Contacts of the helix formed by residues 27 - 59 (chain D) in PDB entry 2FJC
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 PRO 27 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ASP* 1.3 60.2 + - - +
29D ALA 3.5 2.5 - - - -
30D ARG* 3.3 50.7 - - + +
31D ALA* 2.7 46.0 + - + +
148D SER* 5.8 4.0 - - - -
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Residues in contact with ASP 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PRO* 1.3 78.1 - - - +
29D ALA* 1.3 63.5 + - + +
31D ALA* 3.7 3.8 - - - +
32D ILE* 3.2 24.2 + - - +
148D SER* 5.6 2.0 - - - +
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Residues in contact with ALA 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ASP* 1.3 79.8 - - + +
30D ARG* 1.3 61.7 + - - +
31D ALA 3.3 0.4 - - - -
32D ILE* 2.9 36.9 - - + +
33D ALA* 3.4 8.0 + - - +
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Residues in contact with ARG 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PRO* 3.3 42.0 + - + +
29D ALA* 1.3 76.2 - - - +
31D ALA* 1.3 64.7 + - - +
33D ALA* 3.4 7.4 + - + +
34D ALA* 3.1 22.3 + - + +
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Residues in contact with ALA 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PRO* 2.7 29.5 + - + +
28D ASP* 3.7 4.0 - - - +
30D ARG* 1.3 75.2 - - - +
32D ILE* 1.3 60.0 + - + +
34D ALA* 3.1 7.7 + - - +
35D ILE* 2.8 36.5 + - + +
144D LEU* 5.9 4.7 - - + -
148D SER* 3.5 32.3 - - - +
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Residues in contact with ILE 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ASP* 3.2 16.8 - - - +
29D ALA* 2.9 29.4 - - + +
31D ALA* 1.3 77.3 - - + +
33D ALA* 1.3 64.6 - - + +
35D ILE* 3.4 10.3 + - + +
36D CYS* 2.8 40.6 + - - -
93D LEU* 4.9 25.5 - - + +
150D ASP* 6.2 0.2 - - - +
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Residues in contact with ALA 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ALA 3.7 9.6 - - - +
30D ARG* 3.4 11.6 + - + +
31D ALA 3.2 0.6 - - - -
32D ILE* 1.3 85.8 - - + +
34D ALA* 1.3 61.9 + - - +
36D CYS* 3.4 7.2 + - - +
37D GLU* 3.0 24.6 + - - +
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Residues in contact with ALA 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ARG* 3.1 14.3 + - + +
31D ALA* 3.1 10.7 + - - +
33D ALA* 1.3 76.6 - - - +
35D ILE* 1.3 62.5 + - - +
37D GLU* 3.3 8.1 + - - +
38D GLN* 3.1 24.8 + - - +
144D LEU* 4.1 22.6 - - + +
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Residues in contact with ILE 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ALA* 2.8 22.4 + - - +
32D ILE* 3.7 8.7 - - + +
34D ALA* 1.3 77.2 - - - +
36D CYS* 1.3 58.1 + - - +
38D GLN* 3.1 6.1 + - - +
39D LEU* 2.8 47.0 + - + +
93D LEU* 4.1 9.6 - - + -
141D THR* 4.5 3.8 - - + +
144D LEU* 4.0 25.6 - - + -
145D ALA* 3.8 17.3 - - + +
148D SER* 3.5 25.4 - - - +
150D ASP* 3.8 13.9 - - + +
153D THR* 4.0 16.8 - - + -
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Residues in contact with CYS 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D ILE* 2.8 29.9 + - - +
33D ALA* 3.7 7.4 - - - +
35D ILE* 1.3 75.3 - - - +
37D GLU* 1.3 58.0 + - - +
39D LEU* 3.3 1.9 + - - -
40D ARG* 2.8 36.8 + - + +
90D LEU* 3.5 22.8 - - + +
93D LEU* 3.8 35.4 - - - -
95D ALA* 4.1 14.4 - - + -
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Residues in contact with GLU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ALA 3.0 14.0 + - - +
34D ALA* 3.5 11.2 - - - +
35D ILE 3.2 0.2 - - - -
36D CYS* 1.3 76.5 - - - +
38D GLN* 1.3 65.0 + - + +
40D ARG* 3.5 27.3 + - - +
41D GLN* 3.2 20.4 + - - +
107D LEU* 4.9 9.5 - - - +
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Residues in contact with GLN 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ALA 3.1 14.5 + - - +
35D ILE 3.1 9.1 + - - +
37D GLU* 1.3 76.7 - - + +
39D LEU* 1.3 64.8 + - - +
41D GLN* 3.0 11.3 + - - +
42D HIS* 2.9 31.3 + - - -
137D ARG* 3.4 37.4 + - - +
140D GLN* 3.7 16.2 + - - +
141D THR* 3.0 31.9 + - + +
144D LEU* 3.9 18.6 - - + -
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Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ILE* 2.8 24.9 + - + +
36D CYS* 3.6 4.9 - - - +
38D GLN* 1.3 77.3 - - - +
40D ARG* 1.3 62.9 + - - +
42D HIS* 3.1 14.3 + - + +
43D VAL* 3.0 27.2 + - - +
86D ILE* 3.8 16.8 - - + +
89D ARG* 4.2 11.4 - - + -
90D LEU* 3.6 30.3 - - + +
93D LEU* 3.8 29.2 - - + -
141D THR* 3.7 25.1 - - + -
153D THR* 4.3 7.2 - - + -
157D ILE* 4.3 7.4 - - + -
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Residues in contact with ARG 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LYS* 5.4 2.6 - - - +
36D CYS* 2.8 21.6 + - - +
37D GLU* 3.6 29.0 + - - +
39D LEU* 1.3 76.5 - - - +
41D GLN* 1.3 63.0 + - - +
43D VAL* 3.5 3.8 + - - +
44D ALA* 3.2 20.3 + - - +
90D LEU* 3.6 24.4 - - + +
95D ALA* 5.9 2.9 - - - -
96D GLN 3.6 18.8 + - - +
97D ALA 4.4 0.2 - - - -
98D PRO* 3.6 27.6 - - + +
103D GLU* 4.1 10.7 + - - +
107D LEU* 3.4 34.7 - - + +
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Residues in contact with GLN 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D GLU 3.2 9.1 + - - +
38D GLN* 3.0 13.2 + - - +
40D ARG* 1.3 78.1 - - - +
42D HIS* 1.3 70.0 + - - +
44D ALA* 3.1 7.2 + - - +
45D ASP* 2.8 40.1 + - - +
107D LEU* 4.1 25.8 + - + +
109D GLY* 5.3 1.4 - - - +
133D TYR* 3.9 7.9 + - - -
137D ARG* 2.9 51.0 + - - +
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Residues in contact with HIS 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLN* 2.9 29.8 + - - -
39D LEU* 3.1 20.4 + - + +
41D GLN* 1.3 82.8 + - - +
43D VAL* 1.3 56.9 + - - +
45D ASP* 3.3 7.0 + - - +
46D LEU* 2.8 37.4 + - - +
86D ILE* 3.9 13.5 - - + -
134D LEU* 5.3 1.6 - - - +
137D ARG* 3.6 30.8 - - + +
138D PHE* 3.3 44.5 - + + -
141D THR* 2.6 30.8 + - + -
157D ILE* 4.9 0.7 - - + -
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Residues in contact with VAL 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TRP* 4.6 0.2 - - + -
39D LEU 3.0 18.8 + - - +
40D ARG 3.7 7.6 - - - +
42D HIS* 1.3 76.1 - - - +
44D ALA* 1.3 57.6 + - - +
46D LEU* 4.5 2.7 - - - -
47D GLY* 2.8 26.3 + - - -
83D PHE* 3.4 32.6 - - + +
86D ILE* 3.7 17.9 - - + -
87D ALA* 3.8 29.8 - - + +
90D LEU* 4.5 8.3 - - + -
98D PRO* 3.8 12.6 - - + +
104D TYR* 3.7 18.8 - - + +
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Residues in contact with ALA 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ARG 3.2 7.6 + - - +
41D GLN 3.1 8.7 + - - +
43D VAL* 1.3 79.5 - - - +
45D ASP* 1.3 62.5 + - - +
47D GLY* 3.3 1.9 + - - -
48D VAL* 3.0 27.9 + - - +
104D TYR* 3.5 27.4 - - + +
107D LEU* 3.6 32.1 - - + -
108D SER* 3.8 10.8 - - - +
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Residues in contact with ASP 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D GLN* 2.8 36.0 + - - +
42D HIS* 3.8 4.0 + - - +
44D ALA* 1.3 72.1 - - - +
46D LEU* 1.3 58.3 + - - +
48D VAL* 3.2 3.1 + - - +
49D LEU* 2.8 30.0 + - - +
108D SER* 2.7 33.2 + - - -
109D GLY 2.7 16.7 + - - -
110D ILE* 3.7 16.5 + - + +
133D TYR* 3.3 29.1 + - - -
134D LEU* 3.8 15.3 - - + +
137D ARG* 4.7 1.2 - - - +
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D HIS 2.8 26.0 + - - +
43D VAL* 3.7 3.8 - - - +
45D ASP* 1.3 72.8 - - - +
47D GLY* 1.3 59.2 + - - +
49D LEU* 3.2 2.1 + - + -
50D TYR* 2.8 31.0 + - - +
79D VAL* 3.4 32.0 - - + +
82D ALA* 4.1 7.0 - - + -
83D PHE* 3.9 28.3 - - + +
86D ILE* 3.9 16.8 - - + -
134D LEU* 3.5 33.9 - - + -
138D PHE* 3.8 22.9 - - + -
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Residues in contact with GLY 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ILE* 5.7 1.1 - - - -
101A MET* 3.2 21.7 - - - +
43D VAL 2.8 17.1 + - - -
44D ALA 3.7 1.8 - - - -
46D LEU* 1.3 77.0 - - - +
48D VAL* 1.3 62.1 + - - +
50D TYR* 3.3 20.0 - - - +
51D ILE* 3.5 5.0 + - - +
83D PHE* 3.7 18.3 - - - -
104D TYR* 4.7 3.8 - - - -
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Residues in contact with VAL 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A MET* 3.8 22.9 - - - -
44D ALA 3.0 14.1 + - - +
45D ASP 3.2 6.5 + - - +
47D GLY* 1.3 73.0 - - - +
49D LEU* 1.3 65.6 + - - +
51D ILE* 3.3 4.9 + - - +
52D LYS* 3.0 20.5 + - + +
104D TYR* 4.3 8.3 - - + +
105D LEU* 4.7 7.0 - - + -
108D SER* 3.5 22.7 - - - +
110D ILE* 3.6 31.4 - - + +
112D GLU* 3.9 27.1 - - + +
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Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ASP 2.8 16.8 + - - +
46D LEU* 3.6 6.5 - - - +
48D VAL* 1.3 75.0 - - - +
50D TYR* 1.3 58.4 + - - +
52D LYS* 4.0 10.5 - - + -
53D LEU* 2.7 55.3 + - + +
56D TYR* 6.0 0.9 - - + -
79D VAL* 3.8 15.3 - - + -
110D ILE* 4.3 13.9 - - + +
127D VAL* 5.6 2.7 - - + -
130D ASP* 4.3 22.4 - - + +
131D PHE* 3.7 25.4 - - + -
134D LEU* 3.6 27.6 - - + -
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Residues in contact with TYR 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A TYR* 3.6 36.6 + + - -
51A ILE* 6.6 0.2 - - + -
80A THR* 2.8 29.3 + - - +
83A PHE* 5.4 4.7 - + - -
46D LEU 2.8 13.6 + - - +
47D GLY* 3.3 13.9 - - - +
48D VAL 3.2 0.2 - - - -
49D LEU* 1.3 77.9 - - - +
51D ILE* 1.3 73.5 + - + +
53D LEU* 3.6 6.2 + - - +
54D HIS* 2.8 53.7 + + - -
76D TYR* 3.3 37.4 - + + -
77D VAL* 5.3 0.2 - - - -
79D VAL* 4.0 8.0 - - + +
80D THR* 3.6 23.6 - - + +
83D PHE* 6.2 1.3 - - + -
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Residues in contact with ILE 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLY* 5.7 1.1 - - - -
51A ILE* 4.9 2.9 - - + -
83A PHE* 5.1 6.7 - - + -
99A ALA* 3.7 5.2 - - - +
100A SER* 3.7 33.4 - - - +
101A MET* 3.5 38.4 - - + +
104A TYR* 3.7 26.7 - - + +
47D GLY 3.5 3.1 + - - +
48D VAL 3.3 7.2 + - - +
49D LEU 3.2 0.4 - - - -
50D TYR* 1.3 89.3 - - + +
52D LYS* 1.3 65.7 + - - +
54D HIS* 3.1 10.7 + - + +
55D ASN* 3.0 19.4 + - - +
101D MET* 3.8 11.9 - - + -
112D GLU* 4.9 1.6 - - - +
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Residues in contact with LYS 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ALA 5.0 2.2 - - - -
48D VAL* 3.0 18.4 + - + +
49D LEU* 3.4 10.5 - - + +
51D ILE* 1.3 77.5 - - - +
53D LEU* 1.3 62.8 + - - +
55D ASN* 3.0 22.6 + - - +
56D TYR* 3.2 40.0 + - + -
110D ILE* 3.7 11.0 - - + +
111D ALA* 2.7 33.1 + - - +
112D GLU* 4.5 2.9 - - + -
113D GLU* 4.0 25.1 - - + +
126D ARG* 5.3 3.1 + - - +
130D ASP* 2.6 36.6 + - - +
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Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LEU* 2.7 35.7 + - + +
50D TYR 3.7 5.2 - - - +
52D LYS* 1.3 78.3 - - - +
54D HIS* 1.3 56.2 + - - +
56D TYR* 3.4 6.0 + - + +
57D HIS* 2.8 28.5 + - - +
72D LEU* 4.1 14.7 - - + +
75D TYR* 3.9 16.8 - - + -
76D TYR* 3.7 39.9 - - + +
79D VAL* 3.7 22.9 - - + -
127D VAL* 3.9 31.2 - - + -
131D PHE* 4.8 3.1 - - + -
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Residues in contact with HIS 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A THR* 4.8 1.2 + - - -
83A PHE* 3.5 28.6 - + + -
84A ASP* 3.8 13.2 + - - +
50D TYR* 2.8 57.3 + + - -
51D ILE* 3.1 12.5 + - + +
53D LEU* 1.3 74.3 - - - +
55D ASN* 1.3 56.9 + - - +
57D HIS* 3.0 7.6 + - - +
58D TRP* 2.8 65.8 + + + -
76D TYR* 3.4 37.5 + + - -
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Residues in contact with ASN 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ALA* 3.0 44.9 + - + +
51D ILE 3.0 8.5 + - - +
52D LYS* 3.0 15.0 + - - +
54D HIS* 1.3 77.4 - - - +
56D TYR* 1.3 60.2 + - - +
58D TRP* 3.2 1.5 + - - -
59D HIS* 2.9 53.0 + - - +
113D GLU* 3.1 34.8 + - + +
115D GLU 3.4 14.7 + - - +
116D LYS* 4.6 4.4 - - - +
118D ILE* 5.4 0.9 - - - +
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Residues in contact with TYR 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LEU* 6.0 0.7 - - + -
52D LYS* 3.2 46.4 + - + -
53D LEU* 3.8 7.4 - - + +
54D HIS 3.3 0.2 - - - -
55D ASN* 1.3 76.8 - - - +
57D HIS* 1.3 64.7 + - - +
59D HIS 4.5 0.7 - - - +
60D ILE* 3.0 33.5 + - - +
72D LEU* 4.0 13.0 - - + -
113D GLU* 2.6 42.9 + - + -
118D ILE* 3.8 23.8 - - + -
123D ALA* 3.7 25.1 - - + -
126D ARG* 3.3 19.8 - - + +
127D VAL* 3.5 33.4 - - + -
130D ASP* 5.4 0.2 - - - -
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Residues in contact with HIS 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ASP* 4.2 0.2 - - - -
601A FE 2.3 31.1 - - - -
53D LEU 2.8 15.9 + - - +
54D HIS* 3.1 12.1 - - - +
56D TYR* 1.3 78.6 - - - +
58D TRP* 1.3 74.8 + + - +
60D ILE* 4.3 0.9 - - - +
65D PHE* 4.3 5.7 - - - -
69D HIS* 2.7 86.7 + + - -
72D LEU* 3.9 14.1 - - + +
73D GLU* 3.8 26.0 + - + -
76D TYR* 3.9 15.3 + + + -
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Residues in contact with TRP 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A VAL* 4.6 0.9 - - + -
83A PHE* 3.5 32.1 - + - -
84A ASP* 3.2 22.1 + - - -
87A ALA* 3.4 28.6 - - + +
88A GLU* 4.5 8.0 - - + +
91A LEU* 3.5 38.8 - - + +
97A ALA* 4.0 12.6 - - + -
98A PRO 3.6 20.9 - - - -
99A ALA* 3.7 19.5 - - + -
104A TYR* 3.7 2.5 - - - -
601A FE 4.3 0.6 - - - -
54D HIS* 2.8 51.0 + + + +
55D ASN* 3.8 1.8 - - - +
57D HIS* 1.3 91.2 - + - +
59D HIS* 1.3 71.0 + + + +
60D ILE 3.7 4.4 + - - +
65D PHE* 4.8 1.3 - - - -
69D HIS* 5.1 1.3 - + - -
169H TRP* 3.9 11.7 + - - -
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Residues in contact with HIS 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 3.9 15.6 - - + +
96A GLN* 3.8 17.0 - - + +
97A ALA 3.3 41.0 + - - -
99A ALA* 4.1 10.1 - - + -
55D ASN* 2.9 42.7 + - - +
58D TRP* 1.3 85.4 - + + +
60D ILE* 1.3 66.3 + - - +
61D TYR* 4.1 2.4 - - - +
116D LYS* 3.5 15.9 - - + +
117D GLU* 3.3 24.7 - - - +
118D ILE* 3.0 23.7 + - + +
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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