Contacts of the helix formed by residues 60 - 83 (chain A) in PDB entry 3D5K
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 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ALA 3.0 20.7 + - - +
57A LEU 5.5 0.9 - - - +
58A GLU 5.2 1.4 - - - +
59A ASN* 1.3 75.7 - - - +
61A ARG* 1.3 63.3 + - - +
62A ASP* 2.9 33.0 + - - +
63A LEU* 3.1 13.6 + - + +
64A ARG* 3.3 19.4 + - - +
157A LEU* 3.4 27.6 - - + +
236A LEU 4.2 4.4 + - - -
237A LEU* 2.9 36.1 + - - +
238A LEU 3.6 5.1 + - - -
239A GLY* 4.3 4.3 - - - -
360B LYS* 6.4 0.2 - - - +
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Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASN* 2.7 36.3 + - - +
60A ASN* 1.3 73.6 + - - +
62A ASP* 1.3 61.8 + - - +
64A ARG* 3.1 34.2 + - - +
65A VAL* 2.9 33.0 + - - +
239A GLY 3.6 17.0 + - - -
13B PRO* 3.8 15.6 - - - +
356B ALA* 3.4 26.4 - - + +
359B GLU* 2.7 42.8 + - + -
360B LYS* 3.9 21.7 - - + +
363B GLN* 3.6 25.8 + - - +
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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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60A ASN* 2.9 11.2 + - - +
61A ARG* 1.3 74.3 - - - +
63A LEU* 1.3 60.3 + - - +
65A VAL* 3.6 12.0 + - - +
66A ALA* 3.1 25.3 + - - +
153A ALA* 5.2 1.7 - - - +
357B GLN* 5.9 1.6 - - - +
360B LYS* 3.4 41.3 + - - +
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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
----------------------------------------------------------
57A LEU* 3.8 36.3 - - + +
60A ASN* 3.1 13.6 + - + +
62A ASP* 1.3 75.2 - - - +
64A ARG* 1.3 65.4 + - - +
66A ALA* 3.7 3.6 - - + +
67A ALA* 3.1 24.4 + - + +
150A GLN* 4.0 11.9 - - + +
153A ALA* 3.6 17.9 - - + +
154A GLN* 3.5 39.5 - - + +
157A LEU* 3.7 30.3 - - + -
450A TRP* 6.4 0.2 - - + -
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Residues in contact with ARG 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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58A GLU 2.7 30.3 + - - -
59A ASN* 4.0 12.5 + - - +
60A ASN 3.3 11.6 + - - +
61A ARG* 3.1 51.5 + - - +
63A LEU* 1.3 77.6 - - - +
65A VAL* 1.3 55.6 + - - +
67A ALA* 3.4 6.0 + - - +
68A LEU* 3.0 45.4 + - + +
356B ALA* 4.5 9.9 - - + -
359B GLU* 4.4 4.4 + - - -
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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 ARG 2.9 22.3 + - - +
62A ASP* 3.9 13.9 - - - +
63A LEU 3.3 0.2 - - - -
64A ARG* 1.3 75.0 - - - +
66A ALA* 1.3 57.4 + - - +
68A LEU* 3.3 8.5 + - - +
69A ASN* 2.8 42.7 + - - +
353B ILE* 4.0 28.3 - - + +
356B ALA* 3.8 20.4 - - + +
357B GLN* 4.3 22.2 - - + +
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Residues in contact with ALA 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 3.1 17.9 + - - +
63A LEU* 3.7 7.6 - - + +
64A ARG 3.3 0.4 - - - -
65A VAL* 1.3 77.0 - - - +
67A ALA* 1.3 58.7 + - - +
69A ASN* 3.6 10.7 + - - +
70A VAL* 3.3 23.6 + - - +
146A THR* 4.8 1.6 - - - +
149A ALA 5.1 0.9 - - - +
150A GLN* 4.0 13.3 - - - +
153A ALA* 3.8 26.9 - - + -
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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 16.6 + - + +
64A ARG* 3.9 5.8 - - - +
66A ALA* 1.3 73.9 - - - +
68A LEU* 1.3 64.6 + - + +
70A VAL* 3.5 15.2 + - - +
71A GLU* 3.7 13.2 + - - +
150A GLN* 4.0 28.2 - - - +
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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 ARG* 3.0 36.8 + - + +
65A VAL* 3.3 4.9 + - - +
67A ALA* 1.3 75.9 - - + +
69A ASN* 1.3 63.4 + - - +
71A GLU* 3.1 23.0 + - - +
72A ALA 3.1 17.2 + - - -
349B ILE* 3.2 22.8 - - + +
352B ASP* 3.7 52.9 - - + +
353B ILE* 3.8 16.6 - - + +
356B ALA* 4.8 1.8 - - + -
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Residues in contact with ASN 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* 2.8 35.0 + - - +
66A ALA* 3.6 10.7 - - - +
67A ALA 3.3 0.2 - - - -
68A LEU* 1.3 78.1 - - - +
70A VAL* 1.3 54.5 - - - +
72A ALA* 3.2 7.3 + - - +
73A PHE* 3.0 44.0 + - + -
146A THR* 3.8 13.7 - - + -
350B GLN* 5.1 1.4 - - - +
353B ILE* 3.6 19.8 - - - +
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Residues in contact with VAL 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 ALA 3.3 17.3 - - - +
67A ALA 3.5 8.1 - - - +
68A LEU 3.2 0.4 - - - -
69A ASN* 1.3 75.7 - - - +
71A GLU* 1.3 57.8 + - + +
73A PHE 3.9 0.2 - - - -
74A ARG* 3.0 29.8 + - - +
143A TYR* 3.6 26.8 - - + +
146A THR* 3.4 31.6 - - + +
147A GLU* 4.1 17.5 - - + +
150A GLN* 3.3 23.8 - - + +
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Residues in contact with GLU 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 3.7 11.6 + - - +
68A LEU* 3.1 27.9 + - - +
70A VAL* 1.3 77.4 - - + +
72A ALA* 1.3 59.2 + - - +
74A ARG* 3.4 37.8 + - - +
75A ALA* 3.0 22.9 + - - +
349B ILE* 3.4 32.5 - - + +
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Residues in contact with ALA 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 LEU 3.1 12.7 + - - +
69A ASN* 3.2 14.8 + - - +
71A GLU* 1.3 77.0 - - - +
73A PHE* 1.3 60.3 + - + +
75A ALA* 3.5 1.1 + - - -
76A GLN* 3.1 22.3 + - - +
346B TYR* 3.4 36.9 - - + -
349B ILE* 3.8 12.5 - - + +
350B GLN* 3.8 16.8 - - - +
353B ILE* 4.7 0.7 - - + -
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Residues in contact with PHE 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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69A ASN* 3.0 38.5 + - + +
70A VAL 4.1 2.2 - - - +
72A ALA* 1.3 78.3 - - + +
74A ARG* 1.3 60.1 + - - +
75A ALA 3.4 0.2 - - - -
76A GLN* 3.4 13.2 + - + +
77A TYR* 3.1 24.8 + - - +
139A ALA 4.3 3.3 - - - +
142A GLN* 3.9 34.5 - - + -
143A TYR* 3.9 16.7 - - - +
146A THR* 3.5 33.4 - - + +
281A GLN* 6.0 2.5 - - - -
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Residues in contact with ARG 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 VAL* 3.0 20.3 + - - +
71A GLU* 3.6 41.8 + - - +
73A PHE* 1.3 74.5 - - - +
75A ALA* 1.3 63.0 + - - +
76A GLN 3.1 0.2 - - - -
77A TYR* 3.1 10.6 + - + +
78A ARG* 3.0 64.7 + - + +
143A TYR* 3.6 41.1 + - + -
349B ILE* 5.9 0.8 - - - +
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Residues in contact with ALA 75 (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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71A GLU 3.0 18.1 + - - +
72A ALA 3.6 6.7 - - - +
74A ARG* 1.3 76.6 - - - +
76A GLN* 1.3 57.4 + - - +
78A ARG* 3.4 13.9 + - - +
79A ILE* 3.1 34.2 + - - +
342B ALA* 3.6 24.2 - - + +
345B ASP* 4.7 4.3 - - + -
346B TYR* 4.0 18.2 - - + +
349B ILE* 4.5 3.4 - - + -
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Residues in contact with GLN 76 (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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72A ALA 3.1 12.8 + - - +
73A PHE* 3.5 20.0 - - + +
75A ALA* 1.3 75.9 - - - +
77A TYR* 1.3 62.3 + - - +
79A ILE* 3.7 25.2 + - - +
80A GLN* 3.5 37.0 + - - +
139A ALA* 4.2 7.7 - - + +
346B TYR* 3.8 27.8 - - + -
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Residues in contact with TYR 77 (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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73A PHE 3.1 14.0 + - - +
74A ARG* 3.1 20.6 + - + +
76A GLN* 1.3 75.7 - - - +
78A ARG* 1.3 64.5 + - + +
80A GLN* 3.4 2.8 + - - +
81A ARG* 3.0 64.5 + - + +
136A ARG* 3.7 39.6 - - + -
139A ALA* 3.8 20.4 - - - +
140A LEU* 3.7 40.0 - - + +
143A TYR* 4.7 6.3 - + + -
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Residues in contact with ARG 78 (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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74A ARG* 3.0 61.9 + - - +
75A ALA* 3.6 13.4 - - - +
76A GLN 3.4 0.2 - - - -
77A TYR* 1.3 82.8 - - + +
79A ILE* 1.3 64.5 + - - +
81A ARG* 3.4 34.2 + - - +
82A ALA* 3.1 23.9 + - - +
337B ALA 5.0 1.2 - - - +
338B GLY 5.1 3.0 - - - +
342B ALA* 4.0 16.6 - - + +
345B ASP* 4.5 14.3 + - - +
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Residues in contact with ILE 79 (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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75A ALA 3.1 21.7 + - - +
76A GLN* 3.9 28.7 - - - +
77A TYR 3.3 0.2 - - - -
78A ARG* 1.3 76.4 - - - +
80A GLN* 1.3 63.8 + - + +
82A ALA* 3.5 11.8 + - - +
83A ASP* 3.3 21.1 + - - +
339B SER* 4.0 19.5 + - - +
342B ALA* 3.7 15.9 - - + +
343B SER* 3.5 34.1 - - - +
346B TYR* 5.0 5.6 - - + -
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Residues in contact with GLN 80 (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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76A GLN* 3.5 24.7 + - - +
77A TYR 3.4 4.9 + - - +
78A ARG 3.3 0.2 - - - -
79A ILE* 1.3 78.6 - - + +
81A ARG* 1.3 62.5 + - - +
82A ALA 3.2 1.3 - - - -
83A ASP* 3.5 26.6 + - - +
84A LEU* 4.3 3.8 + - - +
132A LEU* 4.5 5.5 - - - +
135A LEU* 2.8 47.9 + - + +
136A ARG* 4.0 17.5 - - - +
138A GLN* 5.7 0.8 + - - -
139A ALA* 3.6 14.7 - - + +
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Residues in contact with ARG 81 (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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77A TYR* 3.0 50.9 + - + +
78A ARG* 3.7 37.8 + - - +
80A GLN* 1.3 76.3 - - - +
82A ALA* 1.3 61.0 + - - +
83A ASP 3.6 0.3 + - - -
84A LEU* 3.6 20.9 + - + +
85A PHE* 3.8 14.6 - - + -
136A ARG* 3.9 28.4 - - + +
337B ALA 5.7 5.5 + - - -
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Residues in contact with ALA 82 (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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78A ARG 3.1 16.7 + - - +
79A ILE 3.6 7.2 - - - +
80A GLN 3.2 0.2 - - - -
81A ARG* 1.3 74.6 - - - +
83A ASP* 1.3 55.8 + - - +
84A LEU 3.1 5.4 - - - -
85A PHE* 3.1 28.6 + - - +
336B THR 3.6 15.4 - - - +
337B ALA* 3.5 30.7 - - - +
339B SER* 3.9 16.4 - - - +
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Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ILE* 3.3 21.1 + - - +
80A GLN* 3.6 24.7 - - - +
81A ARG 3.3 1.2 - - - -
82A ALA* 1.3 76.8 - - - +
84A LEU* 1.3 60.3 + - - +
85A PHE 3.3 4.6 - - - +
87A ARG* 4.9 10.4 + - - -
124A TRP* 4.9 5.2 + - - -
125A GLU* 5.8 0.2 - - - +
132A LEU* 3.6 31.8 - - + +
339B SER* 5.1 3.1 + - - -
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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