Contacts of the helix formed by residues 22 - 50 (chain L) in PDB entry 2UX1
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 22 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L SER* 1.3 93.6 - - - +
23L ALA* 1.3 58.6 + - - +
24L ASP 3.3 2.7 - - - -
25L SER* 3.4 5.3 + - - -
26L LYS* 2.9 46.7 + - + +
83L LEU* 3.6 32.1 - - + +
139L GLU* 3.3 36.1 - - + +
140L GLY 4.8 1.1 - - - +
141L ASP* 3.9 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L SER 3.5 8.3 - - - +
22L LEU* 1.3 75.1 - - - +
24L ASP* 1.3 64.9 + - - +
26L LYS* 3.6 17.9 + - - +
27L ALA* 2.9 28.1 + - - +
139L GLU* 3.7 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 24 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L ALA* 1.3 76.6 - - - +
25L SER* 1.3 60.0 + - - +
27L ALA* 3.0 8.8 + - - +
28L VAL* 2.9 30.7 + - - +
135L VAL* 3.1 28.9 - - + +
139L GLU* 3.0 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 25 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L LEU* 3.7 7.9 - - - -
24L ASP* 1.3 76.5 - - - +
26L LYS* 1.3 56.3 + - - +
28L VAL* 3.4 7.1 - - - +
29L LEU* 3.0 35.5 + - - +
83L LEU* 5.1 1.6 - - - -
135L VAL* 3.4 5.1 - - - +
136L SER* 3.2 28.9 + - - +
139L GLU* 2.6 24.9 + - - +
141L ASP* 3.9 21.3 - - - +
144L THR* 4.5 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L SER 5.6 1.8 - - - +
22L LEU* 2.9 39.7 + - + +
23L ALA* 3.7 14.4 - - - +
25L SER* 1.3 76.0 - - - +
27L ALA* 1.3 63.1 + - - +
29L LEU* 3.5 2.8 + - - -
30L ASN* 3.1 24.1 + - - +
80L LEU* 3.6 30.5 - - + +
83L LEU* 4.0 36.0 + - + +
84L GLY 4.8 1.4 + - - -
85L GLY* 4.4 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L ALA 2.9 18.6 + - - +
24L ASP* 3.0 10.7 + - - +
26L LYS* 1.3 77.6 - - - +
28L VAL* 1.3 58.0 - - - +
30L ASN* 3.4 6.2 + - - +
31L GLN* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L ASP 2.9 14.9 + - - +
25L SER* 3.4 19.7 - - - +
27L ALA* 1.3 75.1 - - - +
29L LEU* 1.3 66.1 + - - +
31L GLN* 3.2 5.2 + - + +
32L ALA* 2.8 23.9 + - - +
128L LEU* 4.0 22.9 - - + +
131L LYS* 4.4 6.1 - - + +
132L GLY* 3.7 40.2 - - - +
135L VAL* 4.3 11.0 - - + -
148L PHE* 4.0 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L SER 3.0 21.4 + - - +
26L LYS* 3.7 5.8 - - - +
27L ALA 3.3 0.2 - - - -
28L VAL* 1.3 78.7 - - - +
30L ASN* 1.3 56.9 + - - +
32L ALA* 3.3 5.6 + - - +
33L VAL* 3.0 29.3 + - - +
76L MET* 3.7 40.0 - - + +
79L ARG* 3.8 18.4 - - + -
80L LEU* 3.9 18.2 - - + +
83L LEU* 3.8 28.3 - - + -
144L THR* 3.8 15.3 - - + -
147L ILE* 5.3 2.9 - - + -
148L PHE* 3.7 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 30 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L LYS 3.1 17.7 + - - +
27L ALA* 3.8 5.4 - - - +
29L LEU* 1.3 74.3 - - - +
31L GLN* 1.3 66.5 + - - +
33L VAL* 3.1 13.1 + - - +
34L ALA 3.2 9.7 + - - -
80L LEU* 3.4 15.1 - - + +
86L ALA 3.3 20.8 + - - -
87L PRO* 3.3 5.9 - - - +
88L PHE* 2.9 67.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L ALA 3.0 14.9 + - - +
28L VAL* 3.5 12.8 - - + +
30L ASN* 1.3 75.2 - - - +
32L ALA* 1.3 62.5 + - - +
34L ALA* 3.2 5.1 + - - +
35L ASP* 2.9 59.0 + - - +
88L PHE* 4.3 5.6 - - - -
97L ASN* 2.9 34.0 + - - +
99L GLN* 3.9 9.9 - - - +
124L TYR* 3.8 7.1 + - - +
128L LEU* 3.7 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L VAL 2.8 17.1 + - - +
29L LEU 3.3 10.8 - - - +
31L GLN* 1.3 72.5 - - - +
33L VAL* 1.3 52.5 + - - +
36L LEU* 2.7 44.0 + - + +
76L MET* 3.7 28.3 - - - -
128L LEU* 3.7 21.2 - - + +
129L PHE* 4.3 4.3 - - + -
148L PHE* 4.4 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48J TRP* 4.2 6.5 - - + -
29L LEU 3.0 15.6 + - - +
30L ASN* 3.1 19.0 + - - +
32L ALA* 1.3 73.6 - - - +
34L ALA* 1.3 61.0 + - - +
36L LEU* 5.0 0.4 - - - -
37L SER* 2.8 30.1 + - - -
73L LEU* 3.5 23.9 - - + +
76L MET* 4.6 2.0 - - + -
77L SER* 3.7 34.3 - - - +
80L LEU* 5.1 0.9 - - + -
87L PRO* 4.7 1.8 - - + -
88L PHE* 3.6 26.9 - - + +
94L PHE* 3.6 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L ASN 3.2 7.6 + - - +
31L GLN* 3.2 9.5 + - - +
33L VAL* 1.3 78.3 - - - +
35L ASP* 1.3 58.3 + - - +
37L SER* 3.2 4.3 + - - -
38L VAL* 3.0 31.7 + - - +
88L PHE* 4.0 6.9 - - + -
94L PHE* 3.7 31.7 - - - +
97L ASN* 4.0 15.3 - - + -
98L SER* 3.8 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 35 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L GLN* 2.9 26.4 + - - +
32L ALA 3.9 3.1 - - - +
34L ALA* 1.3 75.5 - - - +
36L LEU* 1.3 54.4 + - - +
38L VAL 3.3 0.7 + - - -
39L ALA* 2.7 36.3 + - - +
98L SER* 2.6 32.0 + - - -
99L GLN 3.1 13.2 + - - -
100L LEU* 3.5 5.7 - - + +
124L TYR* 2.5 42.1 + - + -
125L LEU* 4.2 5.6 - - + -
128L LEU* 3.4 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L ALA* 2.7 28.1 + - + +
33L VAL 4.1 1.3 - - - +
35L ASP* 1.3 73.0 - - - +
37L SER* 1.3 58.5 + - - +
39L ALA* 4.2 2.0 - - - -
40L HIS* 3.0 25.3 + - - +
69L ILE* 3.4 32.9 - - + +
72L TYR* 3.8 12.1 - - + -
73L LEU* 3.7 41.8 - - + +
76L MET* 3.8 20.9 - - + -
125L LEU* 3.8 28.7 - - + -
129L PHE* 3.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 37 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91J LEU* 4.7 6.2 - - - +
33L VAL 2.8 21.4 + - - -
34L ALA 3.4 5.4 - - - -
35L ASP 3.2 0.2 - - - -
36L LEU* 1.3 78.4 - - - +
38L VAL* 1.3 61.5 + - - +
40L HIS* 3.5 6.5 + - - +
41L SER* 3.3 19.6 + - - -
73L LEU* 3.5 20.0 - - - +
94L PHE* 3.5 43.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91J LEU* 3.9 23.3 - - + -
34L ALA 3.0 8.2 + - - +
35L ASP 3.3 1.3 + - - +
37L SER* 1.3 74.8 - - - +
39L ALA* 1.3 65.0 + - - +
41L SER* 3.1 9.0 + - - -
42L ILE* 2.9 23.8 + - + +
94L PHE 4.0 6.1 - - - +
95L SER* 4.4 4.9 - - - +
98L SER* 3.5 31.0 - - - +
100L LEU* 3.8 29.6 - - + +
102L GLU* 3.7 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L ASP 2.7 22.2 + - - +
36L LEU* 3.8 5.4 - - - +
38L VAL* 1.3 73.8 - - - +
40L HIS* 1.3 62.8 + - - +
42L ILE* 3.2 5.6 + - - +
43L LEU* 2.9 30.6 + - + +
69L ILE* 4.7 6.7 - - + -
100L LEU* 4.0 7.4 - - + +
121L VAL* 3.6 28.4 - - + +
125L LEU* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 40 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J ASP* 5.7 4.0 - - - -
36L LEU 3.0 19.1 + - - +
37L SER* 3.6 8.1 - - - +
39L ALA* 1.3 75.7 - - - +
41L SER* 1.3 63.0 + - - +
43L LEU* 3.3 9.6 + - - +
44L HIS* 2.9 25.6 + + - +
66L MET* 3.8 23.5 + - + +
69L ILE* 4.2 7.5 - - + +
70L ASP* 2.7 40.3 + - - +
73L LEU* 5.7 1.6 - - + -
1174L ZN 2.0 37.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 41 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89J SER 3.5 13.0 + - - +
90J THR* 3.9 5.0 - - - -
91J LEU* 3.9 17.8 - - - +
94J PHE* 4.1 6.7 - - - -
37L SER 3.3 10.3 + - - -
38L VAL* 3.1 8.4 + - - -
40L HIS* 1.3 85.9 - - - +
42L ILE* 1.3 61.1 + - - +
44L HIS* 3.3 5.2 + - - +
45L GLN* 3.0 22.5 + - - +
102L GLU* 2.6 28.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L VAL* 2.9 31.2 + - + +
39L ALA* 3.2 8.0 + - - +
41L SER* 1.3 74.6 - - - +
43L LEU* 1.3 67.6 + - + +
45L GLN* 3.1 11.5 + - - +
46L VAL* 3.0 25.6 + - + +
100L LEU* 4.5 9.0 - - + -
101L LYS 4.1 17.9 - - - +
102L GLU* 4.3 16.6 - - + +
117L ARG* 4.2 33.2 - - + +
118L VAL* 5.8 1.3 - - + -
121L VAL* 3.8 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L ALA* 2.9 22.7 + - + +
40L HIS* 3.6 4.5 - - - +
42L ILE* 1.3 77.9 - - + +
44L HIS* 1.3 57.5 + - - +
46L VAL* 3.3 6.7 + - - +
47L HIS* 3.0 26.5 + - - +
62L MET* 3.9 18.4 - - - +
65L TYR* 4.0 24.2 - - + -
66L MET* 3.6 16.4 - - + +
69L ILE* 3.6 31.2 - - + -
118L VAL* 3.9 38.4 - - + -
121L VAL* 5.7 3.8 - - + -
122L PHE* 4.4 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 44 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J ASP* 5.5 3.1 - - + -
73J LEU* 4.9 8.0 - - + +
74J ASP* 2.7 33.8 + - + -
40L HIS* 2.9 18.8 + + + +
41L SER* 3.8 6.1 - - - +
42L ILE 3.2 0.4 - - - -
43L LEU* 1.3 72.3 - - - +
45L GLN* 1.3 64.5 + - - +
47L HIS* 3.3 15.4 - + - +
48L TRP* 3.1 60.0 + + + -
63L ASP* 5.3 0.4 + - - -
66L MET* 3.6 16.8 - - + +
1174L ZN 2.0 34.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 45 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89J SER* 2.6 47.8 + - - +
90J THR* 3.8 1.6 - - - +
41L SER 3.0 12.9 + - - +
42L ILE* 3.2 11.5 - - - +
44L HIS* 1.3 74.9 - - - +
46L VAL* 1.3 61.0 + - - +
48L TRP* 3.1 1.3 + - - -
49L TYR* 2.8 43.4 + - + +
103L VAL* 2.9 29.3 + - - +
104L LEU 4.5 0.2 - - - +
105L GLY* 3.3 15.2 - - - +
117L ARG* 2.5 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42L ILE* 3.0 23.4 + - + +
43L LEU 3.3 8.0 + - - +
45L GLN* 1.3 73.7 - - - +
47L HIS* 1.3 63.1 + - - +
50L MET* 3.1 46.4 + - + +
62L MET* 3.8 30.5 - - + -
114L GLN* 3.5 38.1 - - + +
117L ARG* 4.0 11.9 - - + +
118L VAL* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 47 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C TRP* 4.9 0.2 - - - -
74J ASP* 3.4 10.5 + - - -
78J GLU* 2.9 9.3 + - - -
1174J ZN 2.0 36.8 - - - -
43L LEU 3.0 13.1 + - - +
44L HIS* 3.3 15.9 - + - +
45L GLN 3.2 0.2 - - - -
46L VAL* 1.3 75.6 - - - +
48L TRP* 1.3 72.5 + + - +
50L MET* 4.4 2.7 + - - +
55L PHE* 4.4 6.1 - - - -
59L HIS* 2.7 72.4 + + - -
62L MET* 3.8 16.0 - - + +
63L ASP* 3.3 26.3 + - - -
66L MET* 3.9 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 48 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C TRP* 4.7 6.5 + - - -
33J VAL* 4.2 12.3 - - + -
73J LEU* 4.3 12.3 - - + -
74J ASP* 2.8 19.9 + - - -
77J SER* 3.1 32.5 + - - -
78J GLU* 3.5 30.2 + - + +
81J ILE* 3.5 28.6 - - + +
87J PRO* 3.9 9.4 - - + -
88J PHE 3.4 21.3 - - - -
89J SER* 4.1 17.7 - - - -
94J PHE* 4.8 6.3 - + - -
44L HIS* 3.1 46.9 + + + +
45L GLN* 3.8 2.9 - - - +
47L HIS* 1.3 84.1 - + - +
49L TYR* 1.3 68.3 + - + +
50L MET 3.5 3.7 + - - +
55L PHE* 5.4 0.2 - - - -
59L HIS* 5.1 0.9 - - - -
107L TYR* 3.8 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 49 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86J ALA* 3.1 11.6 - - + +
87J PRO* 2.6 56.5 + - + -
89J SER* 3.7 14.4 - - - -
45L GLN* 2.8 35.2 + - + +
46L VAL 4.0 0.2 - - - -
48L TRP* 1.3 75.1 - - + +
50L MET* 1.3 66.7 + - - +
51L ARG 3.4 1.9 + - - -
105L GLY* 3.5 22.7 + - - -
106L ASP 3.3 23.8 - - - +
107L TYR* 3.6 61.9 - + - +
109L VAL 5.2 0.5 - - - +
114L GLN* 4.0 13.4 + - - +
117L ARG* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 50 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C TRP* 5.4 0.9 + - - -
164C ALA* 3.9 2.3 - - - +
46L VAL* 3.1 42.6 + - + +
47L HIS* 4.6 2.7 - - - +
48L TRP 3.5 3.6 - - - +
49L TYR* 1.3 77.8 - - - +
51L ARG* 1.3 63.7 + - - +
55L PHE* 3.3 37.1 - - + +
58L TRP* 3.7 22.9 - - + +
59L HIS* 3.3 43.3 - - + +
62L MET* 4.8 1.8 - - - -
107L TYR* 5.3 0.2 - - - -
109L VAL 5.8 0.2 - - - -
111L ILE* 3.8 19.3 - - + -
114L GLN* 4.0 19.0 - - + +
115L LEU* 5.3 1.8 - - - -
----------------------------------------------------------
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