Contacts of the helix formed by residues 2 - 35 (chain G) in PDB entry 5NC5
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 2 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET* 1.3 100.9 - - + +
3G GLU* 1.3 62.5 + - + +
5G LEU* 3.4 14.3 + - + +
6G LYS* 3.0 28.1 + - - +
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Residues in contact with GLU 3 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET 3.2 6.9 + - - +
2G LEU* 1.3 81.7 - - + +
4G LEU* 1.3 59.8 + - + +
6G LYS* 3.3 13.2 + - + +
7G SER* 2.9 25.6 + - - -
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Residues in contact with LEU 4 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET* 3.9 16.2 + - - +
2G LEU 3.4 0.2 - - - -
3G GLU* 1.3 78.5 - - + +
5G LEU* 1.3 59.9 + - - +
7G SER* 3.0 12.1 + - - +
8G LEU* 2.8 31.4 + - - +
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Residues in contact with LEU 5 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET 3.3 15.7 + - - +
2G LEU* 3.6 18.2 - - + +
3G GLU 3.4 0.2 - - - -
4G LEU* 1.3 76.3 - - - +
6G LYS* 1.3 56.5 + - - +
8G LEU* 3.2 21.9 + - + +
9G VAL* 2.9 47.5 + - + +
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Residues in contact with LYS 6 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G LEU 3.0 14.4 + - - +
3G GLU* 3.3 16.6 - - + +
5G LEU* 1.3 73.6 - - - +
7G SER* 1.4 65.0 + - - +
9G VAL* 2.9 25.3 - - + +
10G PHE* 3.0 49.0 + - + -
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Residues in contact with SER 7 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A GLU* 5.6 6.5 + - - -
3G GLU 2.9 15.0 + - - -
4G LEU* 3.0 22.5 + - - +
6G LYS* 1.4 71.6 - - - +
8G LEU* 1.3 71.4 + - - +
10G PHE* 3.1 19.1 + - - +
11G ALA* 2.9 22.9 + - - +
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Residues in contact with LEU 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ILE* 4.9 13.0 - - + -
353A LEU* 4.6 13.5 - - + -
4G LEU 2.8 18.6 + - - +
5G LEU* 3.5 21.8 - - + +
7G SER* 1.3 78.0 + - - +
9G VAL* 1.4 53.8 + - + +
11G ALA* 2.9 11.2 + - + +
12G VAL* 2.8 49.3 + - + +
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Residues in contact with VAL 9 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G LEU* 2.9 33.8 + - + +
6G LYS* 2.9 31.0 - - + +
8G LEU* 1.4 72.8 - - + +
10G PHE* 1.3 72.7 + - + +
12G VAL* 3.5 12.1 - - + +
13G ILE* 2.9 27.5 + - - +
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Residues in contact with PHE 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G LYS* 3.0 67.7 + - + -
7G SER* 3.1 17.5 + - - +
9G VAL* 1.3 80.9 - - + +
11G ALA* 1.3 58.6 + - - +
13G ILE* 2.9 26.8 - - + +
14G MET* 3.0 22.8 + - + +
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Residues in contact with ALA 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ILE* 6.0 1.6 - - + -
350A LEU* 3.7 28.7 - - + +
353A LEU* 4.6 7.0 - - + -
7G SER 2.9 12.7 + - - +
8G LEU* 2.9 17.4 + - + +
10G PHE* 1.3 78.2 - - - +
12G VAL* 1.4 60.1 + - - +
14G MET* 3.1 8.1 + - - +
15G VAL* 3.0 27.9 + - - +
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Residues in contact with VAL 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU* 3.7 27.4 - - + -
8G LEU* 2.8 32.0 + - + +
9G VAL* 3.5 19.5 - - + +
11G ALA* 1.4 71.6 - - - +
13G ILE* 1.3 57.5 + - + +
15G VAL* 3.6 4.0 + - - +
16G PRO* 2.6 32.4 - - - +
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Residues in contact with ILE 13 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G VAL 2.9 18.8 + - - +
10G PHE* 2.9 32.8 - - + +
12G VAL* 1.3 81.0 - - + +
14G MET* 1.3 63.1 + - + +
16G PRO* 3.0 18.8 - - + +
17G VAL* 2.9 31.9 - - + +
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Residues in contact with MET 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984A LEU* 4.1 13.9 - - + -
987A MET* 3.5 32.5 - - + -
10G PHE* 3.0 29.2 + - + +
11G ALA* 3.4 8.1 - - - +
13G ILE* 1.3 79.3 - - - +
15G VAL* 1.3 59.8 + - - +
17G VAL* 4.1 23.6 - - + -
18G VAL* 2.9 41.2 + - + +
21G ILE* 6.0 1.6 - - + -
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Residues in contact with VAL 15 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU* 5.1 3.1 - - + -
353A LEU* 4.1 30.5 - - + +
354A VAL* 4.1 20.9 - - + +
357A LEU* 4.0 23.5 - - + +
980A LEU* 5.5 0.3 - - - +
984A LEU* 3.3 24.9 - - + +
11G ALA 3.0 18.3 + - - +
12G VAL* 3.7 4.0 - - - +
14G MET* 1.3 74.6 - - - +
16G PRO* 1.3 70.7 - - + +
18G VAL* 4.2 1.0 - - - +
19G MET* 3.0 24.7 + - + +
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Residues in contact with PRO 16 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 5.6 3.8 - - + -
512A PHE* 6.0 7.9 - - + -
12G VAL 2.6 30.1 - - - +
13G ILE* 3.0 12.8 - - - +
15G VAL* 1.3 81.2 - - + +
17G VAL* 1.3 53.0 + - + +
19G MET* 3.1 7.4 + - + +
20G ALA* 2.7 37.6 + - - +
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Residues in contact with VAL 17 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G ILE* 2.9 40.5 + - + +
14G MET* 3.2 23.5 + - + +
16G PRO* 1.3 78.9 - - + +
18G VAL* 1.3 61.3 + - - +
20G ALA* 3.4 6.5 + - - +
21G ILE* 3.0 43.3 + - + +
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Residues in contact with VAL 18 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980A LEU* 3.8 15.4 - - + +
983A ILE* 4.1 23.1 - - + -
984A LEU* 3.5 30.3 - - + -
987A MET* 5.0 5.2 - - + -
1008A MET* 6.3 0.9 - - - -
14G MET* 2.9 25.4 + - + +
15G VAL 4.2 2.5 - - - +
17G VAL* 1.3 76.3 - - - +
19G MET* 1.3 68.7 + - - +
21G ILE* 3.4 14.4 + - + +
22G ILE* 3.2 29.8 + - + +
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Residues in contact with MET 19 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A VAL* 5.7 0.2 - - + -
357A LEU* 3.0 36.6 - - + -
358A PHE* 3.5 22.9 - - + -
516A PHE* 4.0 13.5 - - + -
520A PHE* 6.2 1.3 - - - -
976A LEU* 6.1 1.3 - - - -
980A LEU* 3.2 40.4 - - + -
15G VAL 3.0 19.4 + - - +
16G PRO* 3.1 6.7 + - + +
18G VAL* 1.3 83.9 - - - +
20G ALA* 1.3 64.6 + - - +
22G ILE* 3.4 3.6 + - - +
23G LEU* 3.2 53.1 + - + +
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Residues in contact with ALA 20 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G PRO 2.7 19.0 + - - +
17G VAL* 3.6 7.0 - - - +
18G VAL 3.3 0.2 - - - -
19G MET* 1.3 75.0 - - - +
21G ILE* 1.3 59.9 + - + +
23G LEU* 3.2 9.3 + - - +
24G GLY* 2.8 28.8 + - - -
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Residues in contact with ILE 21 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G MET* 6.0 1.6 - - + -
17G VAL* 3.0 35.6 + - + +
18G VAL* 3.8 16.8 - - + +
19G MET 3.3 0.4 - - - -
20G ALA* 1.3 78.2 - - + +
22G ILE* 1.3 64.3 + - + +
24G GLY* 3.5 1.7 + - - -
25G LEU* 3.1 39.4 + - + +
----------------------------------------------------------
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Residues in contact with ILE 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976A LEU* 4.0 31.2 - - + -
979A SER* 6.2 4.3 - - - -
980A LEU* 3.8 29.8 - - + -
983A ILE* 4.7 19.1 - - + -
1012A VAL* 5.5 8.1 - - + -
1015A THR* 5.8 6.3 - - + -
1016A VAL* 4.3 8.6 - - + +
18G VAL* 3.2 17.6 + - + +
19G MET* 3.5 9.4 - - - +
21G ILE* 1.3 81.2 - - + +
23G LEU* 1.3 78.3 + - + +
25G LEU* 3.3 12.2 + - + +
26G ILE* 3.2 29.1 + - + +
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Residues in contact with LEU 23 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A PHE* 5.5 2.9 - - + -
519A MET* 3.6 36.8 - - + -
520A PHE* 4.9 9.4 - - + -
523A SER* 4.3 11.5 + - - +
976A LEU* 4.4 13.7 - - + -
19G MET* 3.2 43.6 + - + +
20G ALA* 3.2 7.0 + - - +
22G ILE* 1.3 80.7 - - + +
24G GLY* 1.3 61.2 + - - +
26G ILE* 3.0 23.4 - - + +
27G TYR* 2.9 30.9 + - - +
----------------------------------------------------------
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Residues in contact with GLY 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ALA 2.8 19.5 + - - -
21G ILE* 3.8 2.5 - - - -
23G LEU* 1.3 73.6 - - - +
25G LEU* 1.3 56.3 + - - +
27G TYR* 3.3 6.8 + - - +
28G GLY* 2.9 27.4 + - - -
----------------------------------------------------------
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Residues in contact with LEU 25 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012A VAL* 4.7 20.0 - - + -
1016A VAL* 4.0 17.0 - - + -
21G ILE* 3.1 39.1 + - + +
22G ILE* 3.3 9.2 + - + +
23G LEU 3.2 0.2 - - - -
24G GLY* 1.3 76.4 - - - +
26G ILE* 1.3 58.9 + - - +
28G GLY* 3.8 0.8 - - - -
29G LEU* 2.8 35.9 + - + +
----------------------------------------------------------
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Residues in contact with ILE 26 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A SER* 4.8 7.2 - - - +
526A HIS* 4.2 2.6 + - - -
527A TYR* 6.0 5.6 - - + -
972A LEU* 5.0 6.7 - - + -
976A LEU* 4.3 25.6 - - + -
1015A THR* 5.4 0.7 - - + -
1016A VAL* 3.5 26.0 - - + -
1019A ILE* 3.4 32.1 - - + -
1020A PHE* 3.6 15.3 - - + -
22G ILE* 3.2 7.8 + - + +
23G LEU* 3.0 43.7 - - + +
25G LEU* 1.3 74.9 - - - +
27G TYR* 1.3 64.4 + - - +
29G LEU* 4.6 0.2 - - - -
30G GLY* 3.0 18.2 + - - -
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Residues in contact with TYR 27 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A SER* 4.7 13.0 - - - +
526A HIS* 2.8 62.3 + + + -
23G LEU 2.9 18.9 + - - +
24G GLY* 3.8 6.1 - - - +
26G ILE* 1.3 75.3 - - - +
28G GLY* 1.3 61.3 + - - +
30G GLY 3.1 0.7 + - - -
31G GLU* 3.0 34.0 + - + +
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Residues in contact with GLY 28 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G GLY 2.9 16.1 + - - -
25G LEU* 3.9 0.9 - - - -
27G TYR* 1.3 79.0 - - - +
29G LEU* 1.3 64.8 + - - +
30G GLY 3.0 1.8 - - - -
31G GLU* 3.0 8.4 + - - +
32G VAL* 3.0 29.4 + - - +
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Residues in contact with LEU 29 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016A VAL* 4.1 15.0 - - + +
1017A LEU* 4.0 28.0 - - + -
1020A PHE* 3.7 27.6 - - + -
25G LEU* 2.8 26.4 + - + +
28G GLY* 1.3 73.2 - - - +
30G GLY* 1.3 61.8 + - - +
32G VAL* 3.4 15.3 - - + +
33G PHE* 2.9 53.6 + - + +
----------------------------------------------------------
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Residues in contact with GLY 30 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A HIS* 3.9 4.9 - - - -
527A TYR* 6.3 0.2 - - - -
530A SER* 3.4 24.0 - - - -
1020A PHE* 4.0 6.2 - - - -
26G ILE 3.0 14.0 + - - -
27G TYR 3.5 4.7 - - - -
28G GLY 3.0 0.8 - - - -
29G LEU* 1.3 77.3 - - - +
31G GLU* 1.3 52.8 + - - +
33G PHE* 3.0 5.7 + - - +
34G ASN* 2.2 39.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 31 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A HIS* 3.2 24.5 + - - -
27G TYR* 3.0 33.2 + - + +
28G GLY* 3.0 11.4 + - - +
30G GLY* 1.3 74.1 - - - +
32G VAL* 1.3 64.7 + - + +
34G ASN* 3.6 15.3 + - - +
35G ILE* 3.3 35.5 + - + +
----------------------------------------------------------
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Residues in contact with VAL 32 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G GLY 3.0 16.9 + - - +
29G LEU* 3.4 17.7 - - + +
31G GLU* 1.3 78.2 - - + +
33G PHE* 1.3 84.5 + - + +
35G ILE* 2.9 32.9 - - - +
36G PHE* 3.7 3.6 - - - +
----------------------------------------------------------
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Residues in contact with PHE 33 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A SER* 4.9 2.4 - - - +
533A GLY* 5.7 1.0 - - - -
534A ILE* 3.5 34.8 + - + +
541A TYR* 2.8 33.9 + + - -
544A LEU* 4.0 21.3 - - + -
1017A LEU* 6.4 0.7 - - + -
1020A PHE* 3.5 41.5 - + + -
1021A PHE* 4.3 18.4 - + - -
29G LEU* 2.9 33.4 - - + +
30G GLY* 3.0 6.9 + - - +
32G VAL* 1.3 94.8 - - + +
34G ASN* 1.3 67.3 + - - +
36G PHE* 3.4 9.9 + + + +
----------------------------------------------------------
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Residues in contact with ASN 34 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A HIS* 4.7 4.6 + - - -
529A ASP* 5.7 3.6 - - - +
530A SER* 3.2 25.1 + - - +
533A GLY* 6.5 0.9 - - - -
30G GLY 2.2 31.9 + - - +
31G GLU* 3.9 19.0 + - - +
32G VAL 3.3 0.2 - - - -
33G PHE* 1.3 72.4 - - - +
35G ILE* 1.3 65.7 + - + +
36G PHE 2.4 28.2 + - - +
----------------------------------------------------------
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Residues in contact with ILE 35 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G GLU* 3.3 22.4 - - + +
32G VAL* 2.9 20.0 + - - +
34G ASN* 1.3 80.6 - - + +
36G PHE* 1.4 65.0 + - - +
----------------------------------------------------------
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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