Contacts of the helix formed by residues 14 - 46 (chain B) in PDB entry 5W97
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 SER 14 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ALA* 4.0 2.4 - - - +
13B THR* 1.3 78.7 - - - +
15B PRO* 1.3 69.8 - - - +
16B ILE* 3.3 7.4 - - - +
17B MET* 3.0 16.1 + - - +
18B GLU* 3.2 18.0 + - - +
167B SER 3.9 0.8 + - - -
168B LEU* 2.9 34.5 + - - -
185B MET* 3.2 21.3 - - - -
187B SER* 4.6 1.1 - - - -
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Residues in contact with PRO 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B SER* 1.3 87.1 - - - +
16B ILE* 1.3 55.5 + - - +
18B GLU* 3.3 14.5 + - + +
19B GLU* 3.1 29.7 + - - +
185B MET* 3.5 37.2 - - + +
187B SER* 3.6 9.9 - - - +
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B SER* 3.3 13.7 - - - +
15B PRO* 1.3 75.9 - - - +
17B MET* 1.3 69.8 + - - +
19B GLU* 3.1 7.2 + - + +
20B LEU* 3.0 24.6 + - + +
83B ILE* 4.3 8.7 - - + +
86B MET* 4.1 25.6 - - + +
87B MET* 3.4 53.2 - - + +
168B LEU 3.8 11.2 - - - +
169B GLY* 4.7 7.6 - - - +
170B LEU* 5.7 3.6 - - + -
183B THR 5.9 1.1 - - - +
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Residues in contact with MET 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A VAL* 3.9 12.8 - - + -
9B PHE* 3.9 36.3 - - + -
10B GLN 4.8 3.8 - - - +
12B ALA* 3.7 14.8 - - + +
14B SER* 3.0 21.6 + - - +
16B ILE* 1.3 78.1 - - - +
18B GLU* 1.3 57.0 + - - +
20B LEU* 3.4 18.3 + - + -
21B LEU* 2.9 37.9 + - + +
166B PRO 3.5 18.6 - - - +
167B SER* 3.4 24.2 - - - +
169B GLY* 3.7 16.2 - - - +
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA* 3.6 5.7 - - + +
14B SER 3.2 12.1 + - - +
15B PRO* 3.3 16.2 - - + +
16B ILE 3.2 0.2 - - - -
17B MET* 1.3 74.7 - - - +
19B GLU* 1.3 64.7 + - + +
21B LEU* 3.3 6.1 + - + +
22B HIS* 3.1 51.8 + - - +
47I TYR* 3.4 47.2 - - + +
51I TYR* 4.4 13.5 - - - -
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PRO* 3.1 15.3 + - + +
16B ILE* 3.1 10.7 + - - +
18B GLU* 1.3 76.9 - - + +
20B LEU* 1.3 57.5 + - - +
22B HIS* 3.4 11.4 + - - +
23B PHE* 3.0 28.8 + - - +
82B ARG* 3.0 30.8 + - - -
83B ILE* 3.7 22.6 - - + +
86B MET* 4.0 20.2 - - - +
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A SER* 3.7 36.8 - - - +
363A LEU* 4.0 17.8 - - + +
365A ILE* 5.5 0.9 - - + -
366A VAL* 4.5 15.0 - - + -
9B PHE* 5.3 0.2 - - - -
16B ILE* 3.0 20.0 + - + +
17B MET* 3.6 31.6 - - + +
19B GLU* 1.3 73.6 - - - +
21B LEU* 1.3 59.5 + - - +
23B PHE* 3.3 4.4 + - + +
24B HIS* 2.8 31.9 + - - +
83B ILE* 3.7 28.0 - - + -
87B MET* 4.8 8.3 - - - -
169B GLY* 4.6 10.1 - - - +
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 3.5 40.8 - - + +
10B GLN 4.6 2.7 - - - +
11B ASP* 5.1 0.2 - - - -
12B ALA* 3.7 18.6 - - + +
17B MET* 2.9 20.1 + - + +
18B GLU* 3.4 9.6 - - + +
20B LEU* 1.3 76.2 - - - +
22B HIS* 1.3 63.6 + - - +
24B HIS* 3.3 7.0 + - - +
25B ASP* 3.2 26.2 + - - +
43I ARG* 4.1 23.5 + - - +
47I TYR* 3.2 41.5 - - + +
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Residues in contact with HIS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU* 3.1 49.1 + - + +
19B GLU* 3.9 13.2 - - - +
20B LEU 3.3 0.2 - - - -
21B LEU* 1.3 78.2 - - + +
23B PHE* 1.3 64.0 + - - +
25B ASP* 3.4 9.2 + - - +
26B HIS* 3.2 21.7 + - - +
40I ALA 4.9 0.6 + - - -
43I ARG* 4.2 21.0 - - + +
44I LYS* 3.7 56.0 + - + +
47I TYR* 4.7 4.7 - + - -
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Residues in contact with PHE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ASN* 3.5 29.4 - - + -
362A SER* 4.9 5.4 - - - -
363A LEU* 3.8 23.3 - - + -
19B GLU 3.0 17.7 + - - +
20B LEU* 3.6 4.7 - - + +
22B HIS* 1.3 75.1 - - - +
24B HIS* 1.3 63.0 + - - +
26B HIS* 3.4 10.1 - + - +
27B THR* 3.0 42.6 + - - -
76B ILE* 3.4 22.4 - - + -
79B PRO* 3.8 23.3 - - + -
80B SER* 3.5 31.9 - - - -
83B ILE* 3.6 17.3 - - + -
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Residues in contact with HIS 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A VAL* 4.4 10.9 - - + +
363A LEU* 3.9 24.9 - - + -
367A LEU* 5.5 0.2 - - + -
372A TYR* 4.6 9.3 + - - -
433A LEU* 3.7 27.7 - - + +
608A TGL 3.8 20.6 - - - +
9B PHE* 3.6 25.1 - + + -
20B LEU 2.8 14.8 + - - +
21B LEU 3.5 9.2 + - - +
22B HIS 3.2 0.2 - - - -
23B PHE* 1.3 80.0 - - - +
25B ASP* 1.3 63.6 + - - +
27B THR* 3.8 2.6 - - - +
28B LEU* 2.9 50.7 + - + +
35I TYR* 5.0 1.0 + - - -
43I ARG* 6.0 0.2 + - - -
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Residues in contact with ASP 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU 3.2 13.1 + - - +
22B HIS* 3.7 12.5 + - - +
23B PHE 3.3 0.2 - - - -
24B HIS* 1.3 79.8 + - - +
26B HIS* 1.3 60.0 + - - +
29B MET* 3.0 30.7 + - - +
35I TYR* 2.7 39.1 + - + -
40I ALA* 3.5 33.6 - - + +
43I ARG* 2.7 41.8 + - - +
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Residues in contact with HIS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B HIS 3.2 11.3 + - - +
23B PHE* 3.4 20.4 - + - +
25B ASP* 1.3 77.2 - - - +
27B THR* 1.3 63.9 + - - +
29B MET* 3.4 36.2 - - + +
30B ILE* 3.5 28.2 + - + +
75B LEU* 2.7 36.4 + - + -
76B ILE* 4.6 2.7 - - - -
79B PRO* 4.0 18.1 - - + +
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Residues in contact with THR 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ILE* 5.3 2.7 - - + -
357A VAL* 3.8 35.0 - - + +
360A ASN* 4.7 2.5 - - - +
363A LEU* 5.2 2.2 - - + -
23B PHE* 3.0 43.2 + - - -
24B HIS* 3.9 7.0 - - - -
25B ASP 3.3 0.2 - - - -
26B HIS* 1.3 78.9 - - - +
28B LEU* 1.3 56.6 + - - +
30B ILE* 3.2 11.5 + - - +
31B VAL* 3.0 27.1 + - + +
76B ILE* 3.9 22.8 - - + +
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A VAL* 5.7 2.9 - - + -
372A TYR* 5.3 4.5 - - - +
608A TGL 3.4 53.6 - - + +
24B HIS* 2.9 35.2 + - + +
25B ASP 4.0 2.7 - - - +
27B THR* 1.3 73.6 - - - +
29B MET* 1.3 56.5 + - - +
31B VAL* 3.5 16.9 - - + +
32B PHE* 2.8 63.7 + - + -
35I TYR* 3.5 23.8 - - + +
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Residues in contact with MET 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASP 3.0 19.0 + - - +
26B HIS* 3.4 35.4 - - + +
28B LEU* 1.3 73.9 - - - +
30B ILE* 1.3 58.4 + - + +
32B PHE* 3.2 8.9 + - - +
33B LEU* 2.9 32.4 + - + +
32I ALA* 3.4 38.9 - - + +
35I TYR* 4.3 14.1 - - + -
36I LYS* 3.9 31.6 - - + +
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Residues in contact with ILE 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU* 6.2 0.4 - - + -
602A HEA 5.4 1.3 - - + -
26B HIS* 3.5 34.3 + - + +
27B THR* 3.2 7.9 + - - +
28B LEU 3.2 0.4 - - - -
29B MET* 1.3 80.5 - - + +
31B VAL* 1.3 68.9 + - + +
33B LEU* 3.1 17.0 + - + +
34B ILE* 2.9 44.4 + - + +
72B ILE* 3.6 25.4 - - + +
75B LEU* 5.1 4.9 - - + -
76B ILE* 3.9 32.3 - - + -
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Residues in contact with VAL 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU* 3.7 40.5 - - + +
354A THR* 5.6 2.5 - - + -
356A ILE* 6.0 2.7 - - + -
357A VAL* 4.0 25.1 - - + -
608A TGL 3.8 30.1 - - + -
27B THR* 3.0 21.1 + - + +
28B LEU* 3.5 17.7 - - + +
30B ILE* 1.3 76.4 - - + +
32B PHE* 1.3 59.0 + - + +
34B ILE 3.4 0.2 + - - -
35B SER* 2.9 31.2 + - - -
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Residues in contact with PHE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A TGL 3.9 85.1 - - + +
28B LEU* 2.8 49.9 + - + +
29B MET* 3.4 5.2 - - - +
31B VAL* 1.3 71.1 - - + +
33B LEU* 1.3 62.2 + - - +
35B SER* 3.6 1.9 + - - -
36B SER* 2.9 30.4 + - - -
31I PHE* 4.8 20.2 - - + +
32I ALA 5.2 0.4 - - - +
35I TYR* 3.7 35.0 - + + -
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B MET* 2.9 14.2 + - + +
30B ILE* 3.1 22.4 + - + +
32B PHE* 1.3 75.5 - - - +
34B ILE* 1.3 67.4 + - + +
36B SER* 3.1 6.8 + - - -
37B LEU* 3.0 36.8 + - + +
72B ILE* 5.6 9.6 - - + -
302B PSC 6.0 2.7 - - + -
25I PHE* 5.6 6.3 - - + -
28I SER* 3.6 31.0 - - - +
29I LEU* 4.7 17.5 - - + +
32I ALA* 4.1 11.4 - - + +
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Residues in contact with ILE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PHE* 5.8 2.7 - - + -
349A THR* 4.7 0.7 - - + -
353A LEU* 3.9 19.3 - - + -
602A HEA 3.7 62.1 - - + -
30B ILE* 2.9 39.5 + - + +
31B VAL 4.0 2.0 - - - +
33B LEU* 1.3 87.6 - - + +
35B SER* 1.3 61.8 + - - +
37B LEU* 3.4 6.8 + - + +
38B VAL* 3.1 27.3 + - + +
72B ILE* 4.6 10.3 - - + -
302B PSC 5.5 7.9 - - + -
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A PHE* 3.7 14.1 - - - -
349A THR* 5.1 3.4 - - - -
350A VAL* 4.6 9.9 - - - -
353A LEU* 4.0 13.7 - - - -
608A TGL 3.7 32.1 - - - +
31B VAL 2.9 18.5 + - - -
32B PHE* 3.6 8.3 + - - -
34B ILE* 1.3 77.6 - - - +
36B SER* 1.3 59.1 + - - +
38B VAL* 3.6 4.3 + - - +
39B LEU* 3.1 28.6 + - - +
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Residues in contact with SER 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A TGL 4.1 17.9 - - - +
32B PHE 2.9 22.0 + - - -
33B LEU* 3.1 5.5 + - - -
35B SER* 1.3 74.4 + - - +
37B LEU* 1.3 63.0 + - - +
39B LEU* 3.4 5.0 + - - +
40B TYR* 2.9 31.6 + - - +
27I VAL* 5.7 1.9 - - - +
28I SER* 3.4 20.5 + - - -
31I PHE* 4.0 26.5 - - - -
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PHE* 5.4 4.7 - - + -
33B LEU* 3.0 22.6 + - + +
34B ILE* 3.5 8.7 - - + +
35B SER 3.3 0.2 - - - -
36B SER* 1.3 82.8 + - - +
38B VAL* 1.3 57.8 + - + +
40B TYR* 3.4 3.4 + - - +
41B ILE* 2.9 50.2 + - + +
302B PSC 4.1 31.2 - - + -
21I ILE* 6.0 0.4 - - + -
24I ALA* 3.8 24.5 - - + +
25I PHE* 3.8 32.3 - - + -
28I SER* 3.2 15.9 - - - +
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Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A VAL* 4.6 9.2 - - + -
321A PHE* 4.3 22.7 - - + -
324A LEU* 4.7 8.9 - - + +
345A ILE* 4.8 2.9 - - + +
346A PHE* 4.4 11.4 - - + -
349A THR* 4.3 29.2 - - + +
602A HEA 4.6 9.4 - - + -
34B ILE* 3.1 18.1 + - + +
35B SER 3.9 3.8 - - - +
37B LEU* 1.3 78.7 - - + +
39B LEU* 1.3 58.2 + - - +
41B ILE* 3.5 6.7 + - - +
42B ILE* 3.0 46.1 + - + +
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A PHE* 3.9 26.7 - - + -
608A TGL 3.9 38.4 - - + -
35B SER 3.1 18.4 + - - +
36B SER* 3.7 4.5 - - - +
38B VAL* 1.3 73.6 - - - +
40B TYR* 1.3 66.8 + - - +
42B ILE* 3.5 8.4 + - + +
43B SER* 3.2 22.6 + - - -
201D TGL 4.0 31.0 - - + -
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Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B SER 2.9 18.7 + - - +
37B LEU* 3.7 4.9 - - - +
39B LEU* 1.3 78.1 - - - +
41B ILE* 1.3 59.3 + - - +
43B SER* 2.8 23.3 + - - -
44B LEU* 2.9 28.1 + - + -
20I HIS* 3.7 31.0 + + - -
23I GLY* 3.9 5.8 - - - -
24I ALA* 3.5 44.7 + - + +
27I VAL* 4.4 31.8 - - + +
28I SER* 5.5 0.4 - - - +
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Residues in contact with ILE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PHE* 5.0 9.0 - - + -
324A LEU* 3.9 19.7 - - + -
37B LEU* 2.9 48.4 + - + +
38B VAL* 3.9 4.7 - - - +
39B LEU 3.3 0.2 - - - -
40B TYR* 1.3 73.5 - - + +
42B ILE* 1.3 64.6 + - - +
44B LEU* 3.3 8.7 + - + +
45B MET* 2.9 50.1 + - + +
302B PSC 4.2 26.5 - - + -
21I ILE* 4.3 23.3 - - + -
24I ALA* 4.6 5.8 - - + -
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Residues in contact with ILE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 3.4 24.2 - - + -
327A LEU* 5.3 2.7 - - + -
342A LEU* 4.4 14.8 - - + +
345A ILE* 4.1 14.8 - - + -
346A PHE* 4.0 22.4 - - + +
38B VAL* 3.0 38.5 + - + +
39B LEU* 3.7 11.2 - - + +
40B TYR 3.3 0.2 - - - -
41B ILE* 1.3 75.1 - - - +
43B SER* 1.3 62.8 + - - +
45B MET* 3.1 14.2 + - - +
46B LEU* 3.3 34.1 + - + +
201D TGL 4.1 19.7 - - + -
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Residues in contact with SER 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.2 11.7 + - - -
40B TYR* 2.8 24.1 + - - -
42B ILE* 1.3 75.8 - - - +
44B LEU* 1.3 54.2 + - - +
46B LEU* 3.6 3.4 + - - +
47B THR* 2.5 40.2 + - - +
201D TGL 4.1 32.5 - - - -
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 2.9 27.8 + - + +
41B ILE* 3.4 13.9 - - - +
43B SER* 1.3 77.0 + - - +
45B MET* 1.3 71.0 + - + +
47B THR* 3.0 13.0 + - - -
16I ARG* 2.9 48.2 + - - +
17I LEU* 4.2 23.6 - - + -
20I HIS* 3.4 51.8 - - + -
21I ILE* 4.5 8.1 - - + +
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Residues in contact with MET 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 3.5 26.5 - - + +
327A LEU* 4.0 30.3 - - + +
328A HIS* 3.6 29.6 - - + +
329A GLY 5.1 3.5 + - - -
330A GLY 5.6 0.5 + - - +
332A ILE* 4.5 6.9 - - - +
41B ILE* 2.9 39.8 + - + +
42B ILE* 3.1 9.8 + - - +
44B LEU* 1.3 85.2 - - + +
46B LEU* 1.3 61.0 + - + +
47B THR 3.5 0.9 + - - -
48B THR* 4.7 11.0 + - - +
302B PSC 4.3 7.0 - - + -
16I ARG* 5.1 2.0 - - - +
17I LEU* 3.8 28.9 - - + -
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU* 4.2 21.1 - - + -
332A ILE* 4.0 33.4 - - + -
334A TRP* 3.4 34.9 - - + -
342A LEU* 3.8 20.6 - - + -
42B ILE* 3.3 32.2 + - + +
43B SER* 3.6 4.4 + - - +
44B LEU 3.2 0.8 - - - -
45B MET* 1.3 81.2 - - + +
47B THR* 1.3 60.8 + - - +
48B THR 3.8 2.5 - - - -
201D TGL 3.8 40.8 - - + +
----------------------------------------------------------
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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