Contacts of the helix formed by residues 45 - 72 (chain A) in PDB entry 2K21
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 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LYS 3.8 4.7 + - - +
42A LEU 3.6 8.7 + - - +
43A GLU 3.2 9.5 + - - +
44A ALA* 1.4 86.0 - - - +
46A TYR* 1.4 70.0 + - + +
47A VAL* 4.6 21.1 - - + +
48A LEU* 3.8 28.5 - - + +
49A MET* 3.5 17.8 + - - +
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Residues in contact with TYR 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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41A LYS 4.1 7.8 + - - +
42A LEU* 4.3 28.5 - - + -
45A LEU* 1.4 76.6 - - + +
47A VAL* 1.4 76.9 + - + +
49A MET* 3.9 5.2 - - - +
50A VAL* 3.2 31.4 + - - +
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Residues in contact with VAL 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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45A LEU* 3.3 14.6 - - + +
46A TYR* 1.4 100.0 - - + +
48A LEU* 1.4 62.1 + - - +
49A MET 3.2 2.0 - - - -
50A VAL* 3.0 25.4 + - + +
51A LEU* 3.2 12.1 + - - +
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Residues in contact with LEU 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 4.7 9.9 - - - +
45A LEU* 3.8 30.5 + - + +
47A VAL* 1.4 76.9 - - - +
49A MET* 1.4 63.4 + - - +
51A LEU* 3.4 21.3 + - + +
52A GLY* 3.5 8.3 + - - -
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Residues in contact with MET 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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44A ALA* 4.9 10.5 + - + +
45A LEU 3.5 17.4 + - - +
46A TYR* 3.9 6.1 - - - +
47A VAL 3.2 0.4 - - - -
48A LEU* 1.4 74.0 - - - +
50A VAL* 1.4 54.6 + - - +
52A GLY* 3.1 10.3 + - - -
53A PHE* 2.7 40.7 + - + +
114A ALA* 3.4 50.5 - - + +
115A ILE* 3.9 21.5 - - + -
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Residues in contact with VAL 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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17A TRP* 6.2 5.4 - - + -
46A TYR 3.2 24.0 + - - +
47A VAL* 3.0 18.3 + - + +
49A MET* 1.4 71.3 - - - +
51A LEU* 1.4 52.7 + - - +
53A PHE* 4.2 15.7 - - + -
54A PHE* 2.4 49.8 + - + +
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Residues in contact with LEU 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 VAL* 3.2 10.2 + - + +
48A LEU* 3.7 17.5 - - + +
49A MET 3.1 0.6 + - - -
50A VAL* 1.4 74.6 - - - +
52A GLY* 1.4 61.5 - - - +
54A PHE* 3.5 9.2 + - + +
55A GLY* 3.3 18.9 + - - -
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Residues in contact with GLY 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 LEU 3.5 5.5 + - - -
49A MET* 3.1 10.7 + - - -
51A LEU* 1.4 73.8 - - - +
53A PHE* 1.4 62.6 + - - +
55A GLY* 3.6 3.3 + - - -
56A PHE* 3.4 19.8 + - - +
114A ALA* 4.9 4.0 - - - -
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Residues in contact with PHE 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 MET* 2.7 28.8 + - + +
50A VAL* 3.5 16.8 - - + +
52A GLY* 1.4 69.0 - - - +
54A PHE* 1.4 59.5 + + + +
56A PHE* 3.2 7.2 + + + +
57A PHE* 2.7 76.7 + + + +
113A LEU* 4.3 16.4 - - + -
114A ALA* 4.0 24.7 - - + +
115A ILE* 4.0 28.5 - - + -
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Residues in contact with PHE 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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8A ALA* 5.7 8.3 - - + -
50A VAL* 2.4 45.6 + - + +
51A LEU* 3.8 9.9 - - + +
53A PHE* 1.4 70.0 - + + +
55A GLY* 1.4 53.9 + - - +
57A PHE* 4.5 20.4 - + - -
58A THR* 2.7 67.3 + - + -
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Residues in contact with GLY 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 LEU 3.3 14.3 + - - -
52A GLY 3.6 4.2 + - - -
53A PHE 3.3 0.2 - - - -
54A PHE* 1.4 79.6 - - - +
56A PHE* 1.4 57.3 + - - +
58A THR* 4.0 7.9 - - - +
59A LEU* 4.0 16.6 + - - +
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Residues in contact with PHE 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 GLY 3.4 12.5 + - - +
53A PHE* 3.2 12.8 + + - +
55A GLY* 1.4 76.3 - - - +
57A PHE* 1.4 56.9 + - + +
58A THR 3.4 0.4 - - - -
59A LEU* 3.4 6.1 + - + +
60A GLY* 2.6 37.5 + - - -
63A LEU* 4.9 17.9 - - + +
111A ASN* 4.1 24.0 - - + -
112A HIS* 3.2 59.0 - + - -
113A LEU* 5.4 4.0 - - + -
114A ALA* 5.1 11.4 - - + -
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Residues in contact with PHE 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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4A SER* 4.5 17.9 - - - -
5A ASN* 6.2 0.9 - - - -
8A ALA* 5.2 12.3 - - + -
53A PHE* 2.7 58.9 + + + +
54A PHE* 4.0 20.6 - + - +
56A PHE* 1.4 70.5 - - + +
58A THR* 1.4 64.2 + - - +
59A LEU 3.2 2.2 - - - -
60A GLY* 3.3 13.8 + - - +
61A ILE* 3.3 42.3 + - + +
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Residues in contact with THR 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 PHE* 2.7 59.8 + - + -
55A GLY* 4.0 9.0 - - - +
56A PHE 3.4 0.2 - - - -
57A PHE* 1.4 72.5 - - - +
59A LEU* 1.4 66.8 + - + +
61A ILE* 3.2 24.2 - - + +
62A MET* 5.2 1.7 - - - +
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Residues in contact with LEU 59 (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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55A GLY 4.0 10.0 + - - +
56A PHE* 3.4 7.8 + - - +
57A PHE 3.2 0.2 - - - -
58A THR* 1.4 84.4 - - + +
60A GLY* 1.4 56.4 + - - +
61A ILE* 3.1 2.2 - - - -
62A MET* 2.8 41.4 + - + +
63A LEU* 2.9 43.1 + - + +
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Residues in contact with GLY 60 (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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56A PHE* 2.6 29.4 + - - -
57A PHE* 3.3 11.5 + - - -
59A LEU* 1.4 70.0 - - - +
61A ILE* 1.4 50.2 - - - +
63A LEU* 3.6 10.8 + - - +
64A SER* 2.9 35.6 + - - -
111A ASN* 4.6 8.9 + - - -
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Residues in contact with ILE 61 (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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1A MET* 3.2 33.8 - - - +
2A ILE* 3.8 12.5 + - + -
4A SER* 3.9 11.7 - - - -
5A ASN* 4.1 28.0 - - + +
57A PHE* 3.3 37.4 + - + +
58A THR* 3.2 30.5 - - + +
59A LEU 3.0 0.4 + - - -
60A GLY* 1.4 74.7 - - - +
62A MET* 1.4 66.8 + - + +
64A SER* 3.4 7.6 + - - -
65A TYR* 3.0 26.3 + - - +
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Residues in contact with MET 62 (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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2A ILE* 5.4 15.5 - - + +
58A THR 5.2 1.1 - - - +
59A LEU* 2.8 28.3 + - + +
61A ILE* 1.4 78.1 - - + +
63A LEU* 1.4 59.7 + - + +
65A TYR* 3.1 13.6 + - + +
66A ILE* 2.9 51.7 + - + +
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Residues in contact with LEU 63 (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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56A PHE* 4.9 19.7 - - + +
59A LEU* 2.9 49.3 + - + +
60A GLY* 3.9 7.9 - - - +
62A MET* 1.4 78.3 - - + +
64A SER* 1.4 62.9 + - - +
66A ILE* 4.2 19.5 - - + +
67A ARG* 3.5 27.4 + - - +
111A ASN* 4.5 16.2 + - - +
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Residues in contact with SER 64 (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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1A MET* 4.5 11.4 - - - -
60A GLY 2.9 18.3 + - - -
61A ILE* 3.5 9.9 - - - -
62A MET 3.3 0.2 - - - -
63A LEU* 1.4 74.0 - - - +
65A TYR* 1.4 50.2 + - - +
67A ARG* 3.2 8.2 + - - +
68A SER* 2.9 35.6 + - - -
111A ASN* 4.8 10.3 + - - +
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Residues in contact with TYR 65 (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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1A MET* 4.2 25.0 - - + +
2A ILE* 4.5 32.3 - - + +
61A ILE 3.0 14.7 + - - +
62A MET* 3.1 14.8 + - + +
64A SER* 1.4 73.4 - - - +
66A ILE* 1.4 60.7 + - + +
68A SER* 3.7 8.4 - - - -
69A LYS* 2.8 71.2 + - + +
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Residues in contact with ILE 66 (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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62A MET* 2.9 44.7 + - + +
63A LEU* 4.3 20.4 - - + +
64A SER 3.5 0.2 - - - -
65A TYR* 1.4 76.6 - - + +
67A ARG* 1.4 63.9 + - + +
69A LYS* 3.1 21.1 + - - +
70A LYS* 3.1 41.2 + - + +
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Residues in contact with ARG 67 (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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63A LEU 3.5 18.3 + - - +
64A SER* 3.2 5.4 + - - +
66A ILE* 1.4 83.8 - - + +
68A SER* 1.4 57.1 + - - +
70A LYS* 3.6 18.9 + - - +
71A LEU* 3.2 55.9 + - - +
110A GLU* 4.7 27.5 + - + +
111A ASN* 6.1 2.0 - - - +
124A GLU* 5.2 7.7 + - - -
126A LYS* 5.6 6.9 - - - +
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Residues in contact with SER 68 (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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1A MET* 5.1 11.9 - - - -
64A SER 2.9 18.0 + - - -
65A TYR* 3.7 12.6 - - - -
67A ARG* 1.4 74.4 - - - +
69A LYS* 1.4 50.5 + - - +
71A LEU* 3.0 5.4 + - - +
72A GLU* 2.5 41.3 + - - -
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Residues in contact with LYS 69 (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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65A TYR* 2.8 57.5 + - + +
66A ILE* 3.1 19.8 + - - +
68A SER* 1.4 70.1 - - - +
70A LYS* 1.4 59.3 + - - +
72A GLU* 3.4 39.7 - - - +
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Residues in contact with LYS 70 (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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66A ILE* 3.1 29.8 + - + +
67A ARG* 3.8 19.5 - - - +
68A SER 3.3 0.4 - - - -
69A LYS* 1.4 79.3 - - - +
71A LEU* 1.4 70.1 + - + +
72A GLU* 3.7 2.2 - - - -
73A HIS* 5.4 2.3 + - - +
126A LYS* 4.9 6.8 + - - +
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Residues in contact with LEU 71 (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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67A ARG* 3.2 38.1 + - - +
68A SER* 3.0 7.4 + - - +
70A LYS* 1.4 83.7 - - + +
72A GLU* 1.4 57.5 + - - +
73A HIS 3.3 9.2 + - - +
74A SER* 2.9 29.3 + - - +
126A LYS* 3.7 27.4 - - - +
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Residues in contact with GLU 72 (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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68A SER* 2.5 23.4 + - - +
69A LYS* 3.4 41.3 - - - +
70A LYS 3.7 1.3 - - - -
71A LEU* 1.4 70.0 - - - +
73A HIS* 1.4 90.2 + - + +
74A SER* 3.1 12.3 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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