Contacts of the helix formed by residues 37 - 61 (chain A) in PDB entry 2BU6
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 CYS 37 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 4.0 4.7 - - - -
36A ALA* 1.3 86.6 - - - +
38A GLU* 1.3 61.9 + - - +
39A LYS* 2.9 34.5 - - - +
40A THR* 3.2 31.5 + - - +
41A SER 3.5 3.3 + - - -
168A PHE* 4.1 3.0 - - - -
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Residues in contact with GLU 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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37A CYS* 1.3 71.1 - - - +
39A LYS* 1.3 58.5 + - + +
40A THR 3.2 0.2 - - - -
41A SER* 3.5 2.1 - - - -
42A PHE* 2.6 37.4 + - - +
101A LEU* 3.4 41.4 - - + +
102A SER* 5.5 0.7 - - - -
105A THR* 4.4 5.7 + - - -
164A HIS* 4.0 5.4 + - + -
168A PHE* 3.3 64.0 - - + +
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Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A CYS* 3.4 28.5 - - + -
38A GLU* 1.3 82.0 - - + +
40A THR* 1.3 62.7 + - - +
42A PHE* 3.2 7.5 + - - +
43A THR* 2.9 31.0 + - - +
95A PRO* 4.4 15.9 - - + -
96A GLU* 4.0 33.1 + - - +
98A HIS* 6.2 3.8 - - + -
101A LEU* 4.2 18.6 - - + -
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Residues in contact with THR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 4.2 16.8 - - + -
36A ALA 4.0 4.3 + - - +
37A CYS* 3.2 27.5 + - - +
39A LYS* 1.3 79.9 - - - +
41A SER* 1.3 58.6 + - - +
43A THR* 3.0 17.7 + - - -
44A PHE* 3.3 13.2 + - - +
1386A TF2 4.3 8.5 - - + +
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 4.3 6.0 - - - -
37A CYS 3.5 3.7 + - - -
38A GLU* 3.2 6.9 + - - -
39A LYS 3.1 0.4 - - - -
40A THR* 1.3 76.9 - - - +
42A PHE* 1.3 55.7 + - - +
44A PHE* 2.9 2.8 + - - +
45A LEU* 2.7 39.4 + - - +
164A HIS* 2.6 32.7 + - - -
168A PHE* 4.0 11.0 - - - -
1386A TF2 2.6 32.8 + - - -
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Residues in contact with PHE 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 GLU 2.6 21.5 + - - +
39A LYS* 3.5 5.8 - - - +
41A SER* 1.3 72.1 - - - +
43A THR* 1.3 64.8 + - - +
45A LEU* 3.9 0.7 - - - +
46A ARG* 2.9 63.4 + - + +
90A PHE* 3.4 31.4 - + + -
93A LYS* 4.5 1.3 - - + -
95A PRO* 3.7 28.5 - - + -
100A THR* 4.4 19.3 - - + -
101A LEU* 4.7 13.0 - - + -
104A PHE* 3.4 55.4 - + + -
164A HIS* 4.2 2.2 - - + -
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Residues in contact with THR 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 LYS 2.9 19.4 + - - +
40A THR* 3.0 16.1 + - - +
42A PHE* 1.3 76.8 - - - +
44A PHE* 1.3 61.8 + - - +
46A ARG* 3.7 37.9 + - - +
47A GLN* 3.9 7.1 + - - +
95A PRO* 4.1 17.5 - - + -
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Residues in contact with PHE 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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21A SER* 4.9 6.5 - - - -
23A LEU* 3.7 24.0 - - + -
40A THR 3.3 4.2 + - - +
41A SER 2.9 7.4 + - - +
43A THR* 1.3 79.7 + - - +
45A LEU* 1.3 71.8 + - + +
47A GLN* 3.1 6.7 + - - +
48A GLU* 3.0 57.3 + - + +
160A LEU* 4.8 1.1 - - + -
1386A TF2 3.3 79.4 - - + -
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Residues in contact with LEU 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 SER* 2.7 36.4 + - - +
44A PHE* 1.3 81.0 - - + +
46A ARG* 1.3 63.1 + - - +
48A GLU* 3.8 2.7 - - + +
49A LEU* 3.0 41.5 + - + +
50A PRO* 3.3 0.5 - - - +
87A ILE* 4.8 0.2 - - - +
104A PHE* 3.8 23.7 - - + -
108A LEU* 4.3 6.1 - - + -
160A LEU* 4.0 25.6 - - + +
164A HIS* 3.6 29.6 - - + +
1386A TF2 3.6 29.2 - - - -
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Residues in contact with ARG 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 PHE* 2.9 66.6 + - + +
43A THR* 3.7 26.4 + - - +
44A PHE 3.1 0.2 - - - -
45A LEU* 1.3 76.0 - - - +
47A GLN* 1.3 58.5 + - + +
50A PRO* 2.8 23.5 - - - +
87A ILE* 4.5 10.5 - - + +
90A PHE* 3.4 20.6 + - + -
91A LEU* 2.6 50.1 + - + +
93A LYS 3.4 20.2 + - - -
95A PRO* 4.4 4.4 - - - +
104A PHE* 4.3 4.0 - - + -
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Residues in contact with GLN 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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14A HIS* 5.4 0.9 + - - -
15A PHE* 3.1 27.1 - - - -
18A PHE* 2.9 47.3 - - + -
43A THR 4.5 6.3 - - - +
44A PHE* 3.1 7.1 + - + +
46A ARG* 1.3 81.2 - - + +
48A GLU* 1.3 62.2 + - - +
50A PRO* 3.5 3.6 - - - +
51A VAL* 2.7 43.8 + - + +
91A LEU* 5.2 4.1 - - + +
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER 4.9 1.0 - - - +
20A PRO* 3.2 9.7 - - - +
21A SER* 2.9 43.1 + - - -
44A PHE* 3.0 45.2 + - + +
45A LEU* 4.4 3.4 - - - -
47A GLN* 1.3 78.3 - - - +
49A LEU* 1.3 66.7 + - - +
51A VAL* 3.0 10.6 + - - +
52A ARG* 2.8 56.7 + - - +
160A LEU* 4.0 10.1 - - + -
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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 LEU* 3.0 39.7 + - + +
48A GLU* 1.3 75.9 - - - +
50A PRO* 1.3 65.8 - - + +
52A ARG* 3.2 3.9 + - - +
53A LEU* 2.8 39.2 + - + +
87A ILE* 3.8 17.5 - - + -
104A PHE* 4.5 1.6 - - + -
108A LEU* 3.7 30.7 - - + -
157A ILE* 3.8 35.4 - - + +
160A LEU* 4.6 13.7 - - + -
161A ILE* 4.3 13.9 - - + -
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Residues in contact with PRO 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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15A PHE* 3.7 32.8 - - + +
45A LEU 3.3 2.7 - - - +
46A ARG* 2.8 30.3 - - - +
47A GLN 3.5 3.8 - - - +
49A LEU* 1.3 96.9 - - + +
51A VAL* 1.3 55.5 + - - +
53A LEU* 3.8 2.5 - - + +
54A ALA* 2.9 32.9 + - - +
84A LEU* 3.9 22.3 - - + +
87A ILE* 4.3 17.9 - - + -
88A MET* 5.3 4.9 - - - -
91A LEU* 5.6 0.9 - - + -
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Residues in contact with VAL 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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15A PHE* 3.8 14.1 - - + +
18A PHE* 3.6 49.1 - - + +
19A SER 3.8 15.5 - - - +
20A PRO* 3.8 6.1 - - + -
47A GLN* 2.7 40.5 + - + +
48A GLU* 3.0 13.4 + - - +
50A PRO* 1.3 76.9 - - - +
52A ARG* 1.3 56.8 + - - +
54A ALA* 3.6 0.7 - - - +
55A ASN* 2.7 38.4 + - - +
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Residues in contact with ARG 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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20A PRO* 3.8 16.7 - - + +
21A SER 3.1 21.2 + - - -
23A LEU* 4.5 2.4 - - - +
48A GLU* 2.8 38.9 + - - +
49A LEU* 3.8 4.9 - - - +
51A VAL* 1.3 74.6 - - - +
53A LEU* 1.3 65.0 + - - +
55A ASN* 3.4 5.3 + - - +
56A ILE* 3.2 24.3 + - - +
153A SER* 4.3 4.9 + - - +
156A SER* 3.3 29.2 + - - +
157A ILE* 3.9 22.0 - - + -
160A LEU* 3.2 33.5 - - - +
361A GLU* 2.9 41.7 + - - -
363A LEU* 3.7 9.9 - - - +
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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 36.5 + - + +
50A PRO* 3.8 6.3 - - + +
52A ARG* 1.3 72.2 - - - +
54A ALA* 1.3 58.5 + - - +
56A ILE* 3.0 9.1 - - - +
57A MET* 2.8 43.3 + - - +
80A TYR* 3.8 22.2 - - + -
83A SER* 4.2 15.7 - - - -
84A LEU* 3.8 31.6 - - + +
87A ILE* 4.2 13.9 - - + -
111A ILE* 5.9 2.5 - - + -
115A HIS* 5.5 1.8 - - + +
157A ILE* 3.8 25.8 - - + -
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Residues in contact with ALA 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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12A ILE* 3.9 19.7 - - + +
15A PHE* 3.6 21.8 - - + -
16A SER* 3.8 12.6 - - - +
50A PRO 2.9 19.6 + - - +
51A VAL 3.6 2.9 - - - +
53A LEU* 1.3 78.6 - - - +
55A ASN* 1.3 51.8 + - - +
57A MET* 3.6 8.6 - - - +
58A LYS* 2.6 39.2 + - - +
84A LEU* 5.1 3.1 - - + +
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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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15A PHE 3.8 5.0 - - - +
16A SER* 4.1 8.6 + - - +
18A PHE 3.2 23.9 + - - +
20A PRO* 3.9 12.2 - - + +
51A VAL* 2.7 30.1 + - - +
52A ARG* 3.9 6.1 - - - +
53A LEU 3.4 0.4 - - - -
54A ALA* 1.3 76.3 - - - +
56A ILE* 1.3 62.7 + - - +
58A LYS* 3.4 6.3 + - - +
59A GLU* 3.2 22.2 + - - +
364A PRO 5.1 6.5 - - - +
365A VAL* 3.7 13.9 - - - +
366A TYR* 3.4 39.2 + - + +
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Residues in contact with ILE 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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52A ARG 3.2 9.1 + - - +
53A LEU* 3.0 20.4 - - - +
55A ASN* 1.3 77.7 - - - +
57A MET* 1.3 60.5 + - - +
59A GLU* 3.4 13.4 + - + +
60A ILE* 3.0 31.6 + - + +
80A TYR* 3.7 28.5 - - + -
146A PHE* 4.9 2.9 - - + -
149A ARG* 4.5 2.2 - - + +
150A PHE* 3.3 55.2 - - + +
153A SER* 3.4 27.1 - - - +
157A ILE* 5.0 0.9 - - + -
364A PRO* 5.8 1.8 - - + -
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Residues in contact with MET 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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12A ILE* 3.4 28.0 - - + -
53A LEU* 2.8 32.9 + - - +
54A ALA* 3.7 4.5 - - - +
56A ILE* 1.3 75.4 - - - +
58A LYS* 1.3 65.4 + - - +
60A ILE* 3.3 6.1 + - + +
61A ASN* 3.1 31.1 + - - +
77A GLN* 3.8 15.6 + - - +
80A TYR* 3.6 33.9 - - + +
81A VAL* 3.2 46.2 - - + +
84A LEU* 4.1 15.7 - - + -
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Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 4.1 13.4 - - + +
13A GLU* 4.3 17.6 + - - +
16A SER* 3.4 30.3 - - - +
54A ALA 2.6 21.3 + - - +
55A ASN* 3.7 6.7 - - - +
56A ILE 3.3 0.2 - - - -
57A MET* 1.3 73.6 - - - +
59A GLU* 1.3 60.7 + - - +
61A ASN* 3.8 7.9 + - + +
62A LEU* 3.5 33.3 + - + +
366A TYR* 3.1 43.4 + - + -
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASN 3.2 16.3 + - - +
56A ILE* 3.7 13.0 - - + +
57A MET 3.2 0.2 - - - -
58A LYS* 1.3 74.7 - - - +
60A ILE* 1.3 67.6 + - + +
62A LEU* 3.2 19.7 + - - +
63A LEU* 3.9 4.0 + - - +
146A PHE* 4.2 9.6 - - + -
149A ARG* 2.8 49.4 + - - +
365A VAL 4.5 0.9 - - - +
366A TYR* 4.7 18.3 - - + +
370A ALA* 4.1 7.3 - - - +
374A TYR* 2.7 41.3 + - + +
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Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 3.0 21.0 + - + +
57A MET* 3.3 8.9 + - + +
59A GLU* 1.3 71.4 - - - +
61A ASN* 1.3 54.6 + - - +
62A LEU 2.7 15.6 + - - -
63A LEU* 2.7 36.9 - - + +
68A LEU* 3.4 5.8 - - + +
73A VAL* 4.1 24.7 - - + -
76A VAL* 5.2 9.4 - - + -
77A GLN* 3.3 30.7 - - + +
80A TYR* 5.7 3.1 - - + -
146A PHE* 3.7 19.7 - - + -
150A PHE* 3.7 29.4 - - + -
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Residues in contact with ASN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 4.4 21.0 - - - +
57A MET* 3.1 21.1 + - - +
58A LYS* 4.0 12.0 - - + +
59A GLU 3.4 0.2 - - - -
60A ILE* 1.3 76.5 - - - +
62A LEU* 1.3 66.7 + - + +
63A LEU 3.5 1.8 + - - +
68A LEU* 3.8 22.8 - - - +
77A GLN* 2.7 25.6 + - - +
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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