Contacts of the helix formed by residues 45 - 71 (chain A) in PDB entry 2X6B
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 45 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A THR 3.9 0.2 + - - -
44A VAL* 1.3 75.9 - - - +
46A TRP* 1.3 67.3 + - - +
47A PRO* 3.2 11.7 - - - -
48A VAL* 3.0 38.5 + - - +
49A PHE* 3.2 8.8 + - - +
134A ARG* 4.2 0.2 - - - +
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Residues in contact with TRP 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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44A VAL 3.6 0.8 + - - -
45A SER* 1.3 70.9 - - - +
47A PRO* 1.3 69.3 - - + +
49A PHE* 3.6 17.6 + + - +
50A ILE* 3.4 34.9 + - + +
131A ILE* 4.6 7.6 - - + -
134A ARG* 3.4 65.0 - - + +
135A PHE* 3.5 35.7 - + - -
137A ARG* 5.1 1.9 - - - +
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Residues in contact with PRO 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A SER* 3.3 14.1 - - - -
46A TRP* 1.3 91.1 - - + +
48A VAL* 1.3 63.3 + - + +
49A PHE 3.0 2.1 + - - -
50A ILE* 3.3 8.9 + - + +
51A THR* 2.9 33.3 + - - +
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 4.0 24.5 - - + -
45A SER* 3.0 28.3 + - - +
47A PRO* 1.3 80.9 - - + +
49A PHE* 1.3 56.1 + - - +
51A THR* 3.3 9.3 - - + -
52A LEU* 2.9 38.3 + - + +
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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
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41A LEU* 3.9 20.9 - - + -
44A VAL* 4.4 5.1 - - + +
45A SER 3.2 5.1 + - - +
46A TRP* 3.6 21.1 - + + +
47A PRO 3.0 0.6 - - - -
48A VAL* 1.3 74.6 - - - +
50A ILE* 1.3 71.1 + - + +
51A THR 2.8 5.0 + - - -
52A LEU* 3.0 6.8 + - + +
53A ILE* 3.0 44.4 + - + +
130A LEU* 3.9 31.9 - - + -
131A ILE* 3.2 36.3 - - + -
134A ARG* 3.2 49.6 - - - +
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Residues in contact with ILE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TRP* 3.4 20.1 + - + +
47A PRO* 3.3 9.3 + - + +
49A PHE* 1.3 86.6 - - + +
51A THR* 1.3 55.2 + - - +
53A ILE* 4.3 4.2 - - - +
54A THR* 2.7 46.2 + - - +
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Residues in contact with THR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 2.9 16.6 + - - +
48A VAL* 3.3 16.0 - - + +
49A PHE 2.8 1.6 - - - -
50A ILE* 1.3 75.8 - - - +
52A LEU* 1.3 71.5 + - + +
54A THR* 3.6 5.1 - - - +
55A GLY* 2.8 21.7 + - - -
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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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41A LEU* 3.9 27.8 - - + -
44A VAL* 4.9 11.2 - - + -
48A VAL* 2.9 35.2 + - + +
49A PHE* 3.0 8.0 + - + +
51A THR* 1.3 75.2 - - + +
53A ILE* 1.3 60.2 + - + +
55A GLY* 3.0 3.9 + - - -
56A LEU* 2.8 27.5 + - - +
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Residues in contact with ILE 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* 3.0 46.3 + - + +
50A ILE* 4.3 4.0 - - - +
52A LEU* 1.3 74.8 - - + +
54A THR* 1.3 73.0 + - - +
55A GLY 2.7 2.9 + - - -
56A LEU* 2.9 19.8 + - + +
57A TYR* 3.0 15.9 + - + +
127A ALA* 3.8 32.3 - - + -
130A LEU* 6.0 2.5 - - + -
131A ILE* 4.3 4.9 - - + -
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Residues in contact with THR 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 ILE* 2.7 33.3 + - - +
51A THR* 3.6 6.5 - - - +
53A ILE* 1.3 81.4 - - - +
55A GLY* 1.3 59.5 + - - +
57A TYR* 3.6 7.8 - - - +
58A LEU* 3.1 36.5 + - + +
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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 THR 2.8 14.2 + - - -
52A LEU* 3.2 5.2 - - - -
53A ILE 2.7 2.6 + - - -
54A THR* 1.3 76.3 - - - +
56A LEU* 1.3 65.5 + - - -
58A LEU* 2.8 23.4 + - - +
59A VAL* 3.1 16.7 + - - +
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Residues in contact with LEU 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 2.8 15.1 + - - +
53A ILE* 2.9 12.0 + - + +
55A GLY* 1.3 68.9 - - - -
57A TYR* 1.3 66.7 + - - +
59A VAL* 3.0 22.5 + - + +
60A THR* 3.1 33.6 + - + +
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Residues in contact with TYR 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 ILE* 3.0 13.0 + - + +
54A THR* 3.6 14.6 - - - +
56A LEU* 1.3 76.1 - - - +
58A LEU* 1.3 78.0 + - + +
60A THR* 2.7 23.2 + - - -
61A ASN* 3.3 23.8 + - - -
87A PHE* 5.9 0.4 - + - -
91A VAL* 3.6 32.4 + - + +
94A MET* 3.5 24.4 - - + +
95A ALA* 4.1 13.1 - - + +
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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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54A THR* 3.1 31.0 - - + +
55A GLY* 2.8 16.2 + - - +
57A TYR* 1.3 91.1 - - + +
59A VAL* 1.3 57.7 + - + +
62A ALA* 2.9 25.3 + - - +
87A PHE* 3.1 33.0 - - + -
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Residues in contact with VAL 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 3.1 15.2 + - - +
56A LEU* 3.0 17.4 + - + +
58A LEU* 1.3 77.3 - - + +
60A THR* 1.3 58.8 + - + +
62A ALA* 3.2 10.1 + - + +
63A LEU* 2.8 42.9 + - + +
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Residues in contact with THR 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 LEU* 3.1 31.5 + - + +
57A TYR* 2.7 20.1 + - - -
59A VAL* 1.3 75.7 - - + +
61A ASN* 1.3 62.5 + - - +
63A LEU* 2.8 16.0 + - + +
64A PHE* 2.6 52.5 + - - -
94A MET* 3.7 13.4 - - - +
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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 TYR* 3.3 28.9 + - - +
60A THR* 1.3 79.1 + - - +
62A ALA* 1.3 58.7 + - - +
64A PHE 3.9 0.2 - - - -
65A ALA* 2.9 31.4 + - - +
87A PHE* 3.2 23.6 - - + -
90A SER* 3.0 28.3 + - - +
91A VAL* 3.3 32.3 - - - +
94A MET* 3.0 25.2 - - - +
116A GLU* 3.2 7.1 - - - +
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Residues in contact with ALA 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 LEU 2.9 15.9 + - - +
59A VAL* 3.2 16.4 - - + +
61A ASN* 1.3 75.5 - - - +
63A LEU* 1.3 59.5 + - + +
66A LEU* 3.0 28.1 + - - +
83A PHE* 3.4 15.6 - - + -
87A PHE* 3.0 16.5 - - + -
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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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59A VAL* 2.8 31.6 + - + +
60A THR* 2.8 19.1 + - + +
62A ALA* 1.3 76.5 - - + +
64A PHE* 1.3 62.3 + - + +
66A LEU* 3.0 24.2 - - + +
67A ALA* 2.8 24.1 + - - +
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Residues in contact with PHE 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 THR* 2.6 40.2 + - - -
61A ASN* 4.7 0.7 - - - -
63A LEU* 1.3 70.5 - - + +
65A ALA* 1.3 59.5 + - - +
66A LEU 2.8 1.3 - - - -
67A ALA* 2.5 31.2 + - + +
68A TYR* 2.9 27.8 + + + -
90A SER* 3.3 15.7 - - - +
94A MET* 4.7 4.3 - - - -
112A LEU* 4.2 9.9 - - + -
115A LEU* 4.4 15.5 - - + -
116A GLU* 3.4 62.8 - - + +
119A CYS* 4.2 18.8 - - + -
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Residues in contact with ALA 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 22.9 + - - +
64A PHE* 1.3 76.4 - - - +
66A LEU* 1.3 59.9 + - - +
68A TYR* 4.2 1.8 - - - -
69A LEU* 3.3 17.0 + - - +
83A PHE* 3.6 18.8 - - + -
86A ALA* 3.1 31.7 - - + +
87A PHE* 3.2 30.7 - - - +
90A SER* 3.9 1.6 + - - -
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Residues in contact with LEU 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 ALA 3.0 16.2 + - - +
63A LEU* 3.0 29.3 + - + +
64A PHE 2.8 0.6 - - - -
65A ALA* 1.3 80.8 - - - +
67A ALA* 1.3 55.8 + - - +
69A LEU* 4.0 7.6 - - + +
70A ALA* 3.1 24.4 + - - +
83A PHE* 4.4 13.2 - - + -
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Residues in contact with ALA 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 2.8 9.8 + - - +
64A PHE* 2.5 28.8 + - + +
66A LEU* 1.3 69.8 - - - +
68A TYR* 1.3 57.7 + - + +
69A LEU 3.0 5.2 - - - -
70A ALA* 2.8 28.9 + - - +
71A CYS* 3.2 12.7 - - - -
112A LEU* 4.3 20.3 - - + +
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Residues in contact with TYR 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 PHE* 2.9 41.0 + + + +
65A ALA* 4.1 7.9 - - - +
67A ALA* 1.3 71.8 - - + +
69A LEU* 1.3 60.1 + - - +
71A CYS* 2.9 23.0 - - - +
72A GLY 3.0 11.6 - - - +
74A VAL* 4.2 6.7 + - + +
75A ILE* 4.3 19.1 - - + -
86A ALA* 4.6 7.6 - - + -
89A PHE* 3.7 35.0 - + - -
90A SER* 4.9 1.6 - - - -
93A THR* 4.1 2.5 - - + +
109A ALA* 4.0 18.6 - - + -
112A LEU* 3.5 33.8 + - + -
113A VAL* 3.6 23.3 + - + +
116A GLU* 2.7 29.6 + - - +
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Residues in contact with LEU 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 ALA 3.3 18.4 + - - +
66A LEU* 4.2 9.2 - - + +
67A ALA 3.0 0.6 - - - -
68A TYR* 1.3 80.3 - - + +
70A ALA* 1.3 60.8 + - - +
71A CYS 2.7 16.6 - - - +
72A GLY 5.5 1.6 - - - +
73A ASP* 5.6 6.1 - - - +
75A ILE* 6.2 1.8 - - + -
79A ARG 5.3 1.6 - - - +
80A PRO* 5.7 0.2 - - + -
81A GLY* 3.8 31.4 - - - +
82A SER 3.8 7.4 - - - +
83A PHE* 3.4 43.1 - - + +
86A ALA* 3.9 8.3 - - + -
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU 3.1 16.8 + - - +
67A ALA* 2.8 17.2 + - - +
69A LEU* 1.3 77.9 - - - +
71A CYS* 1.3 55.6 + - - +
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Residues in contact with CYS 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 ALA 3.2 17.5 - - - -
68A TYR* 2.9 18.6 - - - +
69A LEU* 2.7 16.1 - - - +
70A ALA* 1.3 77.1 - - - +
72A GLY* 1.3 70.4 + - - +
74A VAL* 3.8 18.8 - - + -
108A LEU* 5.2 17.9 - - + -
109A ALA 6.0 0.2 - - - -
112A LEU* 4.1 16.2 - - - -
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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