Contacts of the helix formed by residues 46 - 71 (chain A) in PDB entry 6JOD
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 ALA 46 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A HIS* 2.9 10.2 + - - +
45A ASP* 1.3 78.2 - - + +
47A ILE* 1.3 65.2 + - + +
48A PRO* 3.5 0.4 - - - -
49A ILE* 3.5 7.7 + - - +
50A LEU* 3.2 36.4 + - + +
302A PHE* 5.6 5.2 - - + -
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Residues in contact with ILE 47 (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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43A HIS* 3.5 22.0 + - + +
44A LEU* 3.7 30.3 - - + +
46A ALA* 1.3 77.0 - - - +
48A PRO* 1.3 70.5 - - + +
50A LEU* 3.3 8.1 + - - +
51A TYR* 3.0 47.4 + - + -
104A TYR* 3.6 29.4 - - + -
301A PRO* 3.5 26.7 - - + -
302A PHE* 4.1 20.9 - - + +
305A LEU* 6.2 0.2 - - - -
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Residues in contact with PRO 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU 3.2 18.2 - - - +
45A ASP 3.8 9.6 - - - +
46A ALA 3.6 1.6 - - - -
47A ILE* 1.3 94.1 - - + +
49A ILE* 1.3 68.3 + - + +
51A TYR* 3.1 4.4 + - + +
52A TYR* 2.9 23.9 + - + -
101A ALA* 3.2 27.6 - - + +
104A TYR* 4.5 5.2 - - + +
105A SER* 3.1 33.2 - - - +
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Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASP 4.7 10.8 - - - +
46A ALA* 3.5 9.3 + - - +
47A ILE 3.3 0.4 - - - -
48A PRO* 1.3 82.1 - - + +
50A LEU* 1.3 67.3 + - + +
52A TYR* 3.0 11.6 + - + +
53A ILE* 2.9 39.0 + - + +
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Residues in contact with LEU 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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46A ALA* 3.2 24.4 + - + +
47A ILE* 3.3 7.6 + - - +
49A ILE* 1.3 79.7 - - + +
51A TYR* 1.3 63.5 + - - +
53A ILE* 3.1 22.8 + - + +
54A ILE* 3.0 28.4 + - + +
302A PHE* 4.6 21.5 - - + -
305A LEU* 3.6 26.2 - - + -
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Residues in contact with TYR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 3.0 40.2 + - + +
48A PRO 3.3 9.0 - - - +
50A LEU* 1.3 74.8 - - - +
52A TYR* 1.3 58.1 + - - +
54A ILE* 3.5 2.3 + - - +
55A PHE* 2.9 28.6 + - - +
97A LEU* 3.9 31.6 - - + +
100A TRP* 3.5 34.8 - + + -
101A ALA* 3.6 16.8 - - + -
104A TYR* 3.8 20.9 + + - -
301A PRO 3.5 16.7 + - - -
304A ILE* 4.1 16.3 - - - +
305A LEU* 3.5 37.0 - - + -
308A PHE* 4.8 4.0 - + - -
7B PRO* 4.6 1.5 - - + +
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Residues in contact with TYR 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO* 2.9 12.4 + - + +
49A ILE* 3.0 15.2 + - + +
51A TYR* 1.3 73.8 - - - +
53A ILE* 1.3 61.4 + - - +
55A PHE* 3.2 21.4 + + + +
56A VAL* 2.9 31.6 + - - +
98A PRO* 4.1 29.9 + - + +
101A ALA* 3.4 32.5 - - + -
102A THR* 4.6 7.7 + - - -
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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 ILE* 2.9 36.1 + - + +
50A LEU* 3.4 23.1 - - + +
52A TYR* 1.3 76.7 - - + +
54A ILE* 1.3 71.7 + - + +
56A VAL* 3.1 12.9 - - + +
57A ILE* 3.0 43.2 + - + +
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Residues in contact with ILE 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 LEU* 3.0 17.0 + - + +
51A TYR 3.8 3.6 - - - +
53A ILE* 1.3 85.1 - - + +
55A PHE* 1.3 57.2 + - - +
57A ILE* 3.9 9.9 - - + +
58A GLY* 2.9 28.4 + - - -
94A LEU* 4.5 2.1 - - + +
97A LEU* 3.8 15.9 - - + -
305A LEU* 3.6 19.7 - - + -
308A PHE 4.2 14.4 - - - +
309A THR* 3.5 38.4 - - + +
312A CYS* 4.2 11.4 - - + -
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Residues in contact with PHE 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 TYR 2.9 19.4 + - - +
52A TYR* 3.4 23.3 - + - +
53A ILE 3.1 0.2 - - - -
54A ILE* 1.3 76.4 - - - +
56A VAL* 1.3 70.4 + - + +
59A PHE* 2.9 69.8 + + + +
94A LEU* 3.1 27.5 - - - +
95A ALA* 4.3 5.2 - - - -
97A LEU* 3.7 17.9 - - + +
98A PRO* 3.5 29.4 - - + -
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Residues in contact with VAL 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 TYR 2.9 18.0 + - - +
53A ILE* 3.1 16.4 - - + +
55A PHE* 1.3 85.7 - - + +
57A ILE* 1.3 72.4 + - + +
59A PHE* 3.8 2.4 - - + -
60A LEU* 3.0 48.2 + - + +
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Residues in contact with ILE 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 35.1 + - + +
54A ILE* 3.9 9.2 - - + +
56A VAL* 1.3 84.2 - - + +
58A GLY* 1.3 63.8 + - - +
60A LEU* 3.1 5.3 + - - +
61A VAL* 3.0 37.7 + - + +
312A CYS* 3.6 16.8 - - - -
316A PHE* 5.6 4.5 - - + -
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Residues in contact with GLY 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 ILE 2.9 10.5 + - - -
57A ILE* 1.3 77.1 - - - +
59A PHE* 1.3 57.1 + - - +
61A VAL* 4.4 2.5 - - - -
62A ASN* 2.9 42.6 + - - +
94A LEU* 3.5 19.1 - - - -
312A CYS* 3.4 20.0 - - - -
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Residues in contact with PHE 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 PHE* 2.9 52.1 + + + +
56A VAL* 4.0 3.4 - - - +
58A GLY* 1.3 76.7 - - - +
60A LEU* 1.3 62.7 + - + +
63A ILE* 3.1 54.4 - - + +
91A LEU* 3.7 31.4 - - + -
94A LEU* 4.3 4.5 - - + +
95A ALA* 4.1 24.2 - - + -
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Residues in contact with LEU 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 VAL* 3.0 36.1 + - + +
57A ILE* 3.6 5.2 - - - +
59A PHE* 1.3 83.5 - - + +
61A VAL* 1.3 68.4 + - + +
63A ILE* 3.1 11.4 + - + +
64A VAL* 2.9 29.4 + - + +
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Residues in contact with VAL 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 ILE* 3.0 25.6 + - + +
58A GLY* 4.2 4.5 - - - +
60A LEU* 1.3 75.6 - - + +
62A ASN* 1.3 63.7 + - - +
64A VAL* 2.9 20.6 + - - +
65A VAL* 3.0 12.5 + - - +
312A CYS 4.7 6.1 - - - +
315A PRO* 3.5 23.3 - - + -
316A PHE* 3.8 29.6 - - + -
320A PHE* 3.5 27.8 - - + -
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Residues in contact with ASN 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 GLY* 2.9 38.5 + - - +
61A VAL* 1.3 74.4 - - - +
63A ILE* 1.3 62.3 + - - +
65A VAL* 3.2 4.9 + - - +
66A VAL* 2.9 30.5 + - - +
87A ALA* 3.4 19.3 - - - +
90A ASP* 3.3 22.5 - - - +
91A LEU* 3.9 16.4 - - + -
94A LEU* 3.9 7.7 - - - +
311A SER 3.8 12.7 + - - -
312A CYS* 4.2 1.6 + - - +
315A PRO* 3.2 30.4 - - - +
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Residues in contact with ILE 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 PHE* 3.1 49.5 + - + +
60A LEU* 3.1 12.4 + - + +
62A ASN* 1.3 76.9 - - - +
64A VAL* 1.3 69.1 + - + +
66A VAL* 3.8 4.3 - - - +
67A THR* 2.9 42.2 + - + +
91A LEU* 3.7 20.4 - - + +
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Residues in contact with VAL 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 LEU* 2.9 22.9 + - + +
61A VAL* 2.9 10.6 + - - +
63A ILE* 1.3 79.3 - - + +
65A VAL* 1.3 61.1 + - - +
67A THR* 2.5 22.9 + - - +
68A LEU* 3.0 24.5 + - + +
320A PHE* 4.0 21.5 - - + -
325A PHE* 5.0 4.5 - - + -
329A LEU* 5.2 11.0 - - + -
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Residues in contact with VAL 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 VAL 3.0 12.2 + - - +
62A ASN* 3.2 6.0 + - - +
64A VAL* 1.3 75.5 - - - +
66A VAL* 1.3 64.2 + - - +
68A LEU* 3.1 8.2 + - - +
69A PHE* 3.0 23.7 + - + +
83A ILE* 4.2 11.9 - - + +
84A PHE* 5.5 2.2 - - - -
87A ALA* 3.7 22.7 - - + -
315A PRO* 3.6 27.1 - - + -
319A CYS* 3.7 30.6 - - + -
320A PHE* 3.6 20.0 - - + -
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Residues in contact with VAL 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 ASN 2.9 22.3 + - - +
63A ILE* 4.0 4.9 - - - +
65A VAL* 1.3 76.2 - - - +
67A THR* 1.3 58.9 + - + +
69A PHE* 3.9 5.2 - - - +
70A CYS* 2.8 40.5 + - + +
84A PHE* 3.8 21.1 - - + +
87A ALA* 3.7 34.3 - - + +
88A VAL* 4.2 12.8 - - + +
91A LEU* 4.4 16.2 - - + -
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Residues in contact with THR 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 ILE* 2.9 30.3 + - + +
64A VAL* 2.5 27.5 + - - +
66A VAL* 1.3 73.9 - - + +
68A LEU* 1.3 66.6 + - - +
69A PHE 3.0 2.3 + - - -
70A CYS* 3.3 10.9 + - - +
71A CYS 4.0 2.1 + - - -
72A GLN* 3.2 23.2 + - - +
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Residues in contact with LEU 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 VAL* 3.0 21.7 + - + +
65A VAL* 3.5 7.4 - - - +
67A THR* 1.3 84.4 + - - +
69A PHE* 1.3 57.3 + - - +
72A GLN* 3.1 30.5 - - + +
73A LYS 4.0 5.7 - - - +
74A GLY* 5.1 1.4 - - - -
319A CYS* 4.7 14.1 - - - -
320A PHE* 5.1 0.2 - - + -
325A PHE* 3.9 33.4 - - + +
328A LYS* 4.9 30.6 + - + +
329A LEU* 5.7 3.6 - - + +
332A VAL* 3.9 28.5 - - + -
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Residues in contact with PHE 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 VAL* 3.0 17.1 + - + +
66A VAL* 3.9 0.9 - - - +
67A THR 3.0 0.4 - - - -
68A LEU* 1.3 79.5 - - - +
70A CYS* 1.3 65.3 + - - +
71A CYS 3.8 0.2 - - - -
72A GLN 3.5 4.0 - - - +
74A GLY 4.0 11.2 - - - -
75A PRO* 3.3 42.6 - - + +
80A SER* 3.0 54.3 - - - -
81A ILE* 3.6 12.8 - - + -
83A ILE* 5.6 4.7 - - + -
84A PHE* 3.4 45.3 - + + -
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Residues in contact with CYS 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 VAL* 2.8 23.4 + - + +
67A THR* 3.3 5.8 + - - +
69A PHE* 1.3 81.0 - - - +
71A CYS* 1.3 66.3 + - - +
72A GLN 4.7 0.2 - - - +
75A PRO* 4.9 4.5 - - - +
84A PHE* 4.4 18.2 - - + -
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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 THR 4.0 2.4 + - - -
70A CYS* 1.3 83.6 - - - +
72A GLN* 1.3 80.4 + - - +
73A LYS* 3.5 12.5 + - - +
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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
------------------------------------------------------------
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