Contacts of the helix formed by residues 9 - 38 (chain B) in PDB entry 3ZPL
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 THR 9 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG* 5.2 2.2 - - - +
7B TRP 4.0 1.9 + - - +
8B LEU* 1.3 77.5 - - - +
10B ALA* 1.3 59.0 + - - +
11B GLU* 3.3 9.7 + - - +
12B GLU* 2.9 44.3 + - - +
13B GLN* 3.0 24.1 + - - +
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Residues in contact with ALA 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU 3.8 0.4 + - - -
9B THR* 1.3 74.8 - - - +
11B GLU* 1.3 61.9 + - - +
13B GLN* 3.4 17.0 + - - +
14B LEU* 3.1 30.5 + - + +
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR* 3.1 8.8 + - - +
10B ALA* 1.3 76.5 - - - +
12B GLU* 1.3 64.3 + - + +
14B LEU* 3.0 20.2 + - - +
15B VAL* 3.1 17.1 + - - +
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Residues in contact with GLU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG* 2.9 37.9 + - - -
128A PHE* 3.7 23.1 - - + +
136A GLN* 4.2 22.8 + - - +
8B LEU* 3.6 11.8 - - + -
9B THR* 2.9 45.0 + - - +
11B GLU* 1.3 76.8 - - + +
13B GLN* 1.3 62.3 + - - +
15B VAL* 3.0 8.3 + - - +
16B TRP* 2.9 24.5 + - - +
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Residues in contact with GLN 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLU* 4.3 13.5 - - - +
8B LEU* 3.1 40.3 + - + +
9B THR 3.0 14.9 + - - +
10B ALA* 3.5 15.0 - - - +
11B GLU 3.3 0.2 - - - -
12B GLU* 1.3 73.2 - - - +
14B LEU* 1.3 56.6 + - + +
16B TRP* 3.7 6.5 - - - +
17B ARG* 2.7 39.2 + - - +
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Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ARG* 3.3 24.5 + - - +
10B ALA* 3.1 17.4 + - + +
11B GLU* 3.0 13.6 + - - +
13B GLN* 1.3 82.0 - - + +
15B VAL* 1.3 63.8 + - + +
17B ARG* 4.1 7.0 - - + +
18B SER* 3.1 23.0 + - - -
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Residues in contact with VAL 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE* 4.1 15.7 - - + -
136A GLN* 3.4 34.5 - - + +
137A LYS* 5.0 2.9 - - - +
139A LEU* 3.9 25.2 - - + +
140A GLY* 4.0 16.6 - - - +
144A ARG* 4.7 3.8 - - - +
11B GLU* 3.1 14.6 + - + +
12B GLU* 3.0 9.7 + - - +
14B LEU* 1.3 76.2 - - + +
16B TRP* 1.3 64.9 + - - +
18B SER* 2.9 20.6 + - - -
19B TYR* 2.9 10.7 + - - +
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Residues in contact with TRP 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.2 14.6 - - + -
30A LEU* 3.8 30.5 - - + -
42A HIS* 4.5 5.3 + + - -
119A HIS* 4.8 6.3 + - - -
123A VAL* 3.8 29.8 - - + +
127A VAL* 4.1 21.8 - - + -
128A PHE* 3.8 20.0 - + + -
139A LEU* 6.2 2.0 - - + -
8B LEU* 4.6 12.8 - - + -
12B GLU 2.9 15.5 + - - +
13B GLN* 3.8 6.1 - - + +
15B VAL* 1.3 77.6 - - - +
17B ARG* 1.3 67.0 + - + +
19B TYR* 3.1 24.8 + + + +
20B ILE* 2.9 56.1 + - + +
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Residues in contact with ARG 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR* 2.9 49.5 + - - -
69A LYS* 3.7 25.3 - - - +
13B GLN* 2.7 23.7 + - + +
14B LEU* 4.2 6.5 - - + +
16B TRP* 1.3 74.4 - - + +
18B SER* 1.3 65.7 + - - +
20B ILE* 3.0 14.1 + - - +
21B GLU* 3.0 35.1 + - - +
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Residues in contact with SER 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLY* 3.6 12.3 + - - -
143A MET* 3.4 5.9 - - - +
144A ARG* 3.2 43.6 + - - -
147A ALA* 4.6 2.4 - - - +
14B LEU 3.1 10.6 + - - -
15B VAL* 2.9 18.4 + - - -
17B ARG* 1.3 75.1 - - - +
19B TYR* 1.3 64.4 + - - +
21B GLU* 3.9 6.9 - - - +
22B ALA* 3.1 25.5 + - - +
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Residues in contact with TYR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 4.3 5.1 - + - -
22A ALA* 4.7 0.5 - - - +
23A ALA* 3.4 34.0 + - - +
26A LEU* 3.9 26.9 - - + +
139A LEU* 4.5 13.9 - - + -
143A MET* 3.3 41.0 - - + +
15B VAL 2.9 13.3 + - - +
16B TRP* 3.4 31.6 - + + +
18B SER* 1.3 79.3 + - - +
20B ILE* 1.3 75.5 + - + +
22B ALA* 3.6 0.9 - - - +
23B ALA* 2.9 34.4 + - + +
143B MET* 4.1 21.5 - - + -
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Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A HIS* 3.9 22.0 - - + -
68A ALA 6.0 2.0 - - - +
16B TRP* 2.9 62.8 + - + +
17B ARG* 3.5 13.5 - - - +
19B TYR* 1.3 84.2 - - + +
21B GLU* 1.3 60.5 + - - +
23B ALA* 3.8 2.9 - - - +
24B THR* 2.7 42.1 + - - +
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LYS* 4.3 21.8 - - + -
147A ALA* 4.3 12.3 - - + -
151A GLN* 5.6 1.3 - - - +
17B ARG* 3.0 35.4 + - - +
18B SER* 3.9 7.0 - - - +
20B ILE* 1.3 74.3 - - - +
22B ALA* 1.3 69.2 + - - +
24B THR* 3.1 3.6 + - - -
25B LEU* 2.8 30.8 + - + +
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 4.7 0.2 - - - -
143A MET* 3.4 42.0 - - + +
146A VAL* 3.9 12.6 - - + -
147A ALA* 4.0 12.7 - - - +
150A LEU* 4.4 1.0 - - - +
18B SER 3.1 16.5 + - - +
21B GLU* 1.3 80.0 - - - +
23B ALA* 1.3 52.4 + - - +
25B LEU* 3.1 4.1 + - - +
26B LEU* 2.7 38.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 3.4 24.1 + - - +
23A ALA* 5.3 4.7 - - + -
143A MET* 4.1 0.2 - - - +
19B TYR* 2.9 37.8 + - + +
20B ILE* 3.8 3.4 - - - +
22B ALA* 1.3 76.3 - - - +
24B THR* 1.3 63.8 + - - +
26B LEU* 3.8 0.9 - - - +
27B GLU* 3.0 27.2 + - - +
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Residues in contact with THR 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 6.4 0.4 - - + -
68A ALA 4.1 12.3 + - - +
69A LYS* 3.7 26.6 - - + +
70A ILE* 4.7 7.6 - - + -
74A ARG* 5.2 7.0 - - - +
20B ILE* 2.7 32.4 + - - +
21B GLU* 3.7 3.4 - - - -
23B ALA* 1.3 77.2 - - - +
25B LEU* 1.3 60.9 + - - +
27B GLU* 4.1 5.0 - - - +
28B ASP* 3.3 22.2 + - - +
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LYS* 4.1 27.4 - - + -
147A ALA* 3.9 32.8 - - + +
150A LEU* 4.0 26.0 - - + +
151A GLN* 4.0 20.2 - - + +
159A LEU* 5.7 0.2 - - + -
160A PRO* 4.5 14.8 - - + -
161A TRP* 4.3 15.3 - - + -
21B GLU* 2.8 22.0 + - + +
22B ALA 3.6 2.7 - - - +
24B THR* 1.3 75.7 - - - +
26B LEU* 1.3 59.4 + - - +
28B ASP* 3.4 5.2 + - + +
29B HIS* 2.8 30.7 + - - +
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 4.2 6.5 - - + -
19A TYR* 3.9 33.0 - - + +
143A MET* 5.8 1.1 - - + -
146A VAL* 4.1 12.3 - - + -
150A LEU* 3.8 14.7 - - + +
22B ALA 2.7 17.5 + - - +
23B ALA 3.8 4.0 - - - +
25B LEU* 1.3 70.7 - - - +
27B GLU* 1.3 66.6 + - - +
29B HIS* 3.0 3.4 + - + -
30B LEU* 2.8 54.6 + - + +
123B VAL* 5.9 0.7 - - - -
126B ALA* 3.9 26.9 - - + -
127B VAL* 4.0 21.5 - - + -
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ALA 3.0 18.1 + - - +
24B THR* 4.1 5.6 - - - +
26B LEU* 1.3 75.1 - - - +
28B ASP* 1.3 57.3 + - - +
30B LEU* 4.3 4.0 - - - +
31B ASP* 2.9 42.1 + - - +
42B HIS* 5.7 4.9 - - - -
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Residues in contact with ASP 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LYS 5.4 1.9 - - - +
71A THR* 5.1 1.9 - - - +
158A ASP 4.7 1.2 - - - +
160A PRO* 4.0 18.3 - - + +
163A ARG* 2.7 41.4 + - - -
24B THR 3.3 18.1 + - - +
25B LEU* 3.5 7.7 - - + +
26B LEU 3.1 0.6 - - - -
27B GLU* 1.3 77.9 - - - +
29B HIS* 1.3 68.1 + - - +
31B ASP* 3.9 3.8 - - - +
32B ARG* 3.1 33.3 + - - +
14D T 4.6 12.0 + - - +
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Residues in contact with HIS 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LEU* 3.5 29.8 - - + +
25B LEU 2.8 20.9 + - - +
26B LEU* 3.7 3.6 - - + +
28B ASP* 1.3 78.2 - - - +
30B LEU* 1.3 73.6 + - + +
32B ARG* 3.8 4.5 - - - +
33B GLN* 3.0 31.9 + - + +
36B ARG* 5.5 7.6 - - - -
122B ALA* 4.3 18.5 + - + +
125B GLN* 6.3 0.6 - - - +
126B ALA* 4.3 12.2 + - + +
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 3.6 37.9 - - + -
20A ILE* 5.6 0.2 - - + -
26B LEU* 2.8 34.7 + - + +
27B GLU* 4.3 2.0 - - - +
29B HIS* 1.3 93.0 - - + +
31B ASP* 1.3 65.2 + - - +
32B ARG 3.1 1.1 - - - -
33B GLN* 3.2 4.6 + - - +
34B LEU* 2.9 30.7 + - - +
42B HIS* 4.2 23.6 - - + +
119B HIS* 4.3 8.7 - - + -
122B ALA* 4.1 22.2 - - + -
123B VAL* 4.0 13.9 - - + -
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Residues in contact with ASP 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLU* 2.9 28.4 + - - +
28B ASP* 3.9 4.5 - - - +
30B LEU* 1.3 75.4 - - - +
32B ARG* 1.3 60.0 + - + +
34B LEU* 3.7 1.0 - - - +
35B GLN* 2.8 33.8 + - - +
40B MET 4.4 1.6 - - - +
41B PRO* 4.1 9.0 - - + +
42B HIS* 2.9 39.0 + - - +
43B VAL* 4.7 2.4 + - - +
14D T 5.3 6.8 + - - +
----------------------------------------------------------
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Residues in contact with ARG 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ASP* 3.0 39.1 + - - +
163A ARG* 3.5 37.9 - - - +
28B ASP* 3.1 21.5 + - - +
29B HIS* 3.8 4.5 - - - +
31B ASP* 1.3 80.4 - - + +
33B GLN* 1.3 66.3 + - - +
35B GLN* 3.8 5.8 - - - +
36B ARG* 3.1 33.7 + - - +
15D C 3.2 43.6 + - - +
16D A 5.1 6.7 + - - -
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Residues in contact with GLN 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B HIS* 3.0 22.4 + - + +
30B LEU* 3.2 5.7 + - - +
32B ARG* 1.3 74.6 - - - +
34B LEU* 1.3 66.8 + - - +
36B ARG* 3.7 21.4 - - - +
37B ASP* 3.1 62.1 + - - +
115B THR* 4.9 2.6 + - - -
118B GLY* 3.7 5.9 - - - +
119B HIS* 3.2 53.1 + - - +
122B ALA* 3.9 21.6 - - + +
----------------------------------------------------------
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Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU 2.9 17.0 + - - +
31B ASP 4.0 1.8 - - - +
33B GLN* 1.3 90.7 - - - +
35B GLN* 1.3 60.7 + - - +
38B ALA* 3.1 20.3 + - + +
39B GLY 3.0 20.8 + - - -
40B MET* 3.2 18.8 + - + +
41B PRO 4.6 1.3 - - - -
42B HIS* 3.6 35.2 - - + -
45B TYR* 3.6 37.9 - - + -
115B THR* 5.1 2.2 - - - +
119B HIS* 3.4 31.2 - - + +
----------------------------------------------------------
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Residues in contact with GLN 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASP* 2.8 19.8 + - - +
32B ARG* 3.2 5.8 + - - +
34B LEU* 1.3 76.5 - - - +
36B ARG* 1.3 59.0 + - - +
39B GLY* 3.2 28.0 + - - -
40B MET* 3.1 34.5 + - - +
41B PRO* 3.4 24.3 - - - +
81B ARG* 3.9 8.1 - - - +
12C T 5.3 2.1 + - - +
14D T 5.6 0.7 - - - +
15D C 4.4 20.0 - - - +
----------------------------------------------------------
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Residues in contact with ARG 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B HIS* 5.5 7.7 - - - -
32B ARG* 3.1 20.8 + - - +
33B GLN* 3.7 20.5 - - - +
35B GLN* 1.3 80.4 - - - +
37B ASP* 1.3 104.2 + - - +
38B ALA 3.4 0.5 + - - -
39B GLY* 4.3 1.4 + - - -
----------------------------------------------------------
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Residues in contact with ASP 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLN* 3.1 35.7 + - - +
36B ARG* 1.3 112.8 + - - +
38B ALA* 1.3 58.7 + - + +
115B THR* 3.5 18.7 - - + +
118B GLY* 5.3 4.0 - - - -
----------------------------------------------------------
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 3.1 25.5 + - + +
36B ARG 3.3 0.2 - - - -
37B ASP* 1.3 77.0 - - + +
39B GLY* 1.3 65.0 + - - +
40B MET* 3.3 16.0 + - + +
87B TRP* 3.7 20.1 - - - -
111B VAL* 4.5 6.1 - - + +
115B THR* 3.4 29.2 - - + +
----------------------------------------------------------
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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