Contacts of the helix formed by residues 82 - 112 (chain K) in PDB entry 3IS7
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 82 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K TRP* 4.0 8.5 - - - -
80K GLY 3.6 0.2 - - - -
81K GLU* 1.3 81.9 + - - +
83K THR* 1.3 65.8 + - - +
84K GLN* 3.3 11.1 + - - +
85K GLU* 3.2 37.6 + - - +
86K MET* 3.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K TRP* 2.9 38.5 + - + +
35K TRP* 4.5 3.4 - - - -
37K LEU* 3.8 5.2 - - - +
40K LEU* 3.9 12.3 - - + -
82K ASN* 1.3 74.0 - - - +
84K GLN* 1.3 65.3 + - - +
86K MET* 3.2 4.7 + - - +
87K LEU* 3.1 36.3 + - + +
141K ILE* 4.9 3.1 - - + -
146K LEU* 5.3 2.9 - - - -
149K TYR* 4.4 7.2 - - + -
150K LEU* 3.4 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 84 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82K ASN* 3.3 8.3 + - - +
83K THR* 1.3 80.8 - - - +
85K GLU* 1.3 61.4 + - + +
87K LEU* 3.6 2.6 + - - +
88K GLN* 3.2 22.5 + - + +
138K LEU* 3.9 26.4 + - + +
141K ILE* 3.7 39.8 - - + +
142K GLN* 4.0 15.6 + - - +
146K LEU* 4.7 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K ILE 5.0 0.2 - - - +
80K GLY* 3.8 10.8 - - - -
81K GLU* 3.1 38.0 + - - +
82K ASN* 3.2 31.2 + - - +
84K GLN* 1.3 74.5 - - + +
86K MET* 1.3 55.9 + - - +
88K GLN* 3.6 7.1 - - - +
89K CYS* 2.6 43.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 86 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K HIS* 3.6 57.2 - - + +
31K MET* 3.9 17.0 - - + -
32K TRP* 3.5 35.4 - - + +
35K TRP* 3.5 27.4 - - + -
80K GLY* 3.9 14.1 - - - +
82K ASN* 3.0 24.7 + - - +
83K THR 3.2 4.0 + - - +
85K GLU* 1.3 77.2 - - - +
87K LEU* 1.3 56.9 + - - +
89K CYS* 3.1 5.2 + - - +
90K ASP* 2.9 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K TRP* 4.2 19.9 - - + -
40K LEU* 4.8 6.5 - - + -
44K GLU* 5.8 0.9 - - - +
83K THR* 3.1 25.0 + - + +
84K GLN 3.8 3.4 - - - +
86K MET* 1.3 74.6 - - - +
88K GLN* 1.3 55.8 + - - +
90K ASP* 3.2 9.8 + - - +
91K LEU* 2.8 35.4 + - - +
133K TYR* 4.7 5.6 - - + -
134K LEU* 4.1 23.9 - - + +
137K GLN* 3.9 32.1 - - + -
138K LEU* 3.9 16.4 - - + -
141K ILE* 4.0 23.8 - - + -
149K TYR* 4.4 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 88 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84K GLN* 3.2 15.5 + - + +
85K GLU* 3.8 6.7 - - - +
87K LEU* 1.3 78.6 - - - +
89K CYS* 1.3 58.3 + - - +
91K LEU* 3.1 20.5 + - - +
92K ASN* 2.9 61.2 + - - +
95K LEU* 5.6 1.6 - - - +
138K LEU* 3.8 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 89 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K GLN* 3.2 9.2 + - - +
28K HIS* 4.1 2.5 - - + -
78K LEU* 3.2 43.5 - - + +
79K ILE 4.1 2.0 - - - -
80K GLY* 3.8 17.5 - - - -
85K GLU* 2.6 30.5 + - - +
86K MET 3.1 6.3 + - - +
88K GLN* 1.3 73.4 - - - +
90K ASP* 1.3 61.7 + - - +
92K ASN* 3.5 9.8 + - - +
93K LEU* 3.0 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 90 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K GLN* 3.1 12.3 + - - +
25K TYR* 3.4 19.1 + - + -
28K HIS* 2.8 26.5 + - - -
32K TRP* 4.8 2.6 - - - -
44K GLU* 2.5 32.2 - - - +
86K MET 2.9 18.6 + - - +
87K LEU* 3.5 10.0 - - - +
89K CYS* 1.3 71.2 - - - +
91K LEU* 1.3 63.1 + - - +
93K LEU* 3.3 1.8 + - - +
94K GLU* 3.0 28.4 + - - +
130K HIS* 4.6 0.9 - - - -
134K LEU* 4.0 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87K LEU 2.8 20.1 + - - +
88K GLN* 3.1 19.7 + - - +
90K ASP* 1.3 70.3 - - - +
92K ASN* 1.3 65.5 + - - +
94K GLU* 3.1 2.8 + - - +
95K LEU* 3.0 48.1 + - + +
131K ILE* 4.0 33.2 - - + -
134K LEU* 4.1 16.8 - - + +
135K GLU* 4.0 23.8 - - + +
138K LEU* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K LEU* 3.9 14.9 - - + +
88K GLN* 2.9 53.8 + - - +
89K CYS* 3.7 9.4 - - - +
91K LEU* 1.3 71.3 - - - +
93K LEU* 1.3 62.4 + - - +
95K LEU* 3.6 12.5 + - - +
96K LYS* 3.4 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17K ASN* 5.3 5.6 - - + +
20K ILE* 4.0 27.1 - - + -
21K ALA* 3.6 39.7 - - + +
24K GLN* 3.5 27.8 - - - +
25K TYR* 4.1 7.9 - - + +
76K LYS 5.1 0.9 - - - +
78K LEU* 4.2 13.6 - - + +
89K CYS 3.0 17.9 + - - +
90K ASP 3.6 4.7 - - - +
91K LEU 3.2 0.4 - - - -
92K ASN* 1.3 77.7 - - - +
94K GLU* 1.3 57.1 + - - +
96K LYS* 3.5 10.6 + - + +
97K ALA* 3.0 26.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K ALA* 5.9 0.4 - - - -
25K TYR* 2.4 30.4 + - - +
51K GLU* 4.2 2.1 - - - +
90K ASP 3.0 20.4 + - - +
91K LEU* 3.1 5.4 + - - +
93K LEU* 1.3 75.1 - - - +
95K LEU* 1.3 59.8 + - - +
97K ALA* 3.7 7.8 - - - +
98K THR* 2.9 32.6 + - - -
127K GLU* 2.9 41.2 - - - +
130K HIS* 2.8 29.1 + - + +
131K ILE* 3.7 22.2 - - + +
134K LEU* 4.0 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88K GLN* 5.6 0.9 - - - +
91K LEU* 3.0 45.5 + - + +
92K ASN* 4.0 12.6 - - - +
93K LEU 3.4 0.2 - - - -
94K GLU* 1.3 75.0 - - - +
96K LYS* 1.3 58.5 + - - +
98K THR* 3.0 25.7 - - + +
99K LYS* 3.1 11.1 + - - +
131K ILE* 4.2 20.0 - - + -
135K GLU* 5.5 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13K LYS* 4.3 10.5 - - - +
17K ASN* 5.0 6.2 + - - +
92K ASN 3.4 11.0 + - - +
93K LEU* 3.6 13.2 - - + +
94K GLU 3.3 0.2 - - - -
95K LEU* 1.3 73.9 - - - +
97K ALA* 1.3 65.3 + - - +
98K THR 3.1 1.7 + - - -
99K LYS* 3.2 19.1 + - - +
100K ASP* 2.7 56.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K ILE* 4.9 0.5 - - - +
17K ASN* 3.8 27.4 + - + +
18K GLU* 5.8 2.5 - - - +
51K GLU* 6.1 0.9 - - - +
93K LEU* 3.0 18.4 + - + +
94K GLU* 3.4 17.9 + - - +
96K LYS* 1.3 76.1 - - - +
98K THR* 1.3 58.2 + - - +
100K ASP* 3.4 3.3 + - - +
101K LEU* 3.0 40.6 + - + +
127K GLU* 5.0 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94K GLU 2.9 15.0 + - - +
95K LEU* 3.0 28.9 - - + +
97K ALA* 1.3 76.8 - - - +
99K LYS* 1.3 65.1 + - + +
101K LEU* 3.4 4.0 + - - +
102K ARG* 3.0 45.4 + - - +
124K LEU* 3.0 30.2 - - - +
127K GLU* 4.7 5.7 - - - +
128K GLU* 4.4 2.8 - - - +
131K ILE* 4.3 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 99 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95K LEU 3.1 13.3 + - - +
96K LYS* 3.2 22.4 + - - +
98K THR* 1.3 77.4 - - + +
100K ASP* 1.3 73.4 + - - +
101K LEU 3.2 0.3 + - - -
102K ARG* 3.2 13.2 + - + +
103K GLU* 3.0 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 100 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K HIS* 4.7 2.3 + - - -
13K LYS* 3.7 28.5 + - + +
14K ILE* 3.5 16.7 - - + +
17K ASN* 2.9 33.9 + - - +
96K LYS* 2.7 45.2 + - - +
97K ALA 3.6 2.2 - - - +
99K LYS* 1.3 84.4 + - - +
101K LEU* 1.3 56.2 + - - +
103K GLU* 3.6 11.8 + - - +
104K ALA* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K ILE* 3.2 40.8 - - + +
18K GLU* 5.3 1.1 - - - +
97K ALA* 3.0 25.2 + - + +
98K THR* 3.7 5.2 - - - +
99K LYS 3.2 0.4 - - - -
100K ASP* 1.3 73.9 - - - +
102K ARG* 1.3 61.5 + - - +
104K ALA* 3.8 1.9 - - - +
105K ILE* 2.9 36.4 + - - +
120K LEU* 3.7 28.9 - - + +
123K ILE* 3.9 14.6 - - + -
124K LEU* 4.0 21.8 - - + -
127K GLU* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98K THR* 3.0 36.7 + - - +
99K LYS* 3.8 10.9 - - + +
101K LEU* 1.3 73.5 - - - +
103K GLU* 1.3 64.9 + - - +
105K ILE* 3.3 2.2 + - - +
106K VAL* 3.1 27.4 + - - +
124K LEU* 3.8 18.5 - - + +
128K GLU* 2.8 31.9 + - - +
111T VAL 5.6 0.2 - - - -
112T HIS* 2.7 49.4 + - + +
113T ASP* 4.2 7.7 + - - +
114T TYR* 4.0 17.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K HIS* 4.0 18.6 - - + -
13K LYS* 5.1 5.4 + - - +
99K LYS* 3.0 42.6 + - - +
100K ASP* 3.8 16.6 - - - +
101K LEU 3.3 0.2 - - - -
102K ARG* 1.3 76.0 - - + +
104K ALA* 1.3 62.6 + - - +
106K VAL* 3.2 12.4 + - + +
107K HIS* 3.1 17.3 + - - +
112T HIS* 6.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K HIS* 3.4 34.2 + - + +
14K ILE* 4.4 10.8 - - + -
100K ASP 3.1 17.2 + - - +
101K LEU 3.4 5.1 + - - +
102K ARG 3.3 0.2 - - - -
103K GLU* 1.3 75.8 - - - +
105K ILE* 1.3 64.0 + - - +
107K HIS* 3.2 3.0 + - - +
108K CYS* 2.9 28.8 + - - -
120K LEU* 3.8 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 105 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101K LEU* 2.9 26.9 + - + +
103K GLU 3.3 0.4 - - - -
104K ALA* 1.3 75.4 - - - +
106K VAL* 1.3 63.3 + - - +
108K CYS* 3.4 7.7 + - - +
109K GLU* 3.0 22.3 + - - +
117K ARG* 3.6 26.4 + - + +
120K LEU* 3.8 19.7 - - + +
121K LYS* 3.9 31.2 - - + +
124K LEU* 4.2 11.2 - - + -
114T TYR* 3.4 49.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102K ARG 3.1 10.2 + - - +
103K GLU* 3.3 13.9 - - + +
105K ILE* 1.3 78.2 - - - +
107K HIS* 1.3 66.4 + - + +
109K GLU* 3.3 7.6 + - - +
110K GLN* 3.2 24.2 + - + +
112T HIS* 3.5 30.7 - - + +
114T TYR* 3.0 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 107 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K ASP* 2.8 28.6 + - - -
6K LYS* 3.2 31.3 - - + +
7K VAL* 3.6 21.8 - - + -
10K HIS* 3.8 24.2 + + + +
103K GLU 3.1 5.4 + - - +
104K ALA 3.2 6.5 + - - +
106K VAL* 1.3 81.9 - - + +
108K CYS* 1.3 64.5 + - - +
110K GLN* 3.1 24.5 + - - +
111K VAL* 3.1 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 108 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K VAL* 4.3 17.7 - - - -
10K HIS* 6.0 2.0 - - - -
11K LEU* 5.6 0.4 - - - -
104K ALA* 2.9 25.2 + - - +
105K ILE 3.6 5.4 - - - +
107K HIS* 1.3 70.8 - - - +
109K GLU* 1.3 64.5 + - - +
111K VAL* 3.4 3.5 + - - -
112K HIS 3.0 4.3 + - - -
113K ASP* 2.9 44.7 + - - +
116K SER* 3.7 25.8 - - - -
117K ARG* 3.8 12.1 - - + -
120K LEU* 4.0 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105K ILE 3.0 14.8 + - - +
106K VAL* 3.4 12.6 - - - +
107K HIS 3.2 0.2 - - - -
108K CYS* 1.3 75.8 - - - +
110K GLN* 1.3 62.8 + - - +
112K HIS* 3.3 20.4 + - - -
114K TYR* 3.4 20.9 + - - -
117K ARG* 2.9 39.8 + - - +
109M GLU* 4.0 12.1 - - - +
117M ARG* 2.6 26.5 + - - -
109T GLU* 4.2 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 110 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106K VAL* 3.2 12.7 + - + +
107K HIS* 3.1 36.6 + - - +
109K GLU* 1.3 82.4 - - - +
111K VAL* 1.3 62.6 + - + +
112K HIS* 3.2 12.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K ASP* 4.0 20.2 - - + +
7K VAL* 3.7 29.8 - - + -
107K HIS* 3.1 38.2 + - + +
108K CYS 3.9 4.0 - - - +
110K GLN* 1.3 84.5 - - - +
112K HIS* 1.3 73.2 + - - +
113K ASP* 4.1 6.9 - - + +
102M ARG* 5.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 112 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108K CYS 3.0 6.3 + - - -
109K GLU 3.3 10.9 + - - -
110K GLN* 3.2 10.4 + - - -
111K VAL* 1.3 80.6 + - - +
113K ASP* 1.3 59.2 + - - +
114K TYR* 2.9 46.7 + + + -
102M ARG* 3.0 39.8 + - + +
106M VAL* 3.1 23.2 - - + +
----------------------------------------------------------
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