Contacts of the helix formed by residues 10 - 41 (chain G) in PDB entry 1VEQ
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 10 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G GLY 4.3 0.2 - - - -
9G LEU* 1.3 72.3 - - - +
11G ASP* 1.3 56.3 + - - +
12G LYS* 2.6 22.1 + - - +
13G LYS* 2.8 53.9 + - - +
14G ALA* 2.9 10.4 + - - +
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Residues in contact with ASP 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G SER 4.7 9.9 - - - +
4G PHE 5.0 1.4 - - - +
5G THR* 4.0 25.3 - - - +
9G LEU 3.4 3.0 + - - +
10G SER* 1.3 69.9 - - - +
12G LYS* 1.3 58.0 + - - +
14G ALA* 4.2 9.2 - - - +
15G SER* 3.6 20.1 + - - -
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Residues in contact with LYS 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G SER* 2.6 11.8 + - - +
11G ASP* 1.3 73.9 - - - +
13G LYS* 1.3 75.8 + - + +
14G ALA 3.1 0.7 - - - -
15G SER* 3.1 6.6 + - - -
16G ASP* 2.6 54.3 + - - +
130G LEU* 6.6 0.2 - - - -
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Residues in contact with LYS 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G LEU* 4.5 12.8 - - + -
10G SER* 2.8 35.5 + - - +
12G LYS* 1.3 83.0 - - + +
14G ALA* 1.3 64.3 + - - +
16G ASP* 3.1 7.2 + - - +
17G VAL* 3.0 27.4 + - - +
129G ASP 4.1 17.1 + - - +
130G LEU* 4.4 30.8 + - + +
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Residues in contact with ALA 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G THR* 3.6 24.5 - - - +
9G LEU* 4.2 22.3 - - + +
10G SER 2.9 15.5 + - - +
11G ASP* 4.2 5.8 - - - +
13G LYS* 1.3 77.8 - - - +
15G SER* 1.3 62.3 + - - +
17G VAL* 3.1 6.9 + - - +
18G ALA* 3.1 21.6 + - - +
75G LEU* 3.9 16.8 - - + +
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Residues in contact with SER 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ASP 3.6 16.8 + - - -
12G LYS* 3.1 7.6 + - - -
14G ALA* 1.3 78.8 - - - +
16G ASP* 1.3 59.6 + - - +
18G ALA* 3.4 9.7 - - - +
19G ASP* 3.1 34.2 + - - +
77G LYS* 5.8 3.2 - - - +
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Residues in contact with ASP 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G LYS* 2.6 47.4 + - - +
13G LYS* 3.1 11.2 + - - +
15G SER* 1.3 76.0 - - - +
17G VAL* 1.3 66.4 + - - +
19G ASP* 3.6 12.3 + - - +
20G LEU* 3.3 23.7 + - - +
130G LEU* 4.5 16.9 - - + +
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Residues in contact with VAL 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G LEU* 5.4 2.0 - - + -
13G LYS 3.0 15.8 + - - +
14G ALA* 3.5 7.9 - - - +
16G ASP* 1.3 73.8 - - - +
18G ALA* 1.3 70.8 + - - +
20G LEU* 2.8 17.7 + - - +
21G LEU* 3.0 19.5 + - + +
75G LEU* 3.7 18.4 - - + -
127G LEU* 4.0 16.2 - - + -
130G LEU* 3.7 32.8 - - + -
131G ASP* 4.3 11.9 - - + -
134G SER* 3.9 19.5 - - - +
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Residues in contact with ALA 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G ALA 3.1 10.1 + - - +
15G SER* 3.4 13.9 - - - +
17G VAL* 1.3 81.2 - - - +
19G ASP* 1.3 65.0 + - - +
20G LEU 2.9 1.7 + - - -
21G LEU* 3.0 4.4 + - - +
22G GLN* 2.9 25.6 + - - +
72G ILE* 4.5 11.0 - - + +
75G LEU* 3.9 14.8 - - + +
77G LYS* 3.8 28.9 - - + -
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Residues in contact with ASP 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G SER* 3.1 22.2 + - - +
16G ASP* 3.7 17.0 - - - +
18G ALA* 1.3 79.0 - - - +
20G LEU* 1.3 61.0 + - + +
22G GLN* 3.8 8.6 + - - +
23G LYS* 3.5 17.0 + - - +
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Residues in contact with LEU 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G ASP 3.3 12.6 + - - +
17G VAL* 2.8 11.2 + - - +
19G ASP* 1.3 77.7 - - - +
21G LEU* 1.3 69.9 + - + +
23G LYS* 3.2 16.4 + - + +
24G GLN* 3.2 17.3 + - - +
123G SER* 3.4 35.8 + - - +
126G LYS* 4.5 26.2 - - + +
127G LEU* 4.0 30.5 - - + -
130G LEU* 4.1 12.1 - - + -
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Residues in contact with LEU 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G VAL* 3.4 31.4 - - + +
18G ALA 3.0 2.1 + - - +
20G LEU* 1.3 75.0 - - + +
22G GLN* 1.3 58.0 + - - +
23G LYS 2.8 4.9 - - - -
24G GLN* 2.6 28.5 + - + +
25G LEU* 2.7 13.5 + - - +
68G VAL* 3.6 17.6 - - + +
71G ARG* 3.8 29.8 - - + -
72G ILE* 3.7 21.5 - - + -
75G LEU* 4.5 5.8 - - + -
127G LEU* 4.9 8.7 - - + -
134G SER* 4.5 6.1 - - - +
137G LEU* 6.1 0.4 - - + -
138G LEU* 4.0 28.0 - - + -
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Residues in contact with GLN 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G ALA 2.9 16.5 + - - +
19G ASP* 3.9 11.2 - - - +
21G LEU* 1.3 75.6 - - - +
23G LYS* 1.3 60.8 + - - +
25G LEU* 3.7 6.3 - - - +
26G SER* 3.3 18.0 + - - -
72G ILE* 3.5 13.6 - - + +
78G SER 4.2 2.6 - - - +
79G PRO* 3.5 9.9 - - - +
80G LYS* 2.9 54.5 + - + +
89G ASP* 3.3 26.4 + - - +
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Residues in contact with LYS 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G ASP 3.5 9.6 + - - +
20G LEU* 3.2 17.8 + - + +
21G LEU 2.7 1.0 + - - -
22G GLN* 1.3 78.2 - - - +
24G GLN* 1.3 68.4 + - - +
26G SER* 3.1 5.5 + - - -
27G THR* 2.9 29.2 + - - +
89G ASP* 4.6 27.4 - - + +
91G THR* 5.2 13.6 + - - +
119G ASP* 3.4 26.6 + - + +
123G SER* 5.8 2.9 - - - +
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Residues in contact with GLN 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G LEU 3.2 4.2 + - - +
21G LEU* 2.6 24.4 + - + +
23G LYS* 1.3 74.7 - - - +
25G LEU* 1.3 57.9 + - - +
27G THR* 2.9 15.3 + - - +
28G TYR* 2.8 61.8 + - + +
68G VAL* 4.8 4.9 - - + -
116G VAL* 5.5 0.8 - - - +
119G ASP* 4.6 5.9 - - - +
120G THR* 2.7 35.1 + - - -
123G SER* 4.3 13.4 + - - -
138G LEU* 3.1 32.1 - - + +
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Residues in contact with LEU 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D TRP* 4.5 9.4 - - + -
21G LEU 2.7 17.9 + - - +
22G GLN* 3.7 11.2 - - - +
24G GLN* 1.3 72.0 - - - +
26G SER* 1.3 67.5 + - - +
28G TYR* 3.1 12.9 + - - +
29G ASN* 2.9 55.2 + - - +
65G ALA* 4.4 8.5 - - - +
68G VAL* 4.3 9.3 - - + +
69G ALA* 3.2 43.5 - - + +
72G ILE* 4.5 7.0 - - + -
79G PRO* 4.6 5.8 - - + -
80G LYS 3.4 24.0 - - - +
81G GLY* 4.3 3.6 - - - -
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Residues in contact with SER 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G GLN* 3.3 11.5 + - - -
23G LYS 3.1 8.5 + - - -
25G LEU* 1.3 84.8 - - - +
27G THR* 1.3 62.8 + - - +
29G ASN* 3.4 7.2 + - - +
30G ASP* 3.0 23.4 + - - +
80G LYS 4.5 0.9 + - - -
85G ALA 3.9 0.5 + - - -
86G ILE* 3.7 27.7 + - - +
89G ASP* 3.1 39.3 + - - +
90G ARG* 5.0 4.6 - - - +
92G TRP* 5.6 0.2 - - - -
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Residues in contact with THR 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G LYS* 2.9 23.4 + - - +
24G GLN* 2.9 22.4 + - - +
26G SER* 1.3 78.9 - - - +
28G TYR* 1.3 58.4 + - + +
30G ASP* 3.3 3.6 + - - +
31G LEU* 2.9 24.9 + - - +
90G ARG* 6.5 0.2 - - - +
92G TRP* 3.4 36.1 - - + -
115G GLY 5.6 0.2 - - - +
116G VAL* 3.9 32.3 - - + +
119G ASP* 5.2 8.8 + - + +
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Residues in contact with TYR 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G GLN* 2.8 48.4 + - + +
25G LEU* 3.1 6.9 + - - +
27G THR* 1.3 76.6 - - + +
29G ASN* 1.3 58.9 + - - +
31G LEU* 2.9 13.0 + - + -
32G HIS* 2.7 38.2 + - - +
61G VAL* 3.8 22.9 - - + +
64G TYR* 3.5 28.3 - + + -
65G ALA* 4.3 8.1 - - + -
68G VAL* 3.6 18.8 - - + -
116G VAL* 4.7 9.9 - - + -
120G THR* 4.8 1.3 + - - +
138G LEU* 3.9 2.8 - - - +
141G HIS* 2.7 40.6 + + + +
145G LEU* 4.6 14.7 - - + +
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Residues in contact with ASN 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 3.8 21.1 - - + +
40D TRP* 4.8 6.2 - - - -
25G LEU* 2.9 49.0 + - - +
26G SER* 3.7 6.9 - - - +
28G TYR* 1.3 75.4 - - - +
30G ASP* 1.3 64.8 + - - +
32G HIS* 3.4 23.0 + - - +
33G LEU* 3.1 27.7 + - - +
65G ALA* 4.2 13.0 - - - +
81G GLY* 4.4 10.3 - - - -
86G ILE* 4.0 16.9 - - + +
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Residues in contact with ASP 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PRO* 2.9 31.6 - - - +
26G SER 3.0 12.6 + - - +
27G THR 3.5 8.3 - - - +
29G ASN* 1.3 74.7 - - - +
31G LEU* 1.3 57.7 + - - +
33G LEU* 3.0 3.8 + - - +
34G THR* 2.7 46.8 + - - +
86G ILE* 3.5 14.3 - - + +
90G ARG* 3.2 13.7 + - + -
92G TRP* 3.4 33.2 + - + +
94G ASP* 4.4 4.0 - - - +
95G TYR 5.6 0.7 + - - -
112G VAL* 5.0 9.0 - - - +
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Residues in contact with LEU 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G THR 2.9 13.8 + - - +
28G TYR* 2.9 12.5 + - + +
30G ASP* 1.3 77.4 + - - +
32G HIS* 1.3 51.3 - - - +
34G THR* 2.9 9.8 + - - -
35G LEU* 2.7 60.9 + - + +
61G VAL* 3.6 29.8 - - + -
109G LEU* 5.6 1.3 - - + -
112G VAL* 4.6 11.4 - - + -
113G TYR* 3.4 27.8 - - + +
116G VAL* 4.6 25.1 - - + -
145G LEU* 4.0 15.9 - - + -
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Residues in contact with HIS 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D HIS* 4.4 19.3 - + - -
33D LEU* 4.5 5.6 - - + +
62D ARG* 3.3 24.7 + - - +
28G TYR 2.7 12.2 + - - -
29G ASN* 3.4 41.2 + - - +
31G LEU* 1.3 74.8 - - - +
33G LEU* 1.3 81.9 + - + +
35G LEU* 3.7 11.6 - - - +
36G LYS* 3.3 21.5 + - - +
58G VAL* 4.2 7.9 - - + +
61G VAL* 3.5 24.5 - - + -
62G ARG* 4.2 26.9 + - + +
65G ALA* 5.1 2.9 - - + +
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Residues in contact with LEU 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ASN* 3.8 28.7 - - + +
32D HIS* 4.4 7.4 - - - +
33D LEU* 3.5 30.1 - - + -
81D GLY 3.4 27.3 - - - +
82D THR* 5.2 0.7 - - - -
83D PRO* 4.6 21.8 - - + -
86D ILE* 5.4 4.5 - - + -
29G ASN 3.1 16.9 + - - +
30G ASP* 3.0 5.2 + - - +
32G HIS* 1.3 95.9 + - + +
34G THR* 1.3 57.6 + - - +
36G LYS* 3.5 9.4 + - + +
37G HIS 3.1 19.6 + - - -
40G TRP* 5.0 3.2 - - + -
86G ILE* 5.2 2.2 - - + -
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Residues in contact with THR 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D THR* 4.7 3.2 - - - +
83D PRO* 4.3 7.1 - - - +
30G ASP* 2.7 35.9 + - - +
31G LEU* 3.3 11.4 - - - -
33G LEU* 1.3 75.5 - - - +
35G LEU* 1.3 58.0 + - - +
37G HIS* 2.7 32.5 + - + +
38G VAL* 3.0 12.9 + - + +
95G TYR* 3.5 47.1 + - + +
109G LEU* 4.7 8.1 - - + -
112G VAL* 5.2 8.3 - - + -
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Residues in contact with LEU 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G LEU* 2.7 65.2 + - + +
32G HIS* 3.7 6.5 - - - +
34G THR* 1.3 73.1 - - - +
36G LYS* 1.3 57.6 + - - +
38G VAL* 3.1 12.3 + - + +
39G HIS* 2.9 25.6 + - - +
54G ILE* 3.6 24.6 - - + +
57G GLN* 4.5 5.8 - - + -
58G VAL* 3.3 22.7 - - + -
61G VAL* 5.1 0.7 - - + -
109G LEU* 4.0 26.5 - - + -
113G TYR* 3.5 18.2 - - + +
148G PHE* 4.2 8.3 - - + -
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Residues in contact with LYS 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ARG* 4.5 22.4 - - + +
65D ALA* 6.1 1.1 - - + -
66D ASP* 3.2 27.0 + - - +
32G HIS 3.3 8.7 + - - +
33G LEU* 3.7 12.1 - - + +
34G THR 3.2 0.4 - - - -
35G LEU* 1.3 79.2 - - - +
37G HIS* 1.3 63.4 + - - +
39G HIS* 3.0 43.7 + - + +
40G TRP* 3.0 47.5 + - + -
55G ASP* 3.2 19.4 + - - +
58G VAL* 3.6 28.3 - - + -
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Residues in contact with HIS 37 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D PRO 3.6 1.3 + - - -
80D LYS* 3.5 19.9 - - + -
81D GLY* 2.9 33.3 + - - +
82D THR* 3.7 19.6 - - + +
33G LEU 3.1 12.0 + - - +
34G THR* 2.7 22.8 + - - +
36G LYS* 1.3 77.3 - - - +
38G VAL* 1.3 57.1 + - - -
40G TRP* 3.2 20.2 + - - +
41G ASN* 2.8 45.0 + - - -
95G TYR* 3.5 28.8 + + - -
97G VAL 3.1 18.2 + - - -
98G GLU* 4.7 3.5 + - - -
105G HIS* 5.4 0.4 - + - -
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Residues in contact with VAL 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G THR 3.2 17.0 - - - +
35G LEU 3.6 4.3 - - - +
37G HIS* 1.3 70.1 - - - +
39G HIS* 1.3 66.1 + - - +
40G TRP 2.7 6.9 + - - -
41G ASN 3.2 7.0 + - - +
42G VAL* 2.7 32.1 + - + +
50G VAL* 5.4 0.7 - - + -
54G ILE* 3.1 26.7 - - + -
95G TYR* 3.7 26.7 - - + +
105G HIS* 4.0 26.0 - - + +
106G LEU* 6.5 1.1 - - + -
109G LEU* 4.2 22.4 - - + -
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Residues in contact with HIS 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ASP* 3.0 9.3 + - - -
207D FE 2.7 23.3 - - - -
35G LEU 2.9 13.8 + - - +
36G LYS* 3.0 40.8 + - + +
38G VAL* 1.3 77.3 - - - +
40G TRP* 1.3 64.1 + + - +
42G VAL* 4.9 1.9 + - - +
47G PHE* 5.0 1.6 - - - -
51G HIS* 2.7 86.5 + + - +
54G ILE* 3.9 19.2 - - + +
55G ASP* 3.3 25.1 + - - -
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Residues in contact with TRP 40 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D LEU* 4.5 9.6 - - + -
29D ASN* 4.8 8.5 - - - -
65D ALA* 4.1 10.8 - - + -
66D ASP* 3.2 39.1 + - - +
69D ALA* 3.3 32.5 - - + +
70D GLU* 3.7 22.6 - - + +
73D ALA* 4.4 7.3 - - + +
79D PRO* 4.5 14.6 - - + -
81D GLY* 4.1 21.8 - - - -
150F TRP* 3.7 24.3 - - - -
33G LEU* 5.0 2.7 - - + -
36G LYS* 3.0 46.4 - - + -
37G HIS* 3.2 19.0 + - - +
38G VAL 2.7 1.6 + - - -
39G HIS* 1.3 84.7 - + - +
41G ASN* 1.3 64.1 + - - +
42G VAL 3.3 9.6 + - - +
43G VAL* 5.6 0.7 - - - +
47G PHE* 5.6 0.3 - - - -
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Residues in contact with ASN 41 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D SER* 3.0 14.1 + - - -
79D PRO* 2.9 31.3 + - - +
37G HIS* 2.8 57.5 + - - +
38G VAL* 3.2 2.8 + - - +
40G TRP* 1.3 76.6 - - - +
42G VAL* 1.3 61.1 + - - +
43G VAL* 4.6 2.5 - - - -
98G GLU 3.7 7.5 - - - +
99G ARG* 3.2 24.6 - - - +
100G ASP 3.1 22.9 + - - +
105G HIS* 3.2 8.5 + - + +
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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) + - + + + + + -
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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