Contacts of the helix formed by residues 55 - 80 (chain A) in PDB entry 5AZS
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 ASN 55 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ALA 2.7 22.4 + - - +
52A LEU 4.8 0.9 - - - +
53A ASP 4.0 0.2 - - - -
54A ASN* 1.3 70.5 - - - +
56A ARG* 1.3 63.5 + - - +
57A SER* 3.9 13.5 + - - -
58A LEU* 3.6 23.3 + - + +
59A ARG* 3.1 24.1 + - - +
152A LEU* 3.6 32.4 - - + +
231A LEU* 4.5 4.9 - - - +
232A LEU* 3.5 35.0 - - - +
233A LEU 3.7 3.2 + - - -
234A GLY* 4.9 1.6 - - - -
359C GLN* 5.5 1.0 + - - -
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASN* 3.5 16.7 + - - +
55A ASN* 1.3 74.8 + - - +
57A SER* 1.3 60.2 + - - +
59A ARG* 3.2 43.9 + - - +
60A GLN* 3.0 34.1 + - - +
234A GLY 4.1 12.5 + - - -
13C PRO* 4.3 12.6 - - - +
351C VAL* 5.9 0.6 - - - +
352C ALA* 3.7 22.4 - - - +
355C GLU* 3.4 38.0 + - - +
356C GLY* 3.9 17.0 - - - +
359C GLN* 3.2 30.8 + - - +
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Residues in contact with SER 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASN* 3.4 14.7 + - - -
56A ARG* 1.3 75.3 - - - +
58A LEU* 1.3 62.5 + - - +
60A GLN* 3.5 15.4 + - - +
61A THR* 3.1 25.3 + - - -
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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
----------------------------------------------------------
51A ALA 5.2 0.2 - - - +
52A LEU* 3.9 21.3 - - + +
55A ASN* 3.6 21.5 - - - +
56A ARG 3.4 0.2 - - - -
57A SER* 1.3 76.8 - - - +
59A ARG* 1.3 60.7 + - - +
61A THR* 3.2 5.9 + - - -
62A LEU* 2.8 43.6 + - + +
145A ALA 3.9 8.1 - - - +
148A ALA* 3.6 29.8 - - + -
149A ARG* 3.7 33.2 - - + +
152A LEU* 3.6 25.1 - - + -
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Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASP 3.9 19.8 + - - -
54A ASN* 4.2 13.3 + - - +
55A ASN 3.1 15.1 + - - +
56A ARG* 3.2 49.0 - - - +
57A SER 3.3 0.6 - - - -
58A LEU* 1.3 76.9 - - - +
60A GLN* 1.3 56.1 + - - +
62A LEU* 3.3 13.1 + - + +
63A LEU* 3.0 45.5 + - + +
352C ALA* 4.0 19.7 - - + +
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ARG* 3.0 21.1 + - - +
57A SER* 3.6 15.2 - - - +
58A LEU 3.3 0.4 - - - -
59A ARG* 1.3 76.2 - - - +
61A THR* 1.3 50.8 + - - +
63A LEU* 3.2 8.0 + - - +
64A ASP* 2.8 41.2 + - - +
349C SER* 3.8 23.9 + - - +
352C ALA* 4.1 7.9 + - + -
353C ALA* 3.4 32.6 - - - +
356C GLY* 5.6 2.4 - - - -
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Residues in contact with THR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A SER* 3.1 13.4 + - - -
58A LEU* 3.2 12.6 + - - -
60A GLN* 1.3 74.9 - - - +
62A LEU* 1.3 64.5 + - - +
64A ASP* 3.4 26.0 + - + +
65A ILE* 3.6 12.8 + - - +
141A SER 5.0 0.9 - - - +
144A ALA* 4.1 13.2 - - + +
145A ALA* 3.8 29.2 - - - +
148A ALA* 4.3 12.1 - - + +
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU 5.8 2.7 - - - +
58A LEU* 2.8 35.2 + - + +
59A ARG* 3.5 15.5 - - + +
60A GLN 3.3 0.4 - - - -
61A THR* 1.3 76.6 - - - +
63A LEU* 1.3 61.9 + - + +
65A ILE* 2.9 32.4 - - + +
66A GLU* 3.7 10.1 + - - +
145A ALA* 4.1 21.1 - - + +
149A ARG* 5.6 13.9 - - - +
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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 ARG* 3.0 31.8 + - + +
60A GLN 3.2 1.5 + - - +
62A LEU* 1.3 78.8 - - + +
64A ASP* 1.3 63.5 + - - +
65A ILE 3.3 0.7 - - - -
66A GLU* 3.3 21.1 + - + +
67A ALA* 3.1 21.7 + - - +
345C ALA* 4.2 10.9 - - - +
348C ASP* 3.3 52.7 - - + +
349C SER* 3.2 21.4 + - - +
352C ALA* 4.9 1.3 - - + -
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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
----------------------------------------------------------
60A GLN* 2.8 25.7 + - - +
61A THR* 3.4 23.4 + - + +
62A LEU 3.3 0.2 - - - -
63A LEU* 1.3 77.4 - - - +
65A ILE* 1.3 58.6 + - + +
67A ALA* 3.4 7.9 + - - +
68A ALA* 3.0 27.1 + - - +
141A SER* 4.5 5.9 + - - -
349C SER* 4.4 7.4 + - - -
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Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR 3.6 11.7 - - - +
62A LEU* 2.9 29.8 + - + +
64A ASP* 1.3 74.7 - - + +
66A GLU* 1.3 75.5 - - - +
68A ALA* 3.7 0.8 - - - -
69A ARG* 2.9 37.3 + - - +
138A TYR* 3.7 7.4 - - + +
141A SER* 3.2 46.2 - - - +
142A GLU* 3.6 32.8 - - + +
145A ALA* 4.1 7.6 - - + -
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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 LEU* 3.7 11.7 + - - +
63A LEU* 3.3 25.9 + - + +
64A ASP 3.3 0.4 - - - -
65A ILE* 1.3 94.7 - - - +
67A ALA* 1.3 64.1 + - - +
69A ARG* 3.6 30.2 + - - +
70A ALA* 3.1 21.8 + - - +
73A ARG* 5.9 0.9 + - - -
341C SER* 5.1 1.0 - - - +
345C ALA* 4.0 16.5 - - + +
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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 3.1 13.1 + - - +
64A ASP* 3.5 10.5 - - - +
66A GLU* 1.3 75.3 - - - +
68A ALA* 1.3 58.1 + - - +
70A ALA* 3.0 9.3 + - - +
71A GLN* 3.0 35.6 + - + +
342C LEU* 4.4 16.6 - - + +
345C ALA* 4.0 13.3 - - + +
346C ARG* 5.1 7.6 - - + +
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Residues in contact with ALA 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 ASP 3.0 14.7 + - - +
65A ILE 3.8 4.7 - - - +
66A GLU 3.4 0.2 - - - -
67A ALA* 1.3 75.2 - - - +
69A ARG* 1.3 59.5 + - - +
71A GLN* 3.5 12.4 + - - +
72A TYR* 3.4 15.6 + - - +
134A ALA 4.1 2.8 - - - +
137A GLN* 4.2 7.5 + - + +
138A TYR* 3.7 25.8 - - - +
141A SER* 3.2 28.0 - - - +
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Residues in contact with ARG 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 ILE* 2.9 26.7 + - - +
66A GLU* 3.7 34.2 + - - +
67A ALA 3.2 0.2 - - - -
68A ALA* 1.3 74.8 - - - +
70A ALA* 1.3 59.4 + - - +
72A TYR* 3.3 10.1 + - + +
73A ARG* 3.0 65.1 + - + +
138A TYR* 3.5 41.1 + - + -
142A GLU* 5.0 2.4 + - - -
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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
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66A GLU 3.1 10.8 + - - +
67A ALA 3.0 9.9 + - - +
69A ARG* 1.3 79.2 - - - +
71A GLN* 1.3 57.8 + - - +
73A ARG* 3.5 14.8 + - - +
74A ILE* 2.9 33.3 + - - +
338C ALA* 3.6 21.7 - - - +
341C SER* 4.4 7.4 - - - -
342C LEU* 3.7 21.5 - - + +
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Residues in contact with GLN 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* 3.0 23.2 + - - +
68A ALA* 3.7 11.1 - - - +
69A ARG 3.2 0.4 - - - -
70A ALA* 1.3 73.8 - - - +
72A TYR* 1.3 60.7 + - - +
74A ILE* 3.3 12.8 + - - +
75A GLN* 2.9 28.9 + - - +
134A ALA* 4.2 4.2 - - + +
137A GLN* 3.9 23.3 - - - +
342C LEU* 3.9 20.6 - - + +
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Residues in contact with TYR 72 (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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68A ALA 3.4 6.0 + - - +
69A ARG* 3.3 15.6 + - + +
71A GLN* 1.3 77.6 - - - +
73A ARG* 1.3 59.2 + - + +
75A GLN* 3.2 0.9 + - - -
76A ARG* 2.7 71.1 + - - +
131A THR* 3.4 39.6 - - + +
132A ASP* 5.4 0.4 - - - -
134A ALA* 3.7 21.4 - - - +
135A LEU* 3.5 44.1 - - + +
138A TYR* 4.8 5.4 - + + -
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Residues in contact with ARG 73 (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 5.9 0.6 + - - -
69A ARG* 3.0 59.8 + - + +
70A ALA* 3.6 10.6 - - - +
71A GLN 3.3 0.2 - - - -
72A TYR* 1.3 79.5 - - + +
74A ILE* 1.3 60.4 + - - +
76A ARG* 4.0 28.2 + - - +
77A ALA* 3.3 21.5 + - - +
333C GLY 4.7 1.7 - - - +
334C GLY 4.4 4.7 - - - +
338C ALA* 3.6 22.8 - - + +
341C SER* 3.9 25.9 + - - -
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Residues in contact with ILE 74 (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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70A ALA 2.9 18.5 + - - +
71A GLN* 3.4 14.1 - - - +
72A TYR 3.2 0.4 - - - -
73A ARG* 1.3 76.9 - - - +
75A GLN* 1.3 63.8 + - + +
77A ALA* 3.5 17.4 - - - +
78A ASP* 4.0 9.0 + - - +
335C ARG* 4.2 18.0 - - + +
338C ALA* 3.7 14.6 - - + -
339C ASN* 3.4 35.9 - - - +
342C LEU* 3.8 22.9 - - + -
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Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN 2.9 15.1 + - - +
72A TYR 3.2 3.3 + - - +
74A ILE* 1.3 78.0 - - + +
76A ARG* 1.3 64.2 + - - +
78A ASP* 3.2 26.1 + - - +
79A ARG 4.0 0.5 + - - -
127A VAL* 4.1 8.5 - - - +
130A LEU* 3.3 51.4 - - - +
131A THR* 3.3 29.0 + - - -
134A ALA* 4.1 11.7 - - + -
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Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 2.7 52.2 + - + +
73A ARG* 4.0 25.9 + - - +
75A GLN* 1.3 73.1 - - - +
77A ALA* 1.3 63.0 + - - +
79A ARG* 3.1 25.5 + - + +
80A VAL* 4.0 4.9 + - - +
131A THR* 3.7 18.9 - - + +
333C GLY 4.8 0.9 - - - +
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG 3.3 10.4 + - - +
74A ILE 3.5 13.2 - - - +
75A GLN 3.2 0.2 - - - -
76A ARG* 1.3 78.5 - - - +
78A ASP* 1.3 56.2 + - - +
80A VAL* 3.1 28.3 - - - +
333C GLY* 3.2 40.7 + - - +
335C ARG* 3.7 25.1 + - + +
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Residues in contact with ASP 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE 4.2 7.4 - - - +
75A GLN* 3.2 24.9 + - - +
76A ARG 3.2 1.2 - - - -
77A ALA* 1.3 76.0 - - - +
79A ARG* 1.3 63.4 + - - +
80A VAL 3.4 6.9 + - - +
119A TYR* 4.2 9.4 - - - -
120A GLU* 5.5 3.3 + - - +
126A ARG* 6.0 0.2 + - - -
127A VAL* 3.7 23.9 - - + +
335C ARG* 3.5 28.0 + - - +
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Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ARG* 3.1 16.0 + - + +
78A ASP* 1.3 76.7 - - - +
80A VAL* 1.3 56.3 + - - +
81A PRO* 4.2 0.2 - - - +
119A TYR* 3.2 22.6 + - - -
122A ASP* 4.3 9.2 + - - +
127A VAL* 3.8 13.9 - - + +
128A LYS* 3.6 47.1 - - - +
131A THR* 3.7 36.3 - - - +
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ARG 4.0 2.0 + - - +
77A ALA* 3.1 30.4 - - - +
78A ASP* 3.5 6.9 - - - +
79A ARG* 1.3 77.0 - - - +
81A PRO* 1.4 80.9 - - + +
82A GLY 4.0 0.9 + - - -
119A TYR* 3.7 3.6 - - - -
332C ASP 4.5 3.6 - - - +
333C GLY* 3.4 26.4 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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