Contacts of the helix formed by residues 47 - 73 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B THR 3.2 19.1 + - - -
45B LYS 3.2 0.6 + - - -
46B GLY* 1.3 82.7 - - - +
48B ARG* 1.3 74.3 + - - +
49B PHE* 2.8 23.6 + - - +
50B TYR* 3.8 5.5 - - - +
51B GLY* 3.2 17.0 + - - -
4T G 3.5 17.9 + - - -
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Residues in contact with ARG 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLY 5.6 0.2 - - - +
47B SER* 1.3 76.4 + - - +
49B PHE* 1.3 58.1 + - - +
51B GLY* 3.3 2.4 + - - -
52B ASN* 2.9 27.9 + - - +
424B GLU* 4.5 9.7 + - - -
463B VAL* 3.5 49.2 + - - +
464B ASN* 4.1 20.7 + - - +
465B PHE* 4.0 8.7 - - + -
505B ARG* 4.6 6.2 - - - +
3T T 5.6 6.8 + - - -
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Residues in contact with PHE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B SER* 2.8 9.1 + - - +
48B ARG* 1.3 74.9 - - - +
50B TYR* 1.3 66.5 + - - +
52B ASN* 3.0 5.4 + - - +
53B GLU* 2.9 55.6 + - + +
461B LYS* 5.9 0.9 - - - -
465B PHE* 3.5 46.5 - + + -
4T G 3.3 72.5 - + + +
5T VKJ 4.5 8.1 - - - -
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Residues in contact with TYR 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B MET* 3.8 22.1 - - + +
44B THR* 3.5 47.6 - - + +
45B LYS* 3.7 31.8 - - + +
46B GLY* 3.3 18.4 - - - -
47B SER* 3.3 8.8 + - - +
48B ARG 3.3 0.2 - - - -
49B PHE* 1.3 83.0 - - - +
51B GLY* 1.3 59.1 + - - +
53B GLU* 3.2 12.1 + - + +
54B LEU* 2.9 59.0 + - + +
4T G 5.7 0.2 - - - +
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Residues in contact with GLY 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B SER 3.2 11.5 + - - -
48B ARG* 3.3 4.5 + - - -
49B PHE 3.2 0.2 - - - -
50B TYR* 1.3 81.9 - - - +
52B ASN* 1.3 61.3 + - - +
54B LEU* 3.0 14.2 + - - +
55B LYS* 2.9 21.1 + - - +
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Residues in contact with ASN 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ARG 2.9 8.4 + - - +
49B PHE* 3.0 8.2 + - + +
51B GLY* 1.3 74.6 - - - +
53B GLU* 1.3 59.1 + - + +
55B LYS* 3.4 19.2 + - - +
56B LYS* 2.9 46.5 + - - +
464B ASN 3.4 26.7 + - - +
465B PHE* 3.5 23.9 + - + +
466B GLU* 3.6 23.8 + - - +
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PHE* 2.9 50.4 + - + +
50B TYR* 3.4 13.5 - - + +
51B GLY 3.1 0.2 - - - -
52B ASN* 1.3 76.2 - - + +
54B LEU* 1.3 61.6 + - + +
56B LYS* 2.9 36.0 + - - +
57B GLU* 2.9 31.0 + - - +
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B TYR* 2.9 51.4 + - + +
51B GLY* 3.0 11.9 + - - +
53B GLU* 1.3 78.1 - - + +
55B LYS* 1.3 57.6 + - - +
57B GLU* 3.8 6.8 - - + +
58B LYS* 2.9 31.2 + - - +
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Residues in contact with LYS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLY 2.9 12.1 + - - +
52B ASN* 3.4 21.5 - - - +
54B LEU* 1.3 76.9 - - - +
56B LYS* 1.3 66.2 + - + +
58B LYS* 3.3 16.0 + - + +
59B GLN* 2.9 27.5 + - + +
466B GLU* 3.4 34.6 + - - +
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Residues in contact with LYS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ASN* 2.9 35.8 + - - +
53B GLU* 2.9 34.8 + - - +
55B LYS* 1.3 76.9 - - + +
57B GLU* 1.3 63.3 + - - +
59B GLN* 3.1 11.0 + - + +
60B VAL* 3.0 27.6 + - + +
9P A 6.5 0.2 - - - -
10P T 5.0 14.6 - - - +
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B GLU 2.9 18.0 + - - +
54B LEU* 3.8 8.7 - - + +
56B LYS* 1.3 73.8 - - - +
58B LYS* 1.3 66.3 + - - +
60B VAL* 2.9 12.6 + - - +
61B ASN* 2.9 45.5 + - - +
363B LYS* 2.2 40.9 + - - +
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Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B LEU 2.9 14.0 + - - +
55B LYS* 3.4 17.5 - - + +
57B GLU* 1.3 76.6 - - - +
59B GLN* 1.3 59.0 + - - +
61B ASN* 3.5 10.5 + - - +
62B GLN* 2.9 28.1 + - + +
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Residues in contact with GLN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LYS* 2.9 20.0 + - - +
56B LYS* 3.2 13.5 - - - +
58B LYS* 1.3 78.9 - - - +
60B VAL* 1.3 59.3 + - + +
62B GLN* 3.2 9.3 + - + +
63B ARG* 2.9 39.2 + - + +
8P G 4.3 1.0 + - - -
9P A 2.5 40.2 + - - +
10P T 5.8 1.3 - - - +
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LYS* 3.0 18.6 + - + +
57B GLU* 2.9 16.2 + - - +
59B GLN* 1.3 77.0 - - + +
61B ASN* 1.3 58.9 + - - +
63B ARG* 3.0 14.8 + - + +
64B ILE* 2.9 42.0 + - + +
360B VAL* 4.1 33.2 - - + +
363B LYS* 4.7 11.0 - - + -
364B MET* 5.0 2.9 - - + -
10P T 3.9 21.8 - - - +
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Residues in contact with ASN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B GLU* 2.9 40.0 + - - +
58B LYS* 3.5 12.0 - - - +
60B VAL* 1.3 77.2 - - - +
62B GLN* 1.3 55.5 + - - +
64B ILE* 3.3 10.5 + - - +
65B GLU* 2.9 30.2 + - - +
363B LYS* 3.5 14.4 + - - +
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Residues in contact with GLN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LYS* 2.9 15.7 + - + +
59B GLN* 3.3 13.7 - - + +
60B VAL 3.2 0.2 - - - -
61B ASN* 1.3 74.4 - - - +
63B ARG* 1.3 63.3 + - + +
64B ILE 3.2 0.2 + - - -
65B GLU* 3.2 15.2 + - - +
66B ASN* 2.9 59.6 + - - +
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLN* 2.9 27.0 + - + +
60B VAL* 3.0 15.5 + - + +
62B GLN* 1.3 75.6 - - + +
64B ILE* 1.3 57.7 + - - +
66B ASN* 3.4 11.8 + - - +
67B MET* 2.9 27.4 + - - +
360B VAL* 4.4 12.6 - - - +
364B MET* 4.4 23.4 - - + +
9P A 2.8 18.6 + - - -
10P T 2.6 46.8 + - - -
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B VAL* 2.9 20.1 + - + +
61B ASN* 3.7 13.7 - - - +
63B ARG* 1.3 72.5 - - - +
65B GLU* 1.3 66.8 + - - +
67B MET* 3.0 10.3 + - + +
68B MET* 2.9 29.8 + - + +
363B LYS* 3.9 50.7 - - + +
364B MET* 3.9 24.7 - - + +
367B ALA* 3.7 23.1 - - + -
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Residues in contact with GLU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ASN 2.9 17.4 + - - +
62B GLN* 3.5 16.6 - - - +
64B ILE* 1.3 77.9 - - - +
66B ASN* 1.3 60.2 + - - +
68B MET* 3.2 8.4 + - - +
69B GLN* 2.9 47.4 + - + +
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Residues in contact with ASN 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLN* 2.9 52.2 + - - +
63B ARG* 3.5 12.8 - - - +
65B GLU* 1.3 76.8 - - - +
67B MET* 1.3 58.1 + - - +
69B GLN* 3.3 8.6 + - - +
70B GLN* 2.9 27.6 + - - +
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Residues in contact with MET 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ARG 2.9 14.4 + - - +
64B ILE* 3.0 18.1 + - + +
66B ASN* 1.3 76.5 - - - +
68B MET* 1.3 59.6 + - - +
70B GLN* 3.1 8.3 + - - +
71B LYS* 2.9 26.0 + - - +
364B MET* 3.6 37.5 - - + +
367B ALA* 4.1 11.0 - - + -
368B LEU* 3.6 35.0 - - + -
386B LEU* 3.9 24.9 - - + +
387B PHE* 4.2 19.1 - - + -
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Residues in contact with MET 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ILE* 2.9 27.6 + - + +
65B GLU* 3.2 9.6 + - - +
67B MET* 1.3 77.2 - - - +
69B GLN* 1.3 68.1 + - + +
71B LYS* 3.1 32.2 + - + +
72B ALA* 3.1 13.9 + - - +
367B ALA* 3.5 23.6 - - + +
368B LEU* 4.0 24.9 - - + -
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Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B GLU* 2.9 34.5 + - + +
66B ASN* 3.7 8.1 - - - +
68B MET* 1.3 77.6 - - + +
70B GLN* 1.3 57.9 + - - +
72B ALA* 3.8 8.7 - - - +
73B GLN* 2.6 35.5 + - - +
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Residues in contact with GLN 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ASN 2.9 14.1 + - - +
67B MET* 3.1 11.6 + - - +
69B GLN* 1.3 77.9 - - - +
71B LYS* 1.3 64.9 + - - +
73B GLN* 3.5 12.8 + - - +
74B ILE* 3.8 13.1 + - + +
385B LEU 4.5 13.4 + - - +
386B LEU* 3.8 23.0 + - + +
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B MET 2.9 12.1 + - - +
68B MET* 3.1 30.7 + - + +
70B GLN* 1.3 77.2 - - - +
72B ALA* 1.3 57.4 + - - +
74B ILE* 2.9 38.4 + - + +
368B LEU* 5.0 15.2 + - + +
382B LEU* 4.1 30.9 - - + +
386B LEU* 4.1 8.7 - - + +
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B MET 3.1 9.5 + - - +
69B GLN* 3.8 11.9 - - - +
71B LYS* 1.3 80.3 - - - +
73B GLN* 1.3 68.7 + - - +
74B ILE 3.2 8.0 + - - +
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Residues in contact with GLN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLN* 2.6 33.9 + - - +
70B GLN* 3.5 8.4 + - - +
71B LYS 3.1 2.0 + - - -
72B ALA* 1.3 82.2 - - - +
74B ILE* 1.3 61.9 + - - +
75B THR* 3.9 4.9 + - - +
78B GLN* 3.4 9.4 - - - +
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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