Contacts of the helix formed by residues 47 - 71 (chain B) in PDB entry 2YVE
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B TYR* 3.0 13.4 + - - -
45B PHE 3.9 1.6 - - - +
46B PRO* 1.3 80.8 - - - +
48B ARG* 1.3 64.5 + - - +
49B HIS* 3.5 10.7 + - - +
50B ALA* 3.0 25.5 + - - +
51B LEU* 3.0 18.9 + - - +
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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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22B LEU* 2.8 31.7 + - - +
23B GLU* 4.2 7.6 + - - +
25B LEU* 2.9 27.4 + - + +
26B SER* 4.6 7.8 - - - +
27B TYR* 3.4 19.1 + - + +
47B SER* 1.3 74.9 - - - +
49B HIS* 1.3 63.1 + - - +
51B LEU* 3.1 16.8 + - + +
52B LEU* 3.0 51.0 + - + +
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Residues in contact with HIS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B SER* 3.1 8.8 + - - +
48B ARG* 1.3 79.4 - - - +
50B ALA* 1.3 61.6 + - + +
52B LEU* 3.3 7.9 + - - +
53B LEU* 2.9 30.7 + - + +
106B HIS* 3.6 40.6 + + - -
108B ASP* 2.8 28.0 + - + +
109B PHE* 3.5 30.6 - + - -
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Residues in contact with ALA 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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45B PHE* 3.8 9.7 - - + -
46B PRO* 4.2 19.3 - - + -
47B SER* 3.0 29.3 + - - +
49B HIS* 1.3 77.5 - - + +
51B LEU* 1.3 61.5 + - - +
53B LEU* 3.4 11.2 + - + +
54B GLY* 2.9 25.6 + - - -
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Residues in contact with LEU 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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9B ILE* 4.6 1.1 - - + -
10B LEU* 3.8 12.9 - - + +
13B ALA* 4.5 7.9 - - + -
25B LEU* 4.1 23.6 - - + -
26B SER 5.5 6.1 - - - +
27B TYR* 5.4 9.0 - - + +
30B LEU* 3.8 35.2 - - + -
45B PHE* 3.7 33.3 - - + -
47B SER 3.0 11.6 + - - +
48B ARG* 3.1 21.0 + - + +
50B ALA* 1.3 77.2 - - - +
52B LEU* 1.3 63.3 + - + +
54B GLY* 3.1 3.6 + - - -
55B MET* 3.1 29.6 + - - +
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Residues in contact with LEU 52 (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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22B LEU* 3.6 31.2 - - + -
25B LEU* 4.2 9.0 - - + -
48B ARG* 3.0 45.0 + - + +
49B HIS* 3.7 6.7 - - - +
51B LEU* 1.3 76.0 - - + +
53B LEU* 1.3 64.2 + - - +
55B MET* 3.0 27.8 + - - +
56B HIS* 3.1 23.7 + - + +
99B LEU* 4.7 4.9 - - + -
102B ASP* 4.7 9.4 - - - +
109B PHE* 3.8 26.7 - - + -
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Residues in contact with LEU 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 HIS* 2.9 20.5 + - + +
50B ALA* 3.6 9.6 - - + +
51B LEU 3.3 0.2 - - - -
52B LEU* 1.3 76.6 - - - +
54B GLY* 1.3 59.0 + - - +
56B HIS* 3.2 4.4 + - - +
57B GLU* 2.9 49.5 + - - +
108B ASP* 3.4 56.1 - - - +
109B PHE* 3.8 13.1 - - + -
112B ALA* 3.9 15.0 - - + -
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Residues in contact with GLY 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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6B LYS* 5.1 3.4 - - - -
10B LEU* 3.6 21.5 - - - +
45B PHE* 4.5 4.5 - - - -
50B ALA 2.9 15.5 + - - -
51B LEU 3.1 4.2 + - - -
53B LEU* 1.3 76.6 - - - +
55B MET* 1.3 56.8 + - - +
57B GLU* 3.7 13.5 - - - +
58B LEU* 2.9 30.5 + - - +
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Residues in contact with MET 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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10B LEU* 3.7 15.3 - - + -
13B ALA* 3.7 43.7 - - + +
14B ILE* 3.8 25.1 - - + +
17B ILE* 4.2 7.9 - - + -
25B LEU* 3.8 20.9 - - + -
51B LEU* 3.1 18.8 + - - +
52B LEU* 3.0 18.3 + - + +
54B GLY* 1.3 73.9 - - - +
56B HIS* 1.3 65.7 + - - +
58B LEU* 3.3 2.5 + - - +
59B LEU* 3.1 30.7 + - - +
99B LEU* 4.2 22.2 - - + -
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Residues in contact with HIS 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 LEU* 3.1 27.6 + - - +
53B LEU* 3.6 5.6 - - - +
55B MET* 1.3 75.2 - - - +
57B GLU* 1.3 64.8 + - - +
59B LEU* 3.4 2.1 + - - +
60B ALA* 2.9 25.1 + - - +
99B LEU* 3.1 52.4 + - + +
102B ASP* 4.7 4.2 + - + +
103B ALA* 3.7 15.4 + - + -
109B PHE* 3.7 37.6 - + + -
112B ALA* 3.8 14.8 - - + -
113B TRP* 2.9 34.3 + + - +
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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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6B LYS* 5.1 6.4 + - - -
53B LEU* 2.9 40.7 + - + +
54B GLY* 3.7 14.2 - - - +
56B HIS* 1.3 77.7 - - - +
58B LEU* 1.3 57.3 + - - +
60B ALA* 3.4 4.9 + - - +
61B ASP* 2.9 29.8 + - - +
112B ALA* 3.7 23.2 - - + +
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Residues in contact with LEU 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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7B GLU* 4.1 19.3 - - + +
10B LEU* 3.7 33.0 - - + -
11B ARG* 3.7 49.1 - - - +
14B ILE* 4.2 9.0 - - + -
54B GLY 2.9 18.0 + - - +
55B MET* 3.8 5.2 - - - +
56B HIS 3.3 0.2 - - - -
57B GLU* 1.3 77.4 - - - +
59B LEU* 1.3 58.5 + - - +
61B ASP* 3.2 11.8 + - + +
62B ASP* 2.9 34.2 + - - +
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Residues in contact with LEU 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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11B ARG* 4.9 2.2 - - - +
14B ILE* 3.9 29.4 - - + -
55B MET 3.1 14.6 + - - +
58B LEU* 1.3 76.2 - - - +
60B ALA* 1.3 63.9 + - - +
62B ASP* 3.3 19.8 + - + +
63B TRP* 3.1 21.5 + - - +
96B GLU* 3.5 44.6 - - + +
99B LEU* 3.6 35.7 - - + -
113B TRP* 3.7 14.8 - - + -
1002B MBT 4.3 0.5 + - - -
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Residues in contact with ALA 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 HIS 2.9 18.3 + - - +
57B GLU 3.7 3.6 - - - +
59B LEU* 1.3 76.5 - - - +
61B ASP* 1.3 58.5 + - - +
63B TRP* 3.2 5.0 + - - +
64B ASP* 3.0 26.9 + - - +
112B ALA 3.6 22.2 - - - +
113B TRP* 3.7 25.7 - - + -
116B VAL* 3.9 15.8 - - + +
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Residues in contact with ASP 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 18.5 + - - +
58B LEU* 3.2 13.3 + - + +
60B ALA* 1.3 74.9 - - - +
62B ASP* 1.3 67.9 + - - +
64B ASP* 3.2 12.3 + - - +
65B LYS* 2.9 59.9 + - - +
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Residues in contact with ASP 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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11B ARG* 2.7 46.5 + - - -
58B LEU* 2.9 21.3 + - - +
59B LEU* 3.6 19.6 - - + +
61B ASP* 1.3 78.6 - - - +
63B TRP* 1.3 63.7 + - - +
65B LYS* 3.4 12.0 + - - +
66B GLU* 3.1 22.3 + - - +
1002B MBT 4.5 14.1 - - + -
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Residues in contact with TRP 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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153A HIS* 5.5 0.2 - + - -
59B LEU 3.1 4.3 + - - +
60B ALA 3.6 5.8 - - - +
62B ASP* 1.3 76.9 - - - +
64B ASP* 1.3 66.7 + - - +
66B GLU* 3.2 2.8 + - + +
67B LEU* 2.9 47.4 + - + +
84B VAL* 4.5 11.4 - - + -
87B THR* 3.0 28.0 + - + -
88B LEU* 4.7 3.1 - - + -
113B TRP* 4.4 1.1 - + - -
116B VAL* 3.6 35.4 - - + -
117B ASN* 4.3 11.9 - - - -
120B TRP* 5.3 1.1 - - + -
121B ILE* 3.8 29.8 - - + -
1002B MBT 3.4 93.0 - + + +
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Residues in contact with ASP 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 ALA 3.0 13.2 + - - +
61B ASP* 3.2 18.1 + - - +
63B TRP* 1.3 76.6 - - - +
65B LYS* 1.3 57.9 + - - +
67B LEU* 3.3 5.1 + - - +
68B ARG* 2.9 58.4 + - - +
116B VAL* 3.9 17.9 - - + +
119B GLN* 5.3 2.1 - - - +
120B TRP* 3.0 28.8 + - - -
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Residues in contact with LYS 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 ASP* 2.9 47.0 + - - +
62B ASP* 3.7 11.0 - - - +
64B ASP* 1.3 79.5 - - - +
66B GLU* 1.3 57.1 + - - +
68B ARG* 3.4 9.8 + - - +
69B ASP* 2.9 29.9 + - - +
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Residues in contact with GLU 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 ASP 3.1 14.0 + - - +
63B TRP* 3.7 7.0 - - - +
65B LYS* 1.3 75.2 - - - +
67B LEU* 1.3 63.6 + - - +
69B ASP* 3.1 11.5 + - - +
70B ILE* 3.1 39.6 + - + +
87B THR* 3.7 23.4 - - + +
1002B MBT 3.4 46.9 - - + +
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Residues in contact with LEU 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 TRP* 2.9 50.4 + - + +
64B ASP 3.6 3.6 - - - +
66B GLU* 1.3 76.9 - - - +
68B ARG* 1.3 59.8 + - - +
70B ILE* 3.4 4.1 + - - +
71B THR* 2.7 33.6 + - - -
83B ALA* 3.8 5.6 - - + +
84B VAL* 3.7 40.4 - - + +
87B THR* 3.8 16.4 - - + +
116B VAL* 4.2 1.1 - - + -
120B TRP* 3.5 47.1 - - + +
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Residues in contact with ARG 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 ASP* 2.9 41.3 + - - +
65B LYS* 3.8 8.3 - - - +
67B LEU* 1.3 76.2 - - - +
69B ASP* 1.3 61.8 + - - +
70B ILE 3.5 0.2 + - - -
71B THR* 3.9 10.9 + - - +
120B TRP* 3.9 19.6 - - + -
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Residues in contact with ASP 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 LYS 2.9 17.7 + - - +
66B GLU* 3.1 14.0 + - - +
68B ARG* 1.3 79.5 - - - +
70B ILE* 1.3 67.9 + - + +
71B THR 5.0 0.5 - - - +
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Residues in contact with ILE 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 GLU* 3.1 32.0 + - - +
67B LEU* 3.8 4.7 - - - +
69B ASP* 1.3 89.9 - - - +
71B THR* 1.3 67.1 + - - +
72B ARG* 3.3 17.5 + - - -
83B ALA* 3.7 35.0 - - + +
86B VAL* 3.9 21.3 - - + -
87B THR* 3.8 14.8 - - + -
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Residues in contact with THR 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 LEU 2.7 21.5 + - - -
68B ARG* 3.9 9.6 + - - +
69B ASP 3.6 1.7 - - - +
70B ILE* 1.3 76.8 - - - +
72B ARG* 1.3 64.6 + - - +
73B ASP 3.7 28.3 - - - +
74B PRO* 3.8 16.7 - - + +
79B GLU 4.0 17.5 - - - +
80B ARG* 4.2 6.5 - - + -
83B ALA* 3.1 19.9 - - - +
120B TRP* 3.3 14.4 - - + -
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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
------------------------------------------------------------
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