Contacts of the helix formed by residues 47 - 71 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A TYR* 2.9 14.2 + - - -
45A PHE 3.9 2.3 - - - +
46A PRO* 1.3 81.2 - - - +
48A ARG* 1.3 65.8 + - - +
49A HIS* 3.4 12.9 + - - +
50A ALA* 3.0 32.1 + - - +
51A LEU* 3.1 10.4 + - - +
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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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22A LEU* 3.0 36.2 + - - +
23A GLU* 4.2 7.0 + - - +
25A LEU* 2.8 29.5 + - - +
26A SER* 4.5 8.0 - - - +
27A TYR* 3.4 19.0 + - + +
47A SER* 1.3 73.9 - - - +
49A HIS* 1.3 63.6 + - - +
51A LEU* 3.0 18.3 + - + +
52A LEU* 2.9 49.3 + - + +
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Residues in contact with HIS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 3.5 12.1 - - - +
48A ARG* 1.3 78.8 - - - +
50A ALA* 1.3 60.7 + - + +
52A LEU* 3.3 9.5 + - - +
53A LEU* 2.9 34.3 + - + +
106A HIS* 3.4 42.7 + + - +
108A ASP* 2.7 27.4 + - + +
109A PHE* 3.6 22.6 - + - -
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Residues in contact with ALA 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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45A PHE* 3.6 9.0 - - + -
46A PRO* 4.0 27.8 - - + -
47A SER* 3.0 22.2 + - - +
49A HIS* 1.3 76.6 - - + +
51A LEU* 1.3 60.6 + - - +
53A LEU* 3.4 4.2 + - - -
54A GLY 2.9 23.4 + - - -
2004A GOL 3.0 24.3 + - - +
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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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9A ILE* 4.7 0.7 - - + -
10A LEU* 3.8 20.0 - - + +
13A ALA* 4.4 4.5 - - + -
25A LEU* 4.2 24.5 - - + -
26A SER 5.6 5.6 - - - +
27A TYR* 5.7 7.9 - - + +
30A LEU* 3.8 33.0 - - + -
45A PHE* 3.7 27.7 - - + -
47A SER 3.1 10.8 + - - +
48A ARG* 3.0 20.6 + - + +
50A ALA* 1.3 76.8 - - - +
52A LEU* 1.3 64.7 + - + +
54A GLY* 3.1 3.5 + - - -
55A MET* 3.1 34.4 + - - +
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Residues in contact with LEU 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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22A LEU* 3.7 31.6 - - + -
25A LEU* 4.8 5.6 - - + -
48A ARG* 2.9 48.2 + - + +
49A HIS* 3.7 7.2 - - - +
51A LEU* 1.3 75.0 - - + +
53A LEU* 1.3 64.9 + - - +
55A MET* 3.0 26.1 + - - +
56A HIS* 3.1 23.7 + - + +
99A LEU* 4.4 8.7 - - + -
102A ASP* 4.8 9.2 - - - +
109A PHE* 3.8 27.6 - - + -
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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 HIS* 2.9 22.0 + - + +
50A ALA* 3.7 6.5 - - - +
52A LEU* 1.3 75.6 - - - +
54A GLY* 1.3 65.2 + - - +
56A HIS* 3.2 2.2 + - - +
57A GLU* 2.9 44.5 + - + +
108A ASP* 3.4 49.1 - - + +
109A PHE* 3.7 12.5 - - + -
112A ALA* 4.1 6.5 - - + -
2004A GOL 3.6 31.6 - - - -
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Residues in contact with GLY 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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6A LYS* 6.2 0.4 - - - -
10A LEU* 3.8 21.9 - - - +
45A PHE* 4.6 2.9 - - - -
50A ALA 2.9 15.5 + - - -
51A LEU 3.1 4.2 + - - -
53A LEU* 1.3 77.2 - - - +
55A MET* 1.3 56.0 + - - +
57A GLU* 3.9 9.3 - - - +
58A LEU* 3.0 30.5 + - - +
2004A GOL 3.7 8.7 + - - -
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Residues in contact with MET 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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10A LEU* 3.7 19.7 - - + +
13A ALA* 3.7 22.4 - - + -
14A ILE* 3.7 21.3 - - + -
17A ILE* 3.7 28.0 - - + -
25A LEU* 4.0 7.6 - - + -
51A LEU* 3.2 33.4 - - - +
52A LEU* 3.0 16.9 + - - +
54A GLY* 1.3 74.5 - - - +
56A HIS* 1.3 64.6 + - - +
58A LEU* 3.3 3.1 + - - +
59A LEU* 3.0 31.3 + - - +
99A LEU* 4.3 16.4 - - + -
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Residues in contact with HIS 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 LEU* 3.1 29.1 + - + +
53A LEU* 3.2 6.0 + - - +
55A MET* 1.3 75.5 - - - +
57A GLU* 1.3 58.6 + - - +
59A LEU* 3.8 2.9 - - - +
60A ALA* 2.9 30.5 + - - +
99A LEU* 3.1 52.1 - - + +
102A ASP* 4.8 4.0 + - - -
103A ALA* 3.8 16.4 + - + -
109A PHE* 3.7 36.5 - + + +
112A ALA* 3.8 16.2 - - + -
113A TRP* 3.0 31.4 + - - +
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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 LEU* 2.9 28.2 + - + +
54A GLY* 3.9 6.8 - - - +
56A HIS* 1.3 77.8 - - - +
58A LEU* 1.3 56.6 + - - +
60A ALA* 3.8 3.3 - - - +
61A ASP* 2.9 31.8 + - - +
112A ALA* 3.8 21.8 - - + +
2004A GOL 2.8 51.1 + - - -
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Residues in contact with LEU 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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7A GLU* 4.1 20.4 - - + +
10A LEU* 3.7 31.6 - - + -
11A ARG* 3.6 50.3 - - - +
14A ILE* 4.3 8.7 - - + -
54A GLY 3.0 18.2 + - - +
55A MET* 3.8 4.3 - - - +
56A HIS 3.3 0.2 - - - -
57A GLU* 1.3 77.6 - - - +
59A LEU* 1.3 57.0 + - - +
61A ASP* 3.2 10.3 + - + +
62A ASP* 2.8 35.5 + - - +
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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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11A ARG* 4.8 2.2 - - - +
14A ILE* 4.0 28.5 - - + -
55A MET 3.0 18.8 + - - +
56A HIS* 5.2 0.2 - - - -
58A LEU* 1.3 76.5 - - - +
60A ALA* 1.3 62.1 + - - +
62A ASP* 3.3 18.5 + - + +
63A TRP* 3.2 21.7 + - - +
96A GLU* 3.4 44.0 - - + +
99A LEU* 3.6 34.1 - - + -
113A TRP* 3.8 16.0 - - + -
1001A MBT 4.5 0.7 + - - -
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Residues in contact with ALA 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 HIS 2.9 19.4 + - - +
57A GLU* 3.8 3.6 - - - +
59A LEU* 1.3 75.8 - - - +
61A ASP* 1.3 63.4 + - - +
63A TRP* 3.3 4.3 + - - +
64A ASP* 3.0 22.7 + - - +
112A ALA 3.4 24.7 - - - +
113A TRP* 3.7 27.0 - - + -
116A VAL* 4.1 13.8 - - + +
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Residues in contact with ASP 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 19.6 + - - +
58A LEU* 3.6 10.9 - - + +
60A ALA* 1.3 74.7 - - - +
62A ASP* 1.3 69.1 + - - +
64A ASP* 3.3 8.9 + - - +
65A LYS* 2.9 38.5 + - - +
68A ARG* 4.6 11.5 + - - -
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Residues in contact with ASP 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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11A ARG* 2.7 46.3 + - - -
58A LEU* 2.8 22.3 + - - +
59A LEU* 3.5 19.1 - - + +
60A ALA 3.3 0.2 - - - -
61A ASP* 1.3 81.1 - - - +
63A TRP* 1.3 62.2 + - - +
65A LYS* 3.4 13.4 + - - +
66A GLU* 3.0 23.2 + - - +
1001A MBT 4.4 14.5 - - + -
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Residues in contact with TRP 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 LEU 3.2 4.3 + - - +
60A ALA* 3.7 6.7 - - - +
62A ASP* 1.3 76.9 - - - +
64A ASP* 1.3 64.7 + - - +
66A GLU* 3.2 2.2 + - + +
67A LEU* 2.9 41.7 + - + +
84A VAL* 4.6 4.3 - - + -
87A THR* 3.0 25.5 + - + -
88A LEU* 4.4 6.3 - - + -
113A TRP* 4.3 2.0 - + - -
116A VAL* 3.7 33.0 - - + -
117A ASN* 4.2 11.2 - - - -
120A TRP* 5.5 0.4 - - + -
121A ILE* 3.6 36.3 - - + -
1001A MBT 3.3 97.1 - + + +
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Residues in contact with ASP 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 ALA 3.0 17.0 + - - +
61A ASP* 3.7 12.1 - - - +
63A TRP* 1.3 74.9 - - - +
65A LYS* 1.3 57.7 + - - +
67A LEU* 3.3 1.6 + - - +
68A ARG* 2.9 59.3 + - - +
115A THR* 6.3 0.4 - - - -
116A VAL* 3.8 17.3 - - + +
119A GLN* 3.8 14.5 - - - +
120A TRP* 3.0 26.8 + - - +
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Residues in contact with LYS 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 ASP* 2.9 30.3 + - - +
62A ASP* 3.8 12.4 + - - +
64A ASP* 1.3 76.0 + - - +
66A GLU* 1.3 64.5 + - - +
68A ARG* 3.4 26.6 + - - +
69A ASP* 2.9 45.0 + - - +
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Residues in contact with GLU 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 ASP 3.0 13.5 + - - +
63A TRP* 3.5 8.1 - - + +
65A LYS* 1.3 76.0 - - - +
67A LEU* 1.3 61.5 + - - +
69A ASP* 3.2 10.8 + - - +
70A ILE* 3.2 40.8 + - - +
86A VAL* 5.4 1.4 - - - +
87A THR* 3.5 28.1 - - + +
1001A MBT 3.3 52.4 - - + +
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Residues in contact with LEU 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 TRP* 2.9 49.3 + - + +
64A ASP 3.7 1.3 - - - +
66A GLU* 1.3 73.2 - - - +
68A ARG* 1.3 64.5 + - - +
70A ILE* 3.3 3.7 + - - -
71A THR* 2.7 30.7 + - - -
83A ALA* 4.0 4.9 - - + -
84A VAL* 3.8 31.6 - - + +
87A THR* 3.6 23.1 - - + +
116A VAL* 4.4 0.9 - - + -
120A TRP* 3.5 53.2 - - + +
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Residues in contact with ARG 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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61A ASP* 4.6 8.9 + - - -
64A ASP* 2.9 41.5 + - - +
65A LYS* 3.8 32.8 - - - +
67A LEU* 1.3 76.7 - - - +
69A ASP* 1.3 65.9 + - - +
70A ILE 3.5 0.2 + - - -
71A THR* 3.8 11.5 + - - +
120A TRP* 3.8 19.3 - - + -
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Residues in contact with ASP 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 LYS* 2.9 37.3 + - - +
66A GLU* 3.5 11.1 - - - +
67A LEU 3.2 0.2 - - - -
68A ARG* 1.3 81.9 + - - +
70A ILE* 1.3 64.2 + - + +
71A THR 5.5 0.2 - - - -
72A ARG* 5.5 6.8 + - - -
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Residues in contact with ILE 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 GLU* 3.2 40.4 + - - +
67A LEU* 4.1 4.0 - - - +
69A ASP* 1.3 85.7 - - + +
71A THR* 1.3 61.2 + - - +
72A ARG* 3.7 8.2 + - - +
83A ALA* 3.9 25.6 - - + +
86A VAL* 4.0 20.2 - - + -
87A THR* 3.9 15.7 - - + -
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Residues in contact with THR 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 LEU 2.7 21.7 + - - -
68A ARG 3.8 8.4 + - - +
69A ASP 3.6 2.2 - - - -
70A ILE* 1.3 77.0 - - - +
72A ARG* 1.3 72.9 - - - +
74A PRO* 3.7 33.6 - - + +
79A GLU* 3.8 23.1 - - + +
80A ARG 4.2 0.4 - - - +
83A ALA* 3.0 20.8 - - - +
120A TRP* 3.3 21.6 - - + -
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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
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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