Contacts of the helix formed by residues 28 - 59 (chain A) 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 ASP 28 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PRO* 1.3 79.6 - - + +
29A ALA* 1.3 59.2 - - - +
30A ARG* 3.0 13.9 + - - +
31A ALA* 3.2 35.1 + - + +
32A ILE* 3.6 16.6 + - - +
148A SER* 5.6 2.9 - - - +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PRO 3.7 1.5 - - - +
28A ASP* 1.3 72.2 - - - +
30A ARG* 1.3 60.2 + - - +
31A ALA 3.5 0.2 - - - -
32A ILE* 3.1 35.1 - - + +
33A ALA* 3.3 12.5 + - - +
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Residues in contact with ARG 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ASP* 4.1 11.2 - - - +
29A ALA* 1.3 80.9 - - - +
31A ALA* 1.3 60.6 + - - +
33A ALA* 3.2 11.6 + - - +
34A ALA* 2.9 60.6 + - - +
37A GLU* 5.9 0.6 - - - +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ASP* 3.2 28.7 + - + +
29A ALA 3.5 0.2 - - - -
30A ARG* 1.3 80.5 - - - +
32A ILE* 1.3 57.2 + - + +
34A ALA* 3.2 6.7 + - - +
35A ILE* 2.9 36.4 + - + +
144A LEU 5.6 0.2 - - - +
148A SER* 3.5 31.2 - - - +
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Residues in contact with ILE 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PRO 5.0 2.9 - - - +
28A ASP 3.6 12.3 + - - +
29A ALA* 3.1 31.2 - - + +
31A ALA* 1.3 77.8 - - + +
33A ALA* 1.3 62.7 + - + +
35A ILE* 3.3 10.1 + - + +
36A CYS* 2.8 40.1 + - - -
93A LEU* 5.0 24.2 - - + +
150A ASP* 6.0 1.8 - - - +
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA 3.4 15.7 - - - +
30A ARG* 3.2 19.0 + - - +
31A ALA 3.2 0.6 - - - -
32A ILE* 1.3 83.3 - - + +
34A ALA* 1.3 61.4 + - - +
36A CYS* 3.4 6.8 + - - +
37A GLU* 3.0 24.6 + - - +
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ARG* 2.9 36.4 + - - +
31A ALA* 3.6 9.9 - - - +
33A ALA* 1.3 75.4 - - - +
35A ILE* 1.3 63.8 + - + +
37A GLU* 3.3 8.1 + - - +
38A GLN* 3.1 25.8 + - - +
144A LEU* 4.3 19.1 - - + -
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Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 2.9 22.8 + - + +
32A ILE* 3.7 8.3 - - + +
34A ALA* 1.3 73.9 - - - +
36A CYS* 1.3 61.0 + - - +
38A GLN* 3.1 9.0 + - - +
39A LEU* 2.8 45.8 + - + +
93A LEU* 4.1 9.9 - - + -
141A THR* 4.6 3.6 - - + +
144A LEU* 4.0 22.0 - - + -
145A ALA* 3.8 19.1 - - + +
148A SER* 3.5 24.9 - - - +
150A ASP* 3.8 13.5 - - + +
153A THR* 4.0 16.4 - - + -
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Residues in contact with CYS 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ILE* 2.8 28.6 + - - +
33A ALA* 3.7 7.2 - - - +
34A ALA 3.3 0.2 - - - -
35A ILE* 1.3 76.0 - - - +
37A GLU* 1.3 58.8 + - - +
39A LEU* 4.2 1.1 - - - -
40A ARG* 2.8 38.4 + - - +
90A LEU* 3.5 20.2 - - + +
93A LEU* 3.7 38.1 - - - -
95A ALA* 4.1 14.8 - - + -
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Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ARG* 5.9 0.2 - - - +
33A ALA 3.0 13.8 + - - +
34A ALA* 3.5 11.4 - - - +
35A ILE 3.2 0.2 - - - -
36A CYS* 1.3 77.3 - - - +
38A GLN* 1.3 65.0 + - + +
40A ARG* 3.5 25.8 + - - +
41A GLN* 3.2 20.3 + - - +
107A LEU* 4.9 10.6 - - - +
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Residues in contact with GLN 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ALA 3.1 15.8 + - - +
35A ILE* 3.1 9.5 + - - +
37A GLU* 1.3 77.1 - - + +
39A LEU* 1.3 64.1 + - - +
41A GLN* 3.0 11.8 + - - +
42A HIS* 2.9 31.2 + - - -
137A ARG* 3.2 42.5 + - - +
140A GLN* 3.7 10.1 + - - +
141A THR* 3.1 29.0 + - + +
144A LEU* 4.0 19.7 - - + -
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ILE* 2.8 26.0 + - + +
36A CYS* 4.5 0.2 - - - -
38A GLN* 1.3 77.1 - - - +
40A ARG* 1.3 62.0 + - - +
42A HIS* 3.1 16.0 + - + +
43A VAL* 3.0 26.7 + - - +
86A ILE* 3.8 17.4 - - + +
89A ARG* 4.1 17.5 - - + -
90A LEU* 3.6 27.1 - - + +
93A LEU* 3.8 29.8 - - + -
141A THR* 3.7 24.5 - - + -
153A THR* 4.3 1.1 - - + -
157A ILE* 4.2 14.4 - - + -
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Residues in contact with ARG 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A CYS* 2.8 24.2 + - - +
37A GLU* 3.7 29.3 + - - +
39A LEU* 1.3 77.0 - - - +
41A GLN* 1.3 61.8 + - - +
43A VAL 3.5 0.5 + - - -
44A ALA* 3.2 21.1 + - - +
90A LEU* 3.5 23.6 - - + -
95A ALA* 5.6 3.4 - - - -
96A GLN 3.5 19.5 + - - -
97A ALA 4.3 0.4 - - - -
98A PRO* 3.5 29.7 - - + +
103A GLU* 4.5 10.5 + - - +
107A LEU* 3.7 33.1 - - + +
116D LYS* 6.0 1.2 - - - +
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Residues in contact with GLN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLU 3.2 9.8 + - - +
38A GLN* 3.0 14.0 + - - +
40A ARG* 1.3 75.3 - - - +
42A HIS* 1.3 66.2 + - - +
44A ALA* 3.1 6.4 + - - +
45A ASP* 2.8 40.5 + - - +
107A LEU* 3.9 27.2 + - + +
109A GLY* 5.4 1.4 - - - +
133A TYR* 4.1 6.6 + - - +
137A ARG* 2.7 52.3 + - - +
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Residues in contact with HIS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN* 2.9 29.4 + - - -
39A LEU* 3.1 21.1 + - + +
41A GLN* 1.3 83.3 + - - +
43A VAL* 1.3 57.0 + - - +
45A ASP* 3.2 7.5 + - - +
46A LEU* 2.8 37.9 + - - +
86A ILE* 3.9 12.1 - - + -
134A LEU* 5.3 2.3 - - - +
137A ARG* 3.6 26.8 - - + +
138A PHE* 3.3 46.1 - + + -
141A THR* 2.6 31.4 + - + -
157A ILE* 4.9 0.9 - - + -
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Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU 3.0 20.6 + - - +
40A ARG 3.7 6.3 - - - +
42A HIS* 1.3 74.9 - - - +
44A ALA* 1.3 58.9 + - - +
46A LEU* 3.4 3.1 + - - -
47A GLY* 2.8 25.6 + - - -
83A PHE* 3.4 35.3 - - + +
86A ILE* 3.8 17.3 - - + -
87A ALA* 3.8 27.6 - - + +
90A LEU* 4.5 9.2 - - + -
98A PRO* 3.9 12.3 - - + +
104A TYR* 3.7 18.1 - - + +
58D TRP* 4.6 0.7 - - + -
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ARG 3.2 6.7 + - - +
41A GLN 3.1 8.2 + - - +
43A VAL* 1.3 79.6 - - - +
45A ASP* 1.3 62.7 + - - +
47A GLY* 3.3 1.7 + - - -
48A VAL* 3.0 27.5 + - - +
104A TYR* 3.4 28.4 - - + +
107A LEU* 3.6 31.6 - - + -
108A SER* 3.8 11.9 - - - +
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Residues in contact with ASP 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLN* 2.8 34.5 + - - +
42A HIS* 3.8 3.8 + - - +
44A ALA* 1.3 68.7 - - - +
46A LEU* 1.3 61.5 + - - +
48A VAL* 3.2 3.3 + - - +
49A LEU* 2.8 30.3 + - - +
108A SER* 2.8 19.3 + - - -
109A GLY 2.7 30.1 + - - -
110A ILE* 3.6 17.4 + - + +
133A TYR* 3.1 31.7 + - - -
134A LEU* 3.7 14.4 - - + +
137A ARG* 4.7 1.0 - - - +
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A HIS 2.8 28.2 + - - +
43A VAL* 3.7 4.7 - - - +
45A ASP* 1.3 72.4 - - - +
47A GLY* 1.3 59.5 + - - +
49A LEU* 3.2 1.5 + - + -
50A TYR* 2.8 27.4 + - - +
79A VAL* 3.4 36.0 - - + +
82A ALA* 4.0 7.0 - - + -
83A PHE* 3.9 31.6 - - + +
86A ILE* 4.0 12.1 - - + -
134A LEU* 3.5 34.3 - - + -
138A PHE* 3.9 22.9 - - + -
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Residues in contact with GLY 47 (chain A).
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 2.8 16.9 + - - -
44A ALA 3.7 2.0 - - - -
45A ASP 3.2 0.2 - - - -
46A LEU* 1.3 79.0 - - - +
48A VAL* 1.3 60.8 + - - +
50A TYR* 3.3 18.2 + - - +
51A ILE* 3.5 5.2 + - - +
83A PHE* 3.7 17.4 - - - -
104A TYR* 4.6 3.4 - - - -
51D ILE* 5.7 1.3 - - - -
101D MET* 3.2 22.2 - - - +
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ALA 3.0 19.2 + - - +
45A ASP 3.6 7.2 - - - +
47A GLY* 1.3 74.4 - - - +
49A LEU* 1.3 64.1 + - - +
51A ILE* 3.3 4.5 + - - +
52A LYS* 3.0 20.5 + - + +
104A TYR* 4.3 7.4 - - + +
105A LEU* 4.7 7.2 - - + -
108A SER* 3.4 22.9 - - - +
110A ILE* 3.6 32.5 - - + +
111A ALA 4.7 0.2 - - - +
112A GLU* 4.0 24.7 - - + +
101D MET* 3.6 22.9 - - - +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ASP 2.8 20.4 + - - +
46A LEU* 3.6 6.1 - - - +
48A VAL* 1.3 75.0 - - - +
50A TYR* 1.3 54.9 + - - +
52A LYS* 4.0 10.8 - - + -
53A LEU* 2.8 56.6 + - + +
56A TYR* 6.0 0.7 - - + -
79A VAL* 3.9 14.4 - - + -
110A ILE* 4.2 14.3 - - + +
127A VAL* 5.6 2.7 - - + -
130A ASP* 4.2 23.3 - - + +
131A PHE* 3.7 25.6 - - + -
134A LEU* 3.6 28.0 - - + -
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Residues in contact with TYR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU 2.8 13.8 + - - +
47A GLY* 3.3 13.7 - - - +
49A LEU* 1.3 78.4 - - - +
51A ILE* 1.3 72.9 + - + +
53A LEU* 3.6 3.9 + - - +
54A HIS* 2.8 52.5 + + - -
76A TYR* 3.3 40.3 - + + +
79A VAL* 4.0 8.5 - - + +
80A THR* 3.6 22.6 - - + +
83A PHE* 6.2 1.6 - - + -
50D TYR* 3.6 36.8 + + - -
80D THR* 2.8 28.4 + - - +
83D PHE* 5.4 4.9 - + - -
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Residues in contact with ILE 51 (chain A).
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 3.5 3.3 + - - +
48A VAL 3.3 6.8 + - - +
49A LEU 3.2 0.2 - - - -
50A TYR* 1.3 90.6 - - + +
52A LYS* 1.3 66.5 + - - +
54A HIS* 3.0 18.3 + - + +
55A ASN* 3.0 11.8 + - - +
101A MET* 3.8 11.7 - - + -
112A GLU* 4.9 1.6 - - - +
47D GLY* 5.6 1.3 - - - +
50D TYR* 6.6 0.4 - - + -
51D ILE* 4.9 2.2 - - + -
83D PHE* 5.1 6.7 - - + -
99D ALA* 3.7 4.3 - - - +
100D SER* 3.6 34.3 - - - +
101D MET* 3.6 33.7 - - + +
104D TYR* 3.6 30.5 - - + +
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Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 3.0 17.3 + - + +
49A LEU* 3.5 10.1 - - + +
51A ILE* 1.3 79.7 - - - +
53A LEU* 1.3 61.6 + - - +
55A ASN* 3.0 23.7 + - - +
56A TYR* 3.2 42.8 + - + +
110A ILE* 3.8 10.3 - - + +
111A ALA* 2.7 34.5 + - - +
112A GLU* 4.6 2.7 - - - -
113A GLU* 4.0 20.4 - - + +
126A ARG* 5.3 2.9 - - - +
130A ASP* 2.7 37.1 + - - +
99D ALA 5.0 2.2 - - - -
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 2.8 39.0 + - + +
50A TYR 3.8 4.7 - - - +
51A ILE 3.2 0.2 - - - -
52A LYS* 1.3 69.3 - - - +
54A HIS* 1.3 62.4 + - - +
56A TYR* 3.4 5.2 + - + +
57A HIS* 2.8 28.5 + - - +
72A LEU* 4.1 15.6 - - + +
75A TYR* 3.8 16.2 - - + -
76A TYR* 3.6 40.4 - - + +
79A VAL* 3.8 22.2 - - + -
127A VAL* 3.8 32.3 - - + -
131A PHE* 4.9 3.6 - - + -
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Residues in contact with HIS 54 (chain A).
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* 2.8 58.0 + + - -
51A ILE* 3.0 12.9 + - + +
53A LEU* 1.3 74.9 - - - +
55A ASN* 1.3 60.0 + - - +
57A HIS* 3.1 7.4 - + - +
58A TRP* 2.8 62.4 + + + -
76A TYR* 3.4 39.0 + + - -
80D THR* 4.9 1.4 + - - -
83D PHE* 3.7 26.2 - + + -
84D ASP* 3.8 14.7 + - - +
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Residues in contact with ASN 55 (chain A).
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 3.0 6.7 + - - +
52A LYS* 3.0 19.2 + - - +
54A HIS* 1.3 76.6 - - - +
56A TYR* 1.3 57.0 + - - +
58A TRP* 4.1 1.1 - - - -
59A HIS* 2.8 60.0 + - - +
113A GLU* 3.1 36.0 + - + +
115A GLU 3.4 15.1 + - - +
116A LYS* 4.9 4.0 - - - +
118A ILE* 5.5 0.7 - - - +
99D ALA* 3.0 43.8 + - + +
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Residues in contact with TYR 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 6.0 0.7 - - + -
52A LYS* 3.2 49.0 + - + -
53A LEU* 3.9 7.6 - - + +
55A ASN* 1.3 77.2 - - - +
57A HIS* 1.3 63.7 + - - +
59A HIS 4.4 0.4 - - - +
60A ILE* 3.0 35.1 + - - +
72A LEU* 4.0 13.5 - - + -
113A GLU* 2.6 42.5 + - + -
118A ILE* 3.8 23.6 - - + -
123A ALA* 3.7 26.7 - - + -
126A ARG* 3.4 18.1 - - + +
127A VAL* 3.6 33.4 - - + -
130A ASP* 5.4 0.2 - - - -
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Residues in contact with HIS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU 2.8 19.4 + - - +
54A HIS* 3.1 9.4 - + - +
56A TYR* 1.3 78.3 - - - +
58A TRP* 1.3 80.8 + + - +
60A ILE* 4.2 5.7 - - - +
65A PHE* 4.3 1.6 - - - -
69A HIS* 2.7 77.5 + + - -
72A LEU* 3.9 13.2 - - + +
73A GLU* 3.9 26.8 + - + -
76A TYR* 3.6 15.8 + + + -
84D ASP* 3.8 4.3 - - - -
604D FE 2.2 31.1 - - - -
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Residues in contact with TRP 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A HIS* 2.8 49.8 + + + +
55A ASN* 3.8 2.0 - - - +
57A HIS* 1.3 88.5 - + - +
59A HIS* 1.3 72.1 + + - +
60A ILE 3.7 4.3 + - - +
65A PHE* 4.8 0.7 - - - -
69A HIS* 5.0 0.7 - + - -
43D VAL* 4.6 0.4 - - + -
83D PHE* 3.6 32.3 - + - -
84D ASP* 3.0 22.6 + - - -
87D ALA* 3.4 28.3 - - + +
88D GLU* 4.3 7.0 - - + +
91D LEU* 3.5 39.2 - - + +
97D ALA* 3.9 12.6 - - + -
98D PRO 3.5 21.3 - - - -
99D ALA* 3.7 20.0 - - + -
104D TYR* 3.7 3.4 - - - -
604D FE 4.3 2.9 - - - -
169G TRP* 3.9 10.9 + - - -
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Residues in contact with HIS 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASN* 2.8 42.8 + - - +
58A TRP* 1.3 85.8 - + + +
60A ILE* 1.3 66.4 + - - +
61A TYR* 4.1 2.4 - - - +
116A LYS* 3.1 32.4 - - + +
117A GLU* 3.2 21.9 - - - +
118A ILE* 3.1 22.4 + - + +
91D LEU* 3.8 15.3 - - + +
96D GLN* 3.9 11.0 - - + -
97D ALA 3.3 35.7 + - - -
99D ALA* 4.1 9.4 - - + -
176G LYS* 5.6 0.7 + - - -
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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) + - + + + + + -
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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