Contacts of the helix formed by residues 47 - 73 (chain A) in PDB entry 4U7C
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 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A THR* 3.2 14.3 + - - -
45A LYS 3.3 0.8 + - - -
46A GLY* 1.3 83.6 - - - +
48A ARG* 1.3 65.4 + - - +
49A PHE* 3.3 4.3 + - - +
50A TYR* 2.9 18.2 + - - +
51A GLY* 3.1 17.3 + - - -
4D G 2.9 27.4 + - - -
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Residues in contact with ARG 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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46A GLY 5.6 0.2 - - - +
47A SER* 1.3 72.2 - - - +
49A PHE* 1.3 66.4 + - - +
51A GLY* 3.2 3.1 + - - -
52A ASN* 2.9 22.9 + - - +
424A GLU* 4.5 7.3 + - - -
463A VAL* 3.4 52.4 + - - +
464A ASN* 4.0 22.5 - - - +
465A PHE* 4.0 6.7 - - + -
505A ARG* 4.8 6.9 - - - +
3D T 5.3 8.8 + - - -
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Residues in contact with PHE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 3.3 1.3 + - - +
48A ARG* 1.3 78.0 - - - +
50A TYR* 1.3 57.5 + - - +
52A ASN* 3.0 6.0 + - + +
53A GLU* 2.9 63.5 + - + +
461A LYS* 5.9 1.1 - - - -
465A PHE* 3.5 46.9 - + + -
603A PEG 6.0 1.8 - - - -
4D G 3.4 76.9 - + + +
5D VKJ 4.5 8.1 - - - -
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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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41A MET* 4.6 15.8 - - + +
44A THR* 3.5 37.5 - - + +
45A LYS* 4.1 9.4 - - + +
46A GLY* 3.3 24.7 - - - -
47A SER* 2.9 20.3 + - - +
49A PHE* 1.3 80.4 - - - +
51A GLY* 1.3 59.4 + - - +
53A GLU* 3.1 13.0 + - + +
54A LEU* 2.9 61.8 + - + +
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Residues in contact with GLY 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 SER 3.1 14.4 + - - -
48A ARG* 3.6 4.5 - - - -
49A PHE 3.2 0.4 - - - -
50A TYR* 1.3 77.6 - - - +
52A ASN* 1.3 62.4 + - - +
54A LEU* 3.0 14.0 + - - +
55A LYS* 2.9 21.0 + - - +
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Residues in contact with ASN 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 ARG 2.9 8.3 + - - +
49A PHE 3.0 7.4 + - - +
51A GLY* 1.3 75.1 - - - +
53A GLU* 1.3 59.5 + - + +
55A LYS* 3.3 20.3 + - - +
56A LYS* 2.9 48.9 + - - +
464A ASN 3.4 26.5 + - - +
465A PHE* 3.7 22.0 + - + +
466A GLU* 3.8 21.2 - - - +
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Residues in contact with GLU 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 PHE* 2.9 53.3 + - + +
50A TYR* 3.4 13.9 - - + +
51A GLY 3.1 0.2 - - - -
52A ASN* 1.3 77.0 - - - +
54A LEU* 1.3 61.5 + - + +
56A LYS* 3.0 35.0 + - - +
57A GLU* 2.9 31.1 + - - +
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Residues in contact with LEU 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* 2.9 52.3 + - + +
51A GLY* 3.3 12.6 - - - +
53A GLU* 1.3 77.5 - - + +
55A LYS* 1.3 56.7 + - - +
57A GLU* 3.3 11.7 + - + +
58A LYS* 2.9 32.1 + - - +
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Residues in contact with LYS 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 GLY 2.9 12.2 + - - +
52A ASN* 3.3 26.9 - - - +
54A LEU* 1.3 74.7 - - - +
56A LYS* 1.3 60.3 + - + +
58A LYS* 3.3 32.1 + - - +
59A GLN* 2.9 28.6 + - + +
466A GLU* 4.9 12.8 - - + +
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Residues in contact with LYS 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 ASN* 2.9 37.1 + - - +
53A GLU* 3.0 34.8 + - - +
54A LEU 3.4 0.2 - - - -
55A LYS* 1.3 77.4 - - + +
57A GLU* 1.3 58.4 + - - +
59A GLN* 3.1 13.9 + - + +
60A VAL* 2.9 30.0 + - - +
603A PEG 5.1 9.9 + - - -
9C A 6.1 1.8 - - - +
10C T 5.1 16.5 + - - +
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Residues in contact with GLU 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 GLU 2.9 18.2 + - - +
54A LEU* 3.4 14.4 - - + +
56A LYS* 1.3 72.9 - - - +
58A LYS* 1.3 59.3 + - - +
60A VAL* 3.0 11.8 - - - +
61A ASN* 2.9 43.3 + - - +
359A LYS* 4.7 10.5 + - - +
363A LYS* 2.3 36.0 + - - -
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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
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54A LEU 2.9 11.9 + - - +
55A LYS* 3.3 36.5 - - - +
57A GLU* 1.3 77.3 - - - +
59A GLN* 1.3 61.0 + - + +
61A ASN* 3.4 10.4 - - - +
62A GLN* 2.9 28.1 + - + +
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Residues in contact with GLN 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 LYS* 2.9 14.9 + - + +
56A LYS* 3.1 16.5 + - + +
58A LYS* 1.3 81.3 - - + +
60A VAL* 1.3 58.9 + - + +
62A GLN* 3.1 11.4 + - - +
63A ARG* 3.0 61.2 + - - +
9C A 4.4 31.8 + - - +
10C T 5.1 3.8 - - - +
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Residues in contact with VAL 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 LYS 2.9 14.9 + - - +
57A GLU* 3.0 28.3 - - - +
59A GLN* 1.3 76.2 - - - +
61A ASN* 1.3 65.8 + - - +
63A ARG* 3.0 16.2 + - - +
64A ILE* 2.9 28.7 + - + +
359A LYS* 4.8 10.3 - - - +
360A VAL* 3.7 35.0 - - + +
363A LYS* 4.5 20.9 - - + +
364A MET* 4.8 9.9 - - + -
10C T 4.6 9.9 - - - +
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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
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57A GLU* 2.9 35.7 + - - +
58A LYS* 3.4 12.8 - - - +
60A VAL* 1.3 78.0 - - - +
62A GLN* 1.3 55.8 + - - +
64A ILE* 3.2 12.1 + - - +
65A GLU* 2.9 28.5 + - - +
363A LYS* 3.4 23.7 + - - -
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Residues in contact with GLN 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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58A LYS* 2.9 14.9 + - + +
59A GLN* 3.1 17.7 + - - +
61A ASN* 1.3 73.3 - - - +
63A ARG* 1.3 65.8 + - - +
65A GLU* 3.1 18.4 + - - +
66A ASN* 2.9 55.9 + - - +
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Residues in contact with ARG 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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59A GLN* 3.0 38.9 + - - +
60A VAL* 3.0 16.0 + - + +
62A GLN* 1.3 75.3 - - - +
64A ILE* 1.3 59.2 + - - +
66A ASN* 3.5 12.4 + - - +
67A MET* 3.0 27.4 + - - +
360A VAL* 4.3 11.4 - - - +
364A MET* 4.3 21.8 - - + +
8C G 6.2 0.4 - - - +
9C A 3.1 14.9 + - - -
10C T 2.9 47.5 + - - -
12D C 5.5 9.9 - - - -
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Residues in contact with ILE 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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60A VAL* 2.9 17.0 + - + +
61A ASN* 3.4 14.6 - - - +
63A ARG* 1.3 74.5 - - - +
65A GLU* 1.3 66.0 + - - +
67A MET* 3.0 9.8 + - + +
68A MET* 2.9 30.8 + - + +
363A LYS* 3.9 49.6 - - + +
364A MET* 3.9 23.8 - - + +
367A ALA* 3.9 21.8 - - + -
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Residues in contact with GLU 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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61A ASN 2.9 13.3 + - - +
62A GLN* 3.3 26.6 - - - +
64A ILE* 1.3 78.3 - - - +
66A ASN* 1.3 59.2 + - - +
68A MET* 3.3 7.2 + - - +
69A GLN* 2.9 51.4 + - + +
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Residues in contact with ASN 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 GLN* 2.9 49.6 + - - +
63A ARG* 3.6 12.0 - - - +
65A GLU* 1.3 77.7 - - - +
67A MET* 1.3 56.3 + - - +
69A GLN* 3.3 9.1 + - - +
70A GLN* 2.9 30.0 + - - +
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Residues in contact with MET 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 ARG 3.0 15.2 + - - +
64A ILE* 3.0 15.2 + - - +
66A ASN* 1.3 76.2 - - - +
68A MET* 1.3 58.2 + - - +
70A GLN* 3.3 8.2 + - + +
71A LYS* 2.9 25.5 + - - +
364A MET* 3.6 42.0 - - + +
367A ALA* 4.2 10.1 - - + -
368A LEU* 3.6 33.7 - - + -
386A LEU* 3.9 23.4 - - + +
387A PHE* 4.0 20.9 - - + -
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Residues in contact with MET 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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64A ILE* 2.9 27.8 + - + +
65A GLU* 3.6 9.6 - - - +
67A MET* 1.3 74.3 - - - +
69A GLN* 1.3 67.6 + - + +
70A GLN 3.1 1.3 - - - -
71A LYS* 3.0 25.4 + - + +
72A ALA* 2.9 23.6 + - - +
367A ALA* 3.6 22.0 - - + +
368A LEU* 3.9 25.4 - - + -
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Residues in contact with GLN 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 GLU* 2.9 41.6 + - + +
66A ASN* 3.7 8.5 - - - +
68A MET* 1.3 76.7 - - + +
70A GLN* 1.3 54.5 + - - +
72A ALA* 3.6 10.9 - - - +
73A GLN* 2.4 35.3 + - - +
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Residues in contact with GLN 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 ASN 2.9 17.2 + - - +
67A MET* 3.5 9.4 - - + +
68A MET 3.1 0.2 - - - -
69A GLN* 1.3 75.9 - - - +
71A LYS* 1.3 63.9 + - - +
73A GLN* 3.6 10.7 + - - +
74A ILE* 3.6 18.9 + - + +
385A LEU 4.7 11.4 + - - +
386A LEU* 4.9 19.4 + - + -
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Residues in contact with LYS 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 MET 2.9 13.6 + - - +
68A MET* 3.0 35.0 + - + +
70A GLN* 1.3 77.6 - - - +
72A ALA* 1.3 63.9 + - - +
74A ILE* 3.0 26.2 + - + +
368A LEU* 4.9 13.9 + - + +
382A LEU* 4.0 31.6 - - + +
386A LEU* 4.4 16.4 - - + -
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Residues in contact with ALA 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 MET 2.9 11.9 + - - +
69A GLN* 3.6 17.7 - - - +
71A LYS* 1.3 77.5 - - - +
73A GLN* 1.3 60.2 + - - +
74A ILE 3.2 7.6 + - - +
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Residues in contact with GLN 73 (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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69A GLN* 2.4 33.7 + - - +
70A GLN* 3.6 7.5 + - - +
71A LYS 3.1 2.0 + - - -
72A ALA* 1.3 78.7 - - - +
74A ILE* 1.3 64.7 + - + +
75A THR* 3.8 4.6 + - - +
78A GLN* 3.3 11.1 - - - +
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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