Contacts of the helix formed by residues 64 - 87 (chain A) in PDB entry 1Y67
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 PRO 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A THR* 4.8 10.5 - - + -
48A PHE* 4.1 15.7 - - + -
62A ARG 3.9 1.3 - - - +
63A VAL* 1.3 89.7 - - + +
65A ALA* 1.3 59.9 + - - +
66A ASP* 4.0 21.5 - - - +
67A LYS* 2.9 35.0 + - + +
68A LYS 3.1 9.0 + - - -
71A LEU* 5.9 0.2 - - + -
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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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63A VAL 3.4 4.4 + - - -
64A PRO* 1.3 70.1 - - - +
66A ASP* 1.3 62.5 + - - +
67A LYS 3.4 0.7 + - - -
68A LYS* 3.5 21.4 + - - +
69A GLY 4.6 1.6 + - - -
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Residues in contact with ASP 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PRO* 4.0 13.4 - - - +
65A ALA* 1.3 79.5 + - - +
67A LYS* 1.3 79.5 + - - +
69A GLY 5.1 1.1 + - - -
70A ALA* 5.3 4.2 + - - +
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Residues in contact with LYS 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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41A LYS 3.9 6.3 + - - -
42A ALA* 2.9 42.7 + - + +
45A GLY* 4.5 11.9 - - - +
46A THR* 4.1 14.1 - - + +
63A VAL* 4.4 2.0 - - + -
64A PRO* 2.9 26.9 + - + +
66A ASP* 1.3 93.3 - - - +
68A LYS* 1.3 65.4 + - - +
69A GLY 3.4 2.2 - - - -
70A ALA* 3.3 8.7 + - + +
71A LEU* 2.9 38.9 + - + +
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Residues in contact with LYS 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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60A LEU* 3.7 22.7 - - + +
61A ASP* 2.7 32.3 + - - +
63A VAL* 3.6 16.8 - - + +
64A PRO 3.1 5.8 + - - +
65A ALA* 3.5 20.4 + - + +
67A LYS* 1.3 77.1 - - - +
69A GLY* 1.3 57.6 + - - +
71A LEU* 3.7 0.9 - - - +
72A ARG* 2.8 40.6 + - + +
161A ILE* 4.3 25.1 - - - +
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Residues in contact with GLY 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 4.6 2.4 + - - -
66A ASP 5.1 1.4 + - - -
67A LYS 3.4 0.2 - - - -
68A LYS* 1.3 78.1 - - - +
70A ALA* 1.3 57.1 + - - +
72A ARG* 3.5 9.9 + - - +
73A ASN* 3.0 40.7 + - - -
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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
----------------------------------------------------------
38A ASN 5.5 0.7 - - - +
42A ALA* 4.1 18.8 - - + -
66A ASP 5.3 3.5 + - - +
67A LYS* 3.3 12.9 + - + +
69A GLY* 1.3 75.2 - - - +
71A LEU* 1.3 59.0 + - - +
73A ASN* 4.8 2.0 - - - +
74A ASN* 2.9 47.0 + - - +
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA* 4.2 7.6 - - - +
42A ALA* 3.7 26.2 - - + +
43A LEU* 3.7 37.0 - - + -
46A THR* 5.9 2.5 - - + -
48A PHE* 5.4 1.8 - - + -
56A LEU* 4.3 11.4 - - + -
57A ILE* 5.0 0.2 - - - +
60A LEU* 3.8 14.8 - - + +
63A VAL* 3.8 32.8 - - + -
67A LYS* 2.9 25.8 + - + +
68A LYS* 3.9 0.9 - - - +
70A ALA* 1.3 74.3 - - - +
72A ARG* 1.3 63.0 + - - +
75A ALA* 2.8 40.3 + - + +
76A GLY 3.3 0.5 + - - -
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Residues in contact with ARG 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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60A LEU* 3.8 20.1 - - + +
68A LYS* 2.8 30.6 + - + +
69A GLY* 3.5 9.0 - - - +
71A LEU* 1.3 72.5 - - - +
73A ASN* 1.3 69.4 + - - +
76A GLY* 3.2 19.9 + - - -
152A GLN 4.0 3.5 - - - +
153A ASP* 2.7 42.2 + - - +
157A MET* 3.4 9.9 - - - +
161A ILE* 3.2 40.7 + - + +
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Residues in contact with ASN 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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35A TYR* 4.2 0.9 - - - -
69A GLY* 3.0 24.7 + - - +
70A ALA* 4.0 3.7 - - - +
72A ARG* 1.3 88.9 + - - +
74A ASN* 1.3 66.1 + - - +
77A GLY* 2.9 20.3 + - - -
151A ASN* 5.2 2.6 + - - +
152A GLN* 3.3 15.6 + - - +
153A ASP* 4.9 2.6 - - - +
130B PHE* 3.6 56.1 - - + +
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Residues in contact with ASN 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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35A TYR* 3.5 30.9 - - - +
38A ASN* 3.3 35.3 + - - +
39A ALA* 3.6 23.6 - - - +
70A ALA* 2.9 35.9 + - - +
73A ASN* 1.3 79.7 - - - +
75A ALA* 1.3 62.1 + - - +
76A GLY 3.2 1.1 - - - -
77A GLY* 3.6 0.7 - - - -
78A HIS* 2.9 29.3 + - - +
130B PHE* 4.7 4.2 - - - -
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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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3A TYR* 4.5 2.9 - - + +
39A ALA* 4.0 8.2 - - + +
53A VAL* 3.4 17.1 - - + +
56A LEU* 3.7 29.6 - - + -
57A ILE* 3.8 13.7 - - + -
60A LEU* 5.4 0.7 - - + -
71A LEU* 2.8 28.3 + - + +
74A ASN* 1.3 72.0 - - - +
76A GLY* 1.3 58.6 + - - +
78A HIS* 3.3 1.6 + - - +
79A ALA* 2.9 27.5 + - - +
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Residues in contact with GLY 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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57A ILE* 3.9 6.3 - - - +
71A LEU 3.3 0.6 + - - -
72A ARG 3.2 21.6 + - - -
75A ALA* 1.3 79.2 - - - +
77A GLY* 1.3 54.9 + - - +
79A ALA* 3.4 2.1 + - - +
80A ASN* 2.9 36.9 + - - +
152A GLN 3.5 16.2 - - - -
157A MET* 3.7 11.7 - - - -
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Residues in contact with GLY 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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35A TYR* 3.8 14.5 - - - -
73A ASN 2.9 19.9 + - - -
74A ASN 3.3 3.3 + - - -
75A ALA 3.3 0.4 - - - -
76A GLY* 1.3 75.3 - - - +
78A HIS* 1.3 59.5 + - - +
81A HIS* 2.7 33.2 + - - +
152A GLN* 3.5 23.8 - - - +
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Residues in contact with HIS 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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3A TYR* 3.5 40.7 - + + +
4A THR 3.7 21.0 + - - -
6A PRO* 4.3 4.0 - - + -
32A HIS* 3.0 31.5 + - - +
35A TYR* 3.9 3.4 - - + +
36A VAL* 3.6 17.1 - - + +
53A VAL* 3.7 24.3 - - + +
74A ASN 2.9 17.2 + - - +
75A ALA* 3.3 5.8 + - - +
77A GLY* 1.3 72.4 - - - +
79A ALA* 1.3 57.3 + - - +
82A SER* 2.8 54.5 + - - -
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Residues in contact with ALA 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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53A VAL* 4.0 24.6 - - + +
54A GLU* 5.0 3.6 - - + +
57A ILE* 4.0 27.1 - - + -
75A ALA 2.9 17.0 + - - +
76A GLY 3.7 3.4 - - - +
78A HIS* 1.3 76.1 - - - +
80A ASN* 1.3 64.7 + - - +
82A SER* 3.8 2.9 - - - -
83A MET* 3.2 23.7 + - - +
154A ASN* 4.8 3.9 + - - +
156A LEU* 6.2 0.2 - - + -
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Residues in contact with ASN 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 GLY 2.9 17.1 + - - +
77A GLY 3.9 0.9 - - - +
79A ALA* 1.3 76.6 - - - +
81A HIS* 1.3 57.4 + - - +
83A MET* 3.4 5.5 + - - +
84A PHE* 2.9 27.0 + - - +
134A TRP* 3.5 32.1 - - + +
136A TRP* 3.4 14.6 - - + -
152A GLN* 3.1 46.6 + - - +
153A ASP 3.5 6.9 + - - -
154A ASN* 2.8 36.1 + - - +
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Residues in contact with HIS 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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27A HIS* 3.0 27.3 + + - -
31A HIS* 5.1 0.2 - - - +
32A HIS* 3.4 28.3 - + + +
35A TYR* 3.3 29.2 - + - -
77A GLY 2.7 25.9 + - - +
80A ASN* 1.3 74.2 - - - +
82A SER* 1.3 66.7 + - - +
84A PHE* 3.4 5.2 - + - +
85A TRP* 3.0 42.1 + + - +
134A TRP* 3.8 13.4 - + - -
152A GLN* 3.6 13.2 - - - -
173A ASP* 3.4 2.6 + - - -
177A HIS* 4.1 0.4 + - - -
229A FE 2.2 28.3 - - - -
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Residues in contact with SER 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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6A PRO* 4.0 9.6 - - - +
32A HIS* 3.5 9.3 - - - -
53A VAL* 5.6 3.6 - - - -
78A HIS* 2.8 46.3 + - - -
79A ALA* 3.8 6.1 - - - -
81A HIS* 1.3 77.8 - - - +
83A MET* 1.3 60.7 + - - +
85A TRP* 3.8 6.7 + - - +
86A GLN* 3.4 29.6 + - - +
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Residues in contact with MET 83 (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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79A ALA 3.2 15.5 + - - +
80A ASN* 3.7 3.8 - - - +
82A SER* 1.3 77.3 - - - +
84A PHE* 1.3 65.9 + - - +
86A GLN* 3.0 14.3 + - - +
87A ILE* 3.1 17.5 + - + +
136A TRP* 3.9 25.1 - - - -
154A ASN* 5.5 2.5 - - - +
168A PRO* 3.5 24.2 - - + +
169A ILE* 3.2 38.4 - - - +
170A LEU* 3.5 8.1 - - - +
171A GLY* 4.9 2.7 - - - -
206A ARG* 3.6 37.7 - - - +
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Residues in contact with PHE 84 (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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19A ILE* 4.8 5.8 - - + -
24A MET* 6.0 0.7 - - - -
27A HIS* 3.8 26.7 - + - -
80A ASN 2.9 17.0 + - - +
81A HIS* 3.4 7.6 - + - +
83A MET* 1.3 76.8 - - - +
85A TRP* 1.3 85.5 + + - +
86A GLN 3.2 0.5 + - - -
87A ILE* 3.3 24.1 + - + +
88A MET* 3.5 32.7 + - + +
134A TRP* 3.8 20.4 - + + -
171A GLY 3.6 15.9 - - - -
172A VAL* 4.0 0.2 - - - -
173A ASP* 3.7 16.8 - - + -
178A ALA* 5.3 0.4 - - + -
190A TYR* 3.7 19.7 - - - -
194A PHE* 3.8 24.7 - + - -
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Residues in contact with TRP 85 (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 PRO* 4.3 8.5 - - + -
7A GLN 5.7 1.1 - - - +
8A LEU* 3.3 32.8 - - + -
9A PRO* 3.8 10.0 - - + +
10A TYR* 2.8 32.2 + - - +
24A MET* 3.8 24.7 - - + -
27A HIS* 3.5 36.8 - + + -
28A HIS* 3.7 28.9 - + + -
32A HIS* 2.9 28.6 + + - -
81A HIS* 3.0 36.8 + + + -
82A SER* 4.2 7.0 - - - +
84A PHE* 1.3 93.9 - + - +
86A GLN* 1.3 63.4 + - + +
88A MET* 3.5 13.8 + - + +
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Residues in contact with GLN 86 (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 PRO* 6.2 1.8 - - - +
9A PRO* 4.4 15.7 - - + +
82A SER* 3.4 17.4 - - - +
83A MET* 3.0 8.1 + - - +
85A TRP* 1.3 80.3 - - + +
87A ILE* 1.3 62.1 + - - +
88A MET 3.3 6.6 + - - +
199A ASN* 4.3 4.5 + - - +
202A GLU* 3.3 25.9 - - - +
206A ARG* 2.8 28.7 + - - +
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Residues in contact with ILE 87 (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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83A MET* 3.1 24.5 + - + +
84A PHE* 3.4 17.7 - - + +
86A GLN* 1.3 76.2 - - - +
88A MET* 1.3 63.6 + - + +
169A ILE 3.8 21.5 - - - +
170A LEU* 3.7 18.8 - - + -
171A GLY 3.6 27.4 - - - +
194A PHE* 4.0 5.2 - - + -
198A VAL* 3.5 7.6 - - - +
199A ASN* 2.7 28.4 + - - -
202A GLU* 3.9 11.0 - - + -
203A VAL* 4.2 7.0 - - + -
206A ARG* 3.9 22.9 - - - +
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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