Contacts of the helix formed by residues 67 - 98 (chain A) in PDB entry 6BAA
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 LYS 67 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP 3.7 2.0 + - - +
66A LEU* 1.3 80.4 - - - +
68A TRP* 1.3 65.5 + - - +
69A PRO* 3.4 12.8 - - + -
70A HIS* 3.2 27.4 + - + +
71A THR* 3.2 16.6 + - - -
55E SER* 5.1 10.2 + - - -
56E SER* 5.3 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU 3.8 0.4 + - - -
67A LYS* 1.3 71.6 - - - +
69A PRO* 1.3 71.7 - - + +
71A THR* 3.2 6.5 + - + -
72A LEU* 3.0 50.2 + - + +
167A ILE* 3.9 34.3 - - + -
170A LYS* 3.7 48.4 + - + +
171A THR* 4.6 2.7 - - + -
176A ARG* 6.0 3.8 - - - -
60D PHE* 3.9 36.4 - + - -
162D ILE* 4.9 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS* 3.4 13.0 - - + -
68A TRP* 1.3 95.7 - - + +
70A HIS* 1.3 66.0 + - + +
72A LEU* 3.7 11.6 + - + +
73A LEU* 3.1 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 4.4 18.1 - - + +
67A LYS* 3.2 31.1 + - + +
68A TRP 3.2 0.4 - - - -
69A PRO* 1.3 84.5 - - + +
71A THR* 1.3 66.2 + - - +
72A LEU 3.1 1.6 - - - -
73A LEU* 3.7 18.5 - - + +
74A ILE* 3.0 34.0 + - + +
51E TRP* 4.0 18.8 - + - -
52E GLY* 3.9 20.0 + - - -
55E SER* 3.3 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 3.7 14.6 + - + +
66A LEU* 3.8 3.7 + - - +
67A LYS 3.2 11.1 + - - -
68A TRP* 3.2 11.9 + - + -
70A HIS* 1.3 77.0 - - - +
72A LEU* 1.3 64.3 + - + +
74A ILE* 3.5 8.2 + - - +
75A PHE* 3.2 50.9 + - + -
166A CYS* 5.8 0.7 - - + -
167A ILE* 4.1 8.7 - - + -
170A LYS* 3.2 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TRP* 3.0 50.7 + - + +
69A PRO* 3.8 9.6 - - + +
71A THR* 1.3 76.9 - - + +
73A LEU* 1.3 57.0 + - + +
75A PHE* 3.5 3.7 + - - +
76A THR* 2.6 40.7 + - - +
158D MET* 4.1 32.8 - - + +
162D ILE* 6.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PRO* 3.1 25.7 + - + +
70A HIS* 3.4 21.7 + - + +
72A LEU* 1.3 75.7 - - + +
74A ILE* 1.3 59.4 + - + +
76A THR* 3.7 7.0 - - + -
77A MET* 2.7 41.8 + - + +
48E PHE* 5.2 19.5 - - + -
51E TRP* 5.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 3.6 15.9 - - + -
66A LEU* 3.3 34.3 - - + -
70A HIS* 3.0 19.8 + - + +
71A THR* 3.8 5.4 - - - +
72A LEU 3.3 0.2 - - - -
73A LEU* 1.3 78.1 - - + +
75A PHE* 1.3 59.0 + - + +
77A MET* 3.3 5.7 + - - +
78A SER* 2.6 50.2 + - - +
45E PRO* 5.0 12.9 - - + +
48E PHE* 4.4 20.0 - - + +
49E ILE* 3.4 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 4.9 12.3 - - + -
71A THR* 3.2 42.9 + - + +
72A LEU 4.2 0.2 - - - +
74A ILE* 1.3 84.5 - - + +
76A THR* 1.3 65.9 + - - +
78A SER* 4.0 10.8 - - - -
79A PHE* 3.0 36.4 + + + -
159A ILE* 5.9 1.6 - - + -
162A ILE* 5.1 3.1 - - + -
163A MET* 3.7 38.8 - - + -
166A CYS* 3.5 33.7 - - + -
167A ILE* 3.9 14.8 - - + -
158D MET* 3.4 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 2.6 28.6 + - - +
73A LEU* 3.7 10.5 - - + +
75A PHE* 1.3 77.9 - - - +
77A MET* 1.3 61.9 + - + +
79A PHE* 3.9 1.4 - - - +
80A LEU* 2.9 36.8 + - + +
150D ILE* 6.1 0.2 - - + -
154D ILE* 3.6 39.5 - - + +
158D MET* 5.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 2.7 26.2 + - + +
74A ILE* 3.6 5.6 - - - +
76A THR* 1.3 78.7 - - - +
78A SER* 1.3 59.8 + - - +
80A LEU* 4.3 17.7 - - + -
81A CYS* 2.7 63.2 + - - +
44E PHE* 4.0 25.8 - - + -
45E PRO* 5.7 4.9 - - + -
48E PHE* 3.8 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 2.6 40.0 + - - +
75A PHE* 3.9 11.6 - - - -
77A MET* 1.3 72.1 - - - +
79A PHE* 1.3 65.2 + - - +
81A CYS* 3.8 4.2 - - - +
82A SER* 2.8 32.1 + - - -
159A ILE* 4.8 12.4 - - - +
45E PRO* 4.3 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PHE* 3.0 22.1 + + + +
76A THR 3.9 2.2 - - - +
78A SER* 1.3 77.9 - - - +
80A LEU* 1.3 54.1 + - - +
82A SER* 2.6 21.3 + - - -
83A TRP* 2.7 55.6 + + + -
128A GLN* 5.9 1.6 - - - -
159A ILE* 3.3 34.1 - - + -
160A ASN* 4.0 15.7 - - - -
163A MET* 3.8 21.5 - - + -
154D ILE* 4.5 11.9 - - + -
157D LEU* 3.2 44.9 - - + -
158D MET* 4.2 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A THR* 2.9 24.2 + - + +
77A MET* 3.7 22.2 - - + +
79A PHE* 1.3 77.8 - - - +
81A CYS* 1.3 58.7 + - - +
83A TRP* 3.7 11.2 - - + +
84A LEU* 2.8 50.2 + - + +
121A PHE* 4.7 4.0 - - + -
150D ILE* 4.1 37.7 - - + -
154D ILE* 5.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A MET* 2.7 46.7 + - - +
78A SER* 3.9 4.3 - - - +
80A LEU* 1.3 74.9 - - - +
82A SER* 1.3 54.8 + - - +
84A LEU* 3.0 3.0 + - - +
85A LEU* 2.6 38.8 + - - +
41E PHE* 3.4 54.1 - - + +
44E PHE* 4.0 12.3 - - - -
45E PRO* 4.8 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER 2.8 18.8 + - - -
79A PHE* 2.6 26.2 + - - -
81A CYS* 1.3 74.4 - - - +
83A TRP* 1.3 63.0 + - - +
85A LEU* 4.2 5.5 - - - +
86A PHE* 3.3 21.0 + - - +
128A GLN* 3.0 31.9 + - - +
155A VAL* 5.4 4.5 - - - -
159A ILE* 3.7 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE* 2.7 57.2 + + + +
80A LEU* 3.7 13.0 - - + +
82A SER* 1.3 74.2 + - - +
84A LEU* 1.3 57.7 + - - +
87A ALA* 3.0 15.9 + - - +
121A PHE* 4.9 4.5 - - + -
124A SER* 2.6 31.8 + - - +
125A ILE* 3.4 34.9 + - + +
128A GLN* 3.2 46.3 - - + +
129A VAL* 3.2 30.6 - - + +
150D ILE* 4.2 11.7 - - + -
153D ASN* 4.6 9.6 - - + -
154D ILE* 3.8 31.6 - - + -
157D LEU* 5.0 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 2.8 38.0 + - + +
81A CYS 3.7 2.2 - - - +
83A TRP* 1.3 76.2 - - - +
85A LEU* 1.3 64.7 + - - +
87A ALA* 3.1 13.5 + - - +
88A MET* 3.2 17.1 + - + +
117A PHE* 3.9 26.9 - - + -
121A PHE* 3.4 22.9 - - + -
41E PHE* 3.8 29.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A CYS 2.6 20.1 + - - +
82A SER* 4.2 6.1 - - - +
84A LEU* 1.3 74.3 - - - +
86A PHE* 1.3 72.7 + - + +
88A MET* 3.5 11.4 + - - +
89A VAL* 3.6 15.4 + - + +
34E VAL* 6.3 1.1 - - + -
37E VAL* 4.3 7.2 - - + -
38E PHE* 3.4 56.3 - - + +
41E PHE* 3.7 25.3 - - + -
42E ILE* 5.4 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A SER* 3.3 12.5 + - - +
84A LEU 3.2 0.2 - - - -
85A LEU* 1.3 87.9 - - + +
87A ALA* 1.3 65.7 + - - +
89A VAL* 3.0 27.2 + - + +
90A TRP* 3.0 17.9 + - + -
124A SER* 4.0 0.2 - - - +
128A GLN* 3.5 19.1 - - - -
148A ILE* 4.8 12.8 - - + -
151A VAL* 3.8 24.2 - - + -
152A GLN* 3.2 55.9 - - + +
155A VAL* 3.9 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TRP 3.0 20.2 + - - +
84A LEU* 3.1 9.8 + - - +
86A PHE* 1.3 76.6 - - - +
88A MET* 1.3 62.9 + - - +
90A TRP* 3.2 7.1 + - - +
91A TRP* 3.0 22.5 + - - +
117A PHE* 4.3 7.0 - - + -
120A ALA* 4.1 4.6 - - - +
121A PHE* 3.7 26.9 - - + -
124A SER* 3.6 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.2 12.4 + - + +
85A LEU* 3.6 11.2 - - - +
86A PHE 3.2 0.2 - - - -
87A ALA* 1.3 77.9 - - - +
89A VAL* 1.3 64.9 - - + +
91A TRP* 3.2 33.4 + - + +
92A LEU* 2.9 24.1 + - + +
117A PHE* 4.0 22.3 - - + -
30E ALA 5.2 1.6 - - - +
33E VAL* 3.6 31.2 - - + -
34E VAL* 4.8 13.0 - - + -
37E VAL* 4.0 29.6 - - + -
41E PHE* 6.4 0.7 - - + -
112E MET* 5.6 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 3.8 15.9 - - + +
86A PHE* 3.0 21.4 + - + +
88A MET* 1.3 80.0 - - + +
90A TRP* 1.3 62.2 + - - +
92A LEU* 3.2 9.8 + - + +
93A ILE* 3.0 21.9 + - + +
148A ILE* 3.5 37.0 - - + -
34E VAL* 6.1 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 3.0 25.3 + - + -
87A ALA* 3.2 10.7 + - - +
89A VAL* 1.3 76.4 - - - +
91A TRP* 1.3 64.0 + - - +
93A ILE* 3.2 20.2 - - + +
94A ALA* 3.2 21.0 + - - +
111A VAL* 3.7 28.8 - - + +
114A ILE* 5.6 1.2 - - + +
120A ALA* 4.6 9.9 - - + +
123A PHE* 3.4 38.2 - + + -
124A SER* 4.5 4.0 - - - -
138A VAL* 4.6 3.8 - - + -
145A ALA* 3.2 41.3 - - + -
148A ILE* 3.7 25.9 - - + +
149A LEU* 3.9 20.4 - - + -
152A GLN* 2.6 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA 3.0 12.9 + - - +
88A MET* 3.2 35.2 + - - +
90A TRP* 1.3 75.8 - - - +
92A LEU* 1.3 72.0 + - + +
94A ALA* 3.2 11.0 + - + +
95A PHE* 3.0 36.2 + + - +
100A LEU* 4.2 18.8 - - + +
114A ILE* 5.3 1.8 - - + -
116A SER* 4.3 7.4 - - - +
117A PHE* 3.9 41.6 - + + +
120A ALA* 3.8 14.5 - - + +
30E ALA* 3.9 25.6 - - + -
33E VAL* 5.3 2.9 - - + -
105E HIS* 3.2 41.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A MET* 2.9 18.2 + - + +
89A VAL* 3.6 9.0 - - + +
91A TRP* 1.3 82.5 - - + +
93A ILE* 1.3 64.8 + - + +
95A PHE* 2.9 8.8 + - + +
96A ALA* 2.7 29.6 + - + -
27E PHE* 3.5 27.1 - - + -
30E ALA* 4.2 14.6 - - + +
31E LEU* 3.8 25.6 - - + -
34E VAL* 4.1 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 3.0 12.6 + - + +
90A TRP* 3.2 40.8 - - + +
92A LEU* 1.3 82.4 - - + +
94A ALA* 1.3 63.5 + - - +
96A ALA* 4.0 6.5 - - + +
97A HIS* 3.2 23.2 + - - +
110A CYS* 5.5 2.0 - - + -
111A VAL* 4.9 5.8 - - + -
142A CYS* 4.4 14.0 - - + -
144A LEU* 3.4 43.5 - - + -
145A ALA* 3.5 22.0 - - + +
148A ILE* 3.5 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TRP 3.2 11.5 + - - +
91A TRP 3.2 11.3 + - - +
92A LEU 3.1 0.2 - - - -
93A ILE* 1.3 80.0 - - + +
95A PHE* 1.3 57.6 + - - +
97A HIS* 3.4 2.6 + - - +
98A GLY 2.9 21.3 + - - -
99A ASP* 3.0 33.0 + - - +
100A LEU* 4.3 6.9 + - + -
110A CYS* 6.0 2.2 - - - -
111A VAL* 5.8 4.3 - - + -
114A ILE* 3.8 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TRP* 3.0 40.2 + + - +
92A LEU* 2.9 13.4 + - - +
94A ALA* 1.3 74.9 - - - +
96A ALA* 1.3 62.2 + - - +
98A GLY* 2.8 18.8 + - - +
100A LEU* 3.9 20.8 - - + +
6E CYS* 5.5 1.8 - - + -
12E SER* 2.7 42.6 - - - -
15E TYR* 4.6 10.8 - - + -
16E ARG* 4.0 5.3 - - + +
26E CYS* 4.5 26.2 - - + -
27E PHE* 4.3 32.8 - + + -
30E ALA* 5.1 4.3 - - + -
105E HIS* 5.7 1.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 2.7 21.8 + - + +
93A ILE* 4.0 10.1 - - + +
94A ALA 3.4 0.4 - - - -
95A PHE* 1.3 72.9 - - - +
97A HIS* 1.3 63.4 + - - +
98A GLY 3.2 0.7 + - - -
16E ARG* 3.4 13.6 - - - +
27E PHE* 4.5 22.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE 3.2 15.6 + - - +
94A ALA* 3.6 4.9 - - - +
96A ALA* 1.3 80.5 - - - +
98A GLY* 1.3 58.2 + - - +
99A ASP* 3.4 20.8 + - + +
107A ASN* 3.2 23.5 + - - -
108A VAL 3.1 27.7 + - - -
109A PRO* 4.4 0.4 - - + -
110A CYS* 3.3 32.0 - - - -
141A GLU* 4.4 9.7 + - + +
142A CYS* 4.1 4.5 - - - -
16E ARG* 3.9 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ALA 2.9 3.9 + - - -
95A PHE* 2.8 20.1 + - - -
97A HIS* 1.3 78.6 - - - +
99A ASP* 1.3 59.0 + - - +
100A LEU* 3.3 3.8 - - - -
102A PRO* 3.2 24.3 - - - +
107A ASN* 4.6 2.1 + - - -
13E ALA* 3.4 16.3 - - - +
16E ARG* 3.4 16.2 - - - -
17E VAL* 5.2 1.6 + - - +
----------------------------------------------------------
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