5 + - - +
89F GLU* 3.3 11.4 + - - +
90F GLU* 3.0 22.3 + - - +
180F ARG* 5.9 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F TYR* 3.6 28.4 - - - -
83F PHE* 2.8 49.0 + - - -
84F PHE* 3.6 7.0 - - - -
86F GLU* 1.3 76.2 - - - +
88F SER* 1.3 62.0 + - - +
90F GLU* 3.2 7.2 + - - +
91F GLU* 2.9 28.8 + - - +
180F ARG* 5.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B TYR* 4.6 0.2 + - - -
92B ARG* 2.9 18.6 + - - -
60F SER* 2.8 48.8 + - - +
63F TYR* 3.8 8.0 - - - +
64F HIS* 3.4 23.4 + - - -
84F PHE 2.8 17.1 + - - -
85F LYS 3.5 6.1 - - - -
86F GLU 3.3 0.2 - - - -
87F SER* 1.3 76.8 - - - +
89F GLU* 1.3 62.9 + - - +
91F GLU 3.3 1.0 + - - -
92F ARG* 3.1 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 89 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLU* 4.6 11.6 - - - +
92B ARG* 3.5 23.9 + - - +
93B GLU* 5.5 3.1 - - - +
85F LYS 3.3 10.7 + - - +
86F GLU* 3.6 13.2 - - - +
88F SER* 1.3 79.8 - - - +
90F GLU* 1.3 62.2 + - - +
92F ARG* 3.3 7.1 + - + +
93F GLU* 3.1 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F GLU 3.0 16.6 + - - +
87F SER* 3.2 8.0 + - - +
89F GLU* 1.3 73.3 - - - +
91F GLU* 1.3 63.5 + - - +
93F GLU* 3.1 17.3 + - - +
94F HIS* 2.9 60.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F GLU* 3.1 15.0 - - - +
59F VAL* 3.4 24.2 - - + +
60F SER* 3.5 23.6 - - - +
63F TYR* 3.6 20.9 - - + -
87F SER* 2.9 21.5 + - - +
90F GLU* 1.3 78.5 - - - +
92F ARG* 1.3 63.0 + - - +
94F HIS* 3.1 16.0 + - - +
95F ALA* 3.0 20.8 + - - +
140F GLU* 3.6 14.2 - - - +
143F THR* 5.3 0.2 - - - +
214F CA 2.5 30.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 92 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B SER* 4.7 2.8 + - - -
64B HIS* 3.5 18.0 + - + -
85B LYS 4.6 1.0 + - - -
88B SER* 2.9 30.3 + - - -
89B GLU* 3.5 37.2 + - - +
92B ARG* 3.3 33.3 - - - +
57F TYR* 3.8 30.2 + - + +
60F SER* 3.7 17.4 + - - +
88F SER 3.1 8.2 + - - +
89F GLU* 3.6 11.4 - - - +
90F GLU 3.2 0.2 - - - -
91F GLU* 1.3 76.0 - - - +
93F GLU* 1.3 72.4 + - - +
95F ALA* 3.2 7.2 + - - +
96F GLU* 2.9 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLU* 4.4 10.9 - - - +
89F GLU* 3.1 29.6 + - + +
90F GLU* 3.1 20.2 + - - +
92F ARG* 1.3 86.4 + - - +
94F HIS* 1.3 59.6 + - + +
96F GLU* 3.2 9.7 + - - +
97F LYS* 2.9 32.0 + - - +
216F CA 2.8 27.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 94 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F GLU* 3.6 14.3 + - - +
90F GLU* 2.9 53.6 + - + -
91F GLU* 3.1 16.2 + - - +
93F GLU* 1.3 79.3 - - + +
95F ALA* 1.3 62.1 + - - +
97F LYS* 4.6 9.9 - - - -
98F LEU* 3.3 9.0 + - - +
169F GLU 6.1 0.7 - - - -
170F TYR* 2.8 46.4 + + + -
173F GLU* 5.8 9.7 - - + +
174F GLN* 5.7 1.6 - - - -
214F CA 2.7 25.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F ILE* 3.9 11.3 - - + +
56F GLU* 3.8 23.2 - - + +
57F TYR* 3.8 32.8 - - + +
91F GLU 3.0 9.5 + - - +
92F ARG* 3.2 9.6 + - - +
94F HIS* 1.3 76.1 - - - +
96F GLU* 1.3 58.1 + - - +
98F LEU* 3.1 8.3 + - - +
99F MET* 3.0 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B HIS* 2.7 33.9 + - + +
67B PHE* 4.5 7.2 - - + -
85B LYS* 3.2 34.1 + - - +
92F ARG* 2.9 26.8 + - - +
93F GLU* 3.2 10.8 + - - +
95F ALA* 1.3 77.2 - - - +
97F LYS* 1.3 58.3 + - - +
99F MET* 3.2 10.4 + - - +
100F GLU* 2.9 39.4 + - - +
216F CA 2.6 28.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 97 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F GLU 2.9 17.1 + - - +
94F HIS* 3.8 8.4 - - - +
96F GLU* 1.3 77.1 - - - +
98F LEU* 1.3 58.1 + - - +
100F GLU* 3.4 17.3 + - - +
101F TYR* 2.9 26.3 + - - +
165F PHE* 4.1 13.2 - - + -
169F GLU* 2.8 50.8 + - + +
170F TYR* 3.3 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F VAL* 3.8 23.2 - - + +
52F GLN* 3.6 35.2 - - + -
53F ILE* 3.5 14.4 - - + +
56F GLU* 4.0 11.9 - - + -
94F HIS 3.3 8.8 + - - +
95F ALA 3.1 8.1 + - - +
97F LYS* 1.3 77.6 - - - +
99F MET* 1.3 59.1 + - - +
101F TYR* 3.5 4.2 - - + +
102F GLN* 2.9 29.5 + - - +
147F LEU* 5.4 0.2 - - + -
150F LEU* 4.4 17.7 - - + -
162F LEU* 5.8 0.2 - - + -
165F PHE* 3.7 22.9 - - + -
170F TYR* 3.3 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 99 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B HIS* 3.6 57.2 - - + +
67B PHE* 3.9 16.4 - - + -
68B ALA* 3.9 11.0 - - + -
53F ILE* 3.8 27.1 - - + +
57F TYR* 4.5 3.6 - - - -
95F ALA 3.0 22.2 + - - +
96F GLU* 3.4 16.4 - - - +
98F LEU* 1.3 75.9 - - - +
100F GLU* 1.3 63.0 + - - +
102F GLN* 3.4 3.8 + - - +
103F ASN* 3.3 21.2 + - - -
109F VAL* 3.6 17.3 - - + +
111F LEU* 4.2 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 4.0 18.4 - - + -
71B ASP* 4.1 11.7 - - - +
85B LYS* 2.5 36.6 + - - -
96F GLU* 2.9 23.4 + - - +
97F LYS* 3.6 18.9 - - - +
99F MET* 1.3 75.0 - - - +
101F TYR* 1.3 57.5 + - - +
103F ASN* 3.2 4.5 + - - +
104F LYS* 2.9 42.3 + - - +
179G LYS* 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F TYR* 4.3 9.6 - + - -
49F VAL* 4.7 6.1 - - + -
97F LYS 2.9 17.6 + - - +
98F LEU* 3.2 6.3 + - - +
100F GLU* 1.3 74.9 - - - +
102F GLN* 1.3 70.6 + - - +
104F LYS* 3.0 29.2 + - + +
105F ARG* 3.0 46.9 + - + +
161F GLN* 2.4 34.7 + - - -
162F LEU* 3.2 36.3 - - + -
165F PHE* 3.6 48.2 - + + -
175G VAL* 5.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F TYR* 2.6 41.0 + - - -
46F GLU* 3.0 33.2 + - - +
49F VAL* 3.7 11.7 - - + +
50F ASN* 3.0 26.1 + - - +
53F ILE* 4.8 0.9 - - + -
98F LEU 2.9 12.5 + - - +
99F MET 3.5 10.8 - - - +
101F TYR* 1.3 82.2 - - - +
103F ASN* 1.3 60.8 + - - +
105F ARG* 3.2 2.3 + - - +
106F GLY 3.1 4.0 + - - -
107F GLY* 2.9 40.5 + - - +
109F VAL* 3.6 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 5.5 0.8 - - - -
68B ALA* 2.9 30.3 + - - +
71B ASP* 3.0 47.6 + - - +
72B ARG* 3.5 17.6 - - - +
73B ASP* 4.3 6.6 + - - +
99F MET 3.3 10.0 + - - -
100F GLU 3.2 4.3 + - - +
101F TYR 3.1 0.4 - - - -
102F GLN* 1.3 77.4 - - - +
104F LYS* 1.3 66.2 + - - +
106F GLY* 3.1 11.7 + - - -
107F GLY 3.4 15.7 - - - +
109F VAL* 4.2 9.3 + - - +
179G LYS* 3.7 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ALA* 4.2 7.3 - - - +
100F GLU* 2.9 30.5 + - - +
101F TYR* 3.0 23.5 + - + +
103F ASN* 1.3 76.9 - - - +
105F ARG* 1.3 60.1 + - - +
106F GLY 3.6 0.2 + - - -
165F PHE* 6.1 2.8 - - - -
175G VAL* 3.9 27.4 - - + +
176G GLU* 2.7 42.8 + - - +
178G ILE* 5.8 0.5 - - - +
179G LYS* 3.9 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ALA* 4.5 1.5 - - - +
38F ARG* 3.3 26.8 - - - +
39F GLN 3.4 15.7 + - - +
40F LYS* 3.1 18.6 + - - +
41F TYR* 3.5 40.2 - - + +
101F TYR* 3.0 55.7 + - + +
102F GLN 3.2 0.9 + - - +
103F ASN 3.1 0.2 - - - -
104F LYS* 1.3 76.3 - - - +
106F GLY* 1.3 60.4 + - - +
107F GLY 3.6 0.2 + - - -
159F ASP* 2.8 41.8 + - - -
161F GLN* 3.6 15.8 + - - +
162F LEU* 3.8 1.2 - - - +
144G ASN* 6.2 0.2 - - - +
175G VAL* 3.8 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 106 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ASP* 3.8 9.4 - - - -
35F SER* 3.2 38.7 - - - -
37F ALA* 4.7 0.2 - - - -
38F ARG* 3.6 18.2 + - - -
102F GLN 3.1 2.6 + - - -
103F ASN* 3.1 9.2 + - - -
104F LYS 3.3 0.6 + - - -
105F ARG* 1.3 79.9 - - - +
107F GLY* 1.3 63.3 + - - +
108F LYS* 5.2 3.3 + - - +
217F ACY 4.6 1.4 - - - +
----------------------------------------------------------
Back to top of page
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