Contacts of the helix formed by residues 68 - 97 (chain A) in PDB entry 4U7I
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 GLY 68 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A THR* 1.3 76.1 - - - +
69A PRO* 1.3 77.7 - - - +
70A GLY 3.2 3.1 - - - -
71A TRP 3.1 4.2 + - - -
72A GLU* 3.0 37.3 + - - +
75A ARG* 5.2 0.2 - - - +
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Residues in contact with PRO 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY* 1.3 83.8 - - - +
70A GLY* 1.3 56.9 + - - +
72A GLU* 3.4 18.4 - - - +
73A SER* 2.9 31.0 + - - -
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Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 3.7 21.1 - - - +
67A THR 5.4 0.2 + - - -
68A GLY 3.1 1.2 + - - -
69A PRO* 1.3 80.3 - - - +
71A TRP* 1.3 57.0 + - - +
73A SER* 3.3 7.6 + - - -
74A ALA* 2.9 26.5 + - - +
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Residues in contact with TRP 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PRO* 3.9 23.4 - - + +
12A GLU* 3.5 31.2 - - + -
13A ILE* 3.7 27.9 - - + +
16A ILE* 4.2 11.0 - - + -
60A SER 3.8 9.4 - - - -
61A SER* 3.8 31.9 - - - -
65A GLU 4.0 5.3 + - - -
66A HIS* 3.3 65.2 - + + +
67A THR 3.4 15.7 + - - +
68A GLY 3.1 7.1 + - - +
70A GLY* 1.3 72.4 - - - +
72A GLU* 1.3 61.0 + - - +
74A ALA* 3.2 6.3 + - + +
75A ARG* 2.8 38.1 + - - +
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY* 3.0 31.7 + - - +
69A PRO* 3.4 15.9 - - - +
71A TRP* 1.3 76.0 - - - +
73A SER* 1.3 63.4 + - - +
75A ARG* 3.3 28.6 + - - +
76A GLN* 3.1 32.9 + - - +
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Residues in contact with SER 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PRO 2.9 19.0 + - - -
70A GLY* 3.5 7.6 - - - -
72A GLU* 1.3 76.4 - - - +
74A ALA* 1.3 57.2 + - - +
76A GLN* 3.2 9.1 + - - +
77A MET* 3.0 44.7 + - - +
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 4.2 15.0 - - + -
16A ILE* 3.8 30.4 - - + +
61A SER* 5.5 0.2 - - - -
70A GLY 2.9 16.3 + - - +
71A TRP* 3.2 17.5 + - + +
73A SER* 1.3 74.9 - - - +
75A ARG* 1.3 66.8 + - - +
77A MET* 3.1 9.6 + - - +
78A GLN* 3.0 27.4 + - - +
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Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A SER* 2.9 43.5 + - - +
62A LYS* 4.4 16.0 - - - +
66A HIS* 2.9 27.3 + - - +
67A THR* 4.9 2.0 - - - +
68A GLY 4.7 0.4 + - - +
71A TRP* 2.8 22.9 + - - +
72A GLU* 3.3 37.5 - - - +
74A ALA* 1.3 76.2 - - - +
76A GLN* 1.3 60.2 + - + +
78A GLN* 3.0 11.7 + - - +
79A GLN* 2.9 26.4 + - - +
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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
----------------------------------------------------------
72A GLU* 3.1 20.9 + - - +
73A SER* 3.7 9.4 - - - +
74A ALA 3.2 0.2 - - - -
75A ARG* 1.3 77.5 - - + +
77A MET* 1.3 62.6 + - - +
79A GLN* 3.2 17.6 + - - +
80A LYS* 3.1 28.9 + - + +
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Residues in contact with MET 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 6.5 0.9 - - - -
16A ILE* 4.0 12.6 - - + -
17A ARG* 3.9 35.9 - - + +
20A TYR* 3.6 57.5 - - + -
21A LYS* 6.1 0.7 - - - -
73A SER* 3.0 29.0 + - - +
74A ALA* 3.4 11.2 - - - +
76A GLN* 1.3 77.4 - - - +
78A GLN* 1.3 55.7 + - - +
80A LYS* 3.2 4.0 + - - +
81A MET* 2.9 34.8 + - + +
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Residues in contact with GLN 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.5 23.2 - - + +
56A GLY 2.9 29.7 + - - +
57A ILE* 3.6 13.7 + - + +
59A ILE 2.8 27.1 + - - -
61A SER* 2.5 27.5 + - - -
74A ALA 3.0 12.4 + - - +
75A ARG* 3.0 13.9 + - - +
77A MET* 1.3 73.4 - - - +
79A GLN* 1.3 60.9 + - - +
81A MET* 3.7 9.3 - - + +
82A LYS* 2.9 41.3 + - - +
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Residues in contact with GLN 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG 2.9 12.0 + - - +
76A GLN* 3.4 19.8 - - - +
78A GLN* 1.3 78.2 - - - +
80A LYS* 1.3 70.7 + - + +
82A LYS* 3.3 15.2 + - - +
83A GLU* 3.2 27.8 + - - +
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Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 4.1 15.0 - - + +
76A GLN* 3.1 17.4 + - - +
77A MET* 3.2 7.4 + - - +
79A GLN* 1.3 85.7 - - + +
81A MET* 1.3 62.5 + - - +
83A GLU* 3.3 14.2 + - - +
84A THR* 3.1 26.3 + - - -
321B PHE* 3.9 30.6 - - + +
322B ASP* 2.7 42.1 + - - +
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Residues in contact with MET 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.9 28.7 - - + +
19A ALA* 4.1 7.0 - - - +
20A TYR* 3.7 35.2 - - + -
53A LEU* 3.7 33.5 - - + +
56A GLY* 3.9 30.1 - - - -
57A ILE* 3.7 11.2 - - + -
77A MET 2.9 23.2 + - - +
78A GLN* 3.2 11.6 + - - +
80A LYS* 1.3 78.3 - - - +
82A LYS* 1.3 55.3 + - - +
84A THR* 3.4 1.3 + - - +
85A LEU* 2.8 31.4 + - - +
321B PHE* 4.4 5.2 - - + -
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Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 3.6 36.8 - - + -
78A GLN* 2.9 26.3 + - - +
79A GLN* 3.3 16.2 + - - +
81A MET* 1.3 75.5 - - - +
83A GLU* 1.3 63.3 + - - +
85A LEU* 3.4 4.4 + - + +
86A GLN* 3.2 35.7 + - - +
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLN* 3.2 17.8 + - - +
80A LYS* 3.6 16.4 + - - +
82A LYS* 1.3 79.2 - - - +
84A THR* 1.3 61.9 + - - +
86A GLN* 3.3 17.4 + - - +
87A ASN* 3.2 26.2 + - - +
322B ASP* 4.8 10.7 - - - +
325B SER* 3.4 27.5 + - - +
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Residues in contact with THR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 4.2 15.0 - - + -
53A LEU* 4.0 10.8 - - + -
80A LYS 3.1 12.5 + - - -
81A MET 3.9 2.7 - - - -
83A GLU* 1.3 73.9 - - - +
85A LEU* 1.3 61.4 + - - +
87A ASN* 3.1 9.3 + - - +
88A VAL* 2.8 45.7 + - + +
321B PHE* 3.1 45.5 + - + +
324B LEU* 4.2 5.9 - - + +
325B SER* 4.5 4.5 + - - -
328B PHE* 4.9 4.0 - - + -
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 4.0 22.4 - - + -
53A LEU* 3.7 20.4 - - + +
54A LEU* 3.8 22.9 - - + -
57A ILE* 3.7 23.1 - - + -
81A MET 2.8 18.7 + - - +
82A LYS* 3.7 5.8 - - - +
84A THR* 1.3 77.6 - - - +
86A GLN* 1.3 63.7 + - + +
88A VAL* 3.9 1.0 - - - +
89A ARG* 2.9 63.0 + - + +
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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
----------------------------------------------------------
82A LYS* 3.2 23.9 + - - +
83A GLU* 3.5 12.7 - - - +
84A THR 3.2 0.2 - - - -
85A LEU* 1.3 79.5 - - + +
87A ASN* 1.3 66.1 + - - +
89A ARG* 3.8 5.3 - - - +
90A THR* 3.1 27.5 + - - +
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Residues in contact with ASN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 3.2 20.2 + - - +
84A THR* 3.1 8.7 + - - +
86A GLN* 1.3 81.7 - - - +
88A VAL* 1.3 61.6 + - - +
90A THR* 3.4 7.3 + - - -
91A ARG* 3.0 23.6 + - - +
325B SER* 3.4 37.2 + - - +
328B PHE* 3.7 30.4 - - + +
329B GLU* 5.2 6.2 - - - +
332B LYS* 5.7 1.7 + - - -
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 3.8 16.8 - - + -
46A TYR* 3.7 35.4 - - + +
50A ILE* 3.7 25.1 - - + +
53A LEU* 4.4 2.2 - - + -
84A THR* 2.8 38.9 + - + +
85A LEU* 4.0 3.1 - - - +
87A ASN* 1.3 69.2 - - - +
89A ARG* 1.3 61.0 + - - +
91A ARG* 3.3 1.0 + - - +
92A LEU* 2.8 29.3 + - - +
328B PHE* 3.6 25.4 - - + -
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Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 3.8 24.3 - - + +
54A LEU* 3.8 33.8 - - - +
85A LEU* 2.9 47.8 + - + +
86A GLN* 3.8 5.8 - - - +
88A VAL* 1.3 77.5 - - - +
90A THR* 1.3 63.0 + - - +
92A LEU* 3.5 5.9 + - - +
93A GLU* 3.1 25.5 + - - +
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Residues in contact with THR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLN 3.1 15.1 + - - -
87A ASN* 3.6 10.7 - - - -
88A VAL 3.2 0.2 - - - -
89A ARG* 1.3 77.9 - - - +
91A ARG* 1.3 63.5 + - - +
93A GLU* 3.2 7.4 + - - +
94A ILE* 3.0 32.6 + - + +
332B LYS* 4.8 21.1 - - - +
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Residues in contact with ARG 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 2.7 42.8 + - - +
39A LYS* 5.0 2.8 - - - +
46A TYR* 3.6 17.7 - - + +
87A ASN 3.0 17.5 + - - +
88A VAL 3.9 2.0 - - - +
90A THR* 1.3 77.6 - - - +
92A LEU* 1.3 58.4 + - - +
94A ILE* 3.2 22.6 + - - +
95A LEU* 2.9 47.9 + - + +
100A ALA* 3.9 15.0 - - - +
101A THR* 5.0 4.8 + - - +
328B PHE* 3.7 19.3 - - + -
331B LEU* 3.8 42.5 + - - +
332B LYS* 5.3 4.2 - - - +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS* 3.9 41.3 - - + +
46A TYR* 4.4 11.6 - - + -
47A LYS* 3.6 26.2 - - + +
50A ILE* 3.7 21.5 - - + -
88A VAL 2.8 18.8 + - - +
89A ARG* 3.8 5.2 - - - +
91A ARG* 1.3 78.6 - - - +
93A GLU* 1.3 56.7 + - - +
95A LEU* 3.3 2.8 + - - -
96A GLU* 2.9 57.0 + - - +
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ARG 3.1 18.6 + - - +
90A THR* 3.8 5.6 - - - +
92A LEU* 1.3 76.6 - - - +
94A ILE* 1.3 63.6 + - + +
96A GLU* 3.3 11.1 + - - +
97A LYS* 3.0 54.4 + - + +
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Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A THR* 3.0 27.8 + - + +
91A ARG* 3.5 26.5 - - - +
92A LEU 3.2 0.2 - - - -
93A GLU* 1.3 79.2 - - + +
95A LEU* 1.3 60.3 + - - +
97A LYS* 3.4 1.9 + - - -
98A GLY 3.1 4.2 + - - -
99A LEU* 2.9 54.5 + - + +
100A ALA* 3.8 26.0 - - + +
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 3.8 19.3 - - - +
39A LYS* 3.8 27.5 - - + +
42A ALA* 4.3 9.4 - - + -
43A LYS* 3.9 37.4 + - + -
46A TYR* 3.8 19.5 - - + -
91A ARG* 2.9 32.9 + - - +
92A LEU* 3.8 4.0 - - - +
94A ILE* 1.3 73.7 - - - +
96A GLU* 1.3 65.6 + - - +
98A GLY* 3.2 13.2 + - - +
99A LEU 5.0 0.4 - - - +
100A ALA* 3.8 26.5 - - + -
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS* 3.9 24.3 + - + +
47A LYS* 4.5 10.2 - - - +
92A LEU* 2.9 44.7 + - + +
93A GLU* 3.8 12.3 - - + +
95A LEU* 1.3 77.2 - - - +
97A LYS* 1.3 64.7 + - + +
98A GLY 3.2 0.7 + - - -
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLU* 3.0 44.8 + - + +
94A ILE 4.2 0.2 - - - +
96A GLU* 1.3 80.3 - - + +
98A GLY* 1.3 63.2 + - - +
99A LEU* 3.3 31.4 + - + +
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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