Contacts of the helix formed by residues 64 - 85 (chain A) in PDB entry 1Q4U
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 HIS 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU 2.9 19.0 + - - +
57A ARG 4.2 3.6 - - - -
58A GLN* 3.9 20.6 - - + -
62A LEU 3.2 2.4 + - - -
63A VAL* 1.3 71.8 - - - +
65A GLY* 1.3 69.2 + - - +
66A GLY* 2.8 28.2 + - - -
67A ALA* 2.7 17.9 + - - +
68A TYR* 3.4 7.5 - - - -
371A 4CA 3.6 18.2 - + - -
30B LEU* 3.6 26.0 - - + +
31B ASP* 2.8 41.3 + - - -
36B PHE* 4.8 0.2 - - - -
70B ALA* 3.5 32.8 - - + +
73B GLU* 4.4 2.9 - - + -
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Residues in contact with GLY 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 3.2 + - - -
64A HIS* 1.3 75.0 + - - +
66A GLY* 1.3 60.9 + - - +
68A TYR* 3.0 16.1 + - - -
69A CYS* 3.2 11.0 + - - -
100A PHE* 3.5 27.4 - - - -
371A 4CA 3.7 14.3 - - - +
73B GLU* 3.4 23.4 + - - -
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Residues in contact with GLY 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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64A HIS* 2.8 17.6 + - - -
65A GLY* 1.3 75.4 - - - +
67A ALA* 1.3 57.1 + - - +
69A CYS* 3.6 9.6 - - - +
70A ALA* 2.9 30.5 + - - +
30B LEU* 4.6 1.8 - - - -
66B GLY 4.1 3.8 - - - +
69B CYS 4.6 1.3 - - - -
70B ALA* 3.7 28.5 - - - -
73B GLU* 4.2 3.8 - - - +
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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
----------------------------------------------------------
36A PHE* 3.9 5.5 - - + -
56A LEU* 3.6 43.1 - - + +
63A VAL* 3.9 7.9 - - + -
64A HIS* 2.7 24.4 + - + +
66A GLY* 1.3 69.6 - - - +
68A TYR* 1.3 64.8 + - - +
70A ALA* 3.3 6.0 + - - +
71A LEU* 3.1 24.6 + - - +
30B LEU* 4.2 7.5 - - + +
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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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63A VAL* 3.5 33.8 + - + +
64A HIS 3.4 11.0 - - - -
65A GLY* 3.0 9.5 + - - +
67A ALA* 1.3 78.4 - - - +
69A CYS* 1.3 64.1 + - - +
71A LEU* 3.3 2.9 + - - +
72A ALA* 3.0 26.2 + - - +
98A THR* 4.4 8.3 - - + -
100A PHE* 3.7 24.7 - + + -
102A ARG 4.0 3.5 + - - -
103A PRO* 3.8 5.5 - - - +
104A VAL* 3.1 47.7 + - + +
109A VAL* 4.1 20.2 - - + -
129A LEU* 3.8 25.8 - - + +
137A CYS* 4.3 12.1 - - + -
138A ALA* 4.0 15.5 - - + -
371A 4CA 5.0 5.3 + - - -
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Residues in contact with CYS 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 GLY 3.2 17.4 + - - -
66A GLY* 3.6 4.9 - - - +
67A ALA 3.3 0.2 - - - -
68A TYR* 1.3 79.7 - - - +
70A ALA* 1.4 56.5 + - - +
72A ALA* 3.5 1.1 + - - +
73A GLU* 2.9 23.8 + - - +
96A ASN* 2.9 15.8 + - - +
98A THR* 3.7 33.2 + - - -
100A PHE* 4.0 4.9 - - - -
66B GLY* 4.6 0.4 - - - -
69B CYS* 3.5 38.1 - - + -
96B ASN* 3.9 19.1 - - - -
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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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30A LEU* 4.7 9.6 - - + -
36A PHE* 3.7 14.3 - - + -
66A GLY 2.9 17.9 + - - +
67A ALA* 3.8 5.6 - - - +
68A TYR 3.2 0.4 - - - -
69A CYS* 1.4 75.4 - - - +
71A LEU* 1.3 59.7 + - - +
73A GLU* 4.1 0.4 - - - -
74A MET* 2.8 28.1 + - - +
64B HIS* 3.4 18.4 - - + +
66B GLY* 3.6 25.1 - - - -
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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
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36A PHE* 3.5 36.7 - - + -
48A ALA* 4.1 24.0 - - + -
49A SER* 4.6 5.4 - - - +
50A VAL* 4.0 23.3 - - + -
67A ALA 3.1 16.8 + - - +
68A TYR* 3.8 3.1 - - - +
70A ALA* 1.3 73.0 - - - +
72A ALA* 1.3 62.4 + - - +
74A MET* 3.9 3.7 - - + -
75A LEU* 2.9 33.1 + - - +
109A VAL* 4.2 16.4 - - + +
111A ALA* 3.9 24.7 - - + +
129A LEU* 4.0 11.7 - - + -
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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 TYR 3.0 17.5 + - - +
69A CYS 3.7 3.8 - - - +
71A LEU* 1.3 77.0 - - - +
73A GLU* 1.3 63.9 + - - +
75A LEU* 3.9 2.0 - - - +
76A ALA* 3.0 28.1 + - - +
127A VAL* 4.0 25.0 - - + +
129A LEU* 4.6 2.6 - - + +
140A SER* 3.5 35.2 - - - +
142A MET* 4.0 3.7 - - + +
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Residues in contact with GLU 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 CYS 2.9 17.2 + - - +
70A ALA* 3.4 9.0 - - - +
72A ALA* 1.3 75.8 - - - +
74A MET* 1.3 66.8 + - - +
76A ALA* 4.4 0.2 - - - +
77A THR* 2.7 31.6 + - - +
93A GLY* 4.0 9.7 + - - -
96A ASN* 2.9 30.4 + - - +
142A MET* 3.4 18.0 - - - +
370A 4CA 3.6 36.5 - - + +
64B HIS* 4.4 1.6 - - + -
65B GLY* 3.7 17.1 - - - -
66B GLY 4.2 8.1 - - - +
100B PHE* 3.6 15.4 - - - -
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Residues in contact with MET 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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15A LEU* 4.1 18.4 - - + -
31A ASP* 3.2 28.3 - - + +
36A PHE* 3.7 34.5 - - + -
38A ILE* 3.8 35.0 - - + -
48A ALA* 4.9 2.2 - - + -
70A ALA 2.8 19.1 + - - +
71A LEU* 4.0 10.1 - - + +
73A GLU* 1.3 73.8 - - - +
75A LEU* 1.3 61.8 + - - +
78A GLU* 2.9 37.4 + - - +
370A 4CA 3.5 32.8 - - + +
64B HIS* 4.3 0.2 - - - -
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Residues in contact with LEU 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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38A ILE* 4.0 12.6 - - + -
41A MET* 4.2 2.2 - - + +
46A ALA* 3.5 42.6 - - + +
47A THR* 3.9 15.9 - - - +
48A ALA* 3.9 13.9 - - + +
71A LEU 2.9 18.5 + - - +
72A ALA* 4.0 3.4 - - - +
74A MET* 1.3 82.9 - - - +
76A ALA* 1.4 58.0 + - - +
78A GLU* 3.9 0.7 - - - +
79A ALA* 2.9 31.7 + - - +
111A ALA* 3.8 30.3 - - + +
112A GLU 4.5 0.2 - - - -
113A ALA* 3.7 19.5 - - + +
127A VAL* 4.7 2.7 - - + -
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Residues in contact with ALA 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 3.0 16.8 + - - +
73A GLU 4.4 0.2 - - - +
75A LEU* 1.4 74.2 - - - +
77A THR* 1.3 58.2 + - - +
79A ALA* 3.5 4.1 + - - +
80A THR* 2.7 33.3 + - - -
113A ALA* 4.8 2.0 - - - +
125A TRP* 3.6 34.5 + - + -
127A VAL* 4.6 3.8 - - + -
142A MET* 3.7 23.1 - - + -
144A ILE* 4.1 5.8 - - + -
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Residues in contact with THR 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 GLU* 2.7 29.3 + - - +
74A MET 4.0 1.1 - - - -
76A ALA* 1.3 75.0 - - - +
78A GLU* 1.3 60.5 + - - +
80A THR* 3.0 7.1 + - - -
81A VAL* 2.8 33.9 + - + +
91A ALA 3.4 30.5 - - - +
92A VAL* 4.1 6.3 - - - +
93A GLY 4.1 5.9 + - - +
144A ILE* 3.5 19.6 - - + +
370A 4CA 3.7 27.9 - - + +
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Residues in contact with GLU 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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15A LEU* 3.9 10.5 - - + -
16A PRO* 3.4 26.9 - - + +
38A ILE* 4.4 3.4 - - + -
41A MET* 4.3 0.4 - - - -
74A MET* 2.9 26.4 + - - +
75A LEU 4.2 1.3 - - - +
77A THR* 1.3 78.3 - - - +
79A ALA* 1.3 57.6 + - - +
81A VAL* 3.2 17.3 + - - +
82A ALA* 2.9 25.5 + - - +
370A 4CA 2.6 34.9 + - + +
59B ARG* 2.9 32.5 + - - -
60B TRP* 2.8 24.6 + - - -
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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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41A MET* 3.7 15.1 - - + +
42A THR 4.9 4.2 - - - +
43A PRO* 5.3 0.3 - - - +
46A ALA* 4.0 20.2 - - + -
75A LEU 2.9 19.4 + - - +
76A ALA 3.8 2.5 - - - +
77A THR 3.1 0.2 - - - -
78A GLU* 1.3 77.0 - - - +
80A THR* 1.3 61.5 + - - +
82A ALA* 3.7 11.6 + - - +
83A VAL* 4.0 10.6 + - - +
123A TRP* 4.5 0.2 - - - -
125A TRP* 3.6 34.2 - - + -
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Residues in contact with THR 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 ALA 2.7 19.5 + - - -
77A THR 3.0 8.6 + - - -
79A ALA* 1.3 74.9 - - - +
81A VAL* 1.3 65.6 + - - +
83A VAL* 3.1 4.9 + - - +
84A VAL* 3.0 26.0 + - + +
91A ALA* 3.7 21.3 - - + -
123A TRP* 3.7 34.1 - - + -
125A TRP* 3.0 17.7 + - - -
144A ILE* 3.9 12.6 - - + +
146A VAL* 4.0 11.7 - - + -
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Residues in contact with VAL 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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16A PRO* 5.1 0.4 - - + -
18A VAL* 3.9 26.6 - - + +
77A THR* 2.8 21.0 + - + +
78A GLU* 3.4 27.6 - - - +
80A THR* 1.3 78.1 - - - +
82A ALA* 1.3 61.9 + - - +
84A VAL* 4.2 7.9 - - + -
85A HIS* 3.0 32.4 + - + +
91A ALA* 4.0 11.7 - - + +
372A EDO 3.6 33.2 - - - -
59B ARG* 4.8 0.2 - - - +
60B TRP* 4.1 9.0 - - + -
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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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16A PRO* 3.9 17.9 - - + +
18A VAL* 4.2 9.5 - - - +
41A MET* 3.8 21.8 - - + -
42A THR 6.5 0.7 - - - -
78A GLU 2.9 15.6 + - - +
79A ALA 3.7 8.7 - - - +
80A THR 3.2 0.4 - - - -
81A VAL* 1.3 75.8 - - - +
83A VAL* 1.3 62.9 + - + +
85A HIS 5.0 0.2 + - - -
86A GLU* 4.7 10.2 + - - +
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Residues in contact with VAL 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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42A THR 5.5 0.2 - - - -
43A PRO* 3.7 40.2 - - + -
79A ALA 4.3 6.7 - - - +
80A THR 3.1 3.7 + - - +
82A ALA* 1.3 82.9 - - + +
84A VAL* 1.3 62.3 + - - +
85A HIS 3.5 0.7 - - - -
86A GLU* 3.8 14.3 - - - +
87A LYS* 3.3 40.5 + - + +
123A TRP* 3.7 32.1 - - + -
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Residues in contact with VAL 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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80A THR* 3.0 26.3 + - + +
81A VAL* 4.2 2.5 - - + -
83A VAL* 1.3 75.8 - - + +
85A HIS* 1.3 69.3 + - - +
86A GLU 3.3 2.5 - - - -
87A LYS* 2.8 21.5 + - + +
89A MET* 3.1 45.2 + - + +
90A MET 4.6 0.4 - - - -
91A ALA* 4.1 18.6 - - + -
123A TRP* 3.8 31.4 - - + +
146A VAL* 4.4 12.8 - - + -
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Residues in contact with HIS 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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18A VAL* 3.4 52.0 + - + +
19A ALA* 4.5 7.8 - - + +
81A VAL* 3.0 27.3 + - + +
83A VAL 3.5 0.2 - - - -
84A VAL* 1.3 78.4 - - - +
86A GLU* 1.3 55.8 + - - +
88A GLY* 2.8 22.3 + - - -
89A MET 3.7 11.2 - - - -
149A ARG* 2.9 57.5 + - - -
372A EDO 4.7 8.1 - - - -
60B TRP* 4.2 19.5 - + - -
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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
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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