Contacts of the helix formed by residues 56 - 85 (chain D) in PDB entry 6R93
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 SER 56 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ARG* 3.9 14.5 - - - +
79C ILE 3.1 20.2 + - - -
80C ILE* 4.4 12.8 - - - -
81C PRO* 5.1 1.9 - - - +
55D ILE* 1.3 80.7 - - - +
57D SER* 1.3 73.7 + - - +
58D LYS* 3.3 17.4 + - - +
59D ALA 3.4 5.8 + - - -
60D MET* 3.2 19.6 + - - +
19I A 2.8 16.7 + - - -
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Residues in contact with SER 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D SER* 1.3 76.1 + - - +
58D LYS* 1.3 66.4 + - - +
60D MET* 3.2 8.7 + - - +
61D GLY* 2.9 24.8 + - - -
18I G 5.5 0.3 - - - -
19I A 2.8 27.3 + - - -
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Residues in contact with LYS 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PRO* 4.0 21.1 - - + -
104C ALA* 5.9 2.6 - - - +
105C GLN* 4.0 24.2 - - + +
56D SER* 3.3 9.3 + - - +
57D SER* 1.3 87.5 + - - +
59D ALA* 1.3 62.6 + - - +
61D GLY* 3.1 3.8 + - - +
62D ILE* 2.9 28.6 + - + +
100F GLY* 5.2 11.0 + - - +
101F PHE* 5.5 10.7 - - - -
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Residues in contact with ALA 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ILE* 4.2 14.6 - - + +
80C ILE 4.4 1.3 - - - -
81C PRO* 4.2 12.3 - - + +
84C LEU* 3.7 17.9 - - + +
55D ILE* 3.7 25.1 - - + -
56D SER* 3.4 4.0 + - - +
57D SER 3.3 0.8 - - - -
58D LYS* 1.3 79.1 - - - +
60D MET* 1.3 58.1 + - - +
62D ILE* 3.1 14.0 + - - +
63D MET* 2.9 31.2 + - - +
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Residues in contact with MET 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D SER* 5.4 0.2 - - - +
39D SER* 3.3 50.9 - - - +
42D VAL* 3.5 38.6 - - + -
43D TYR* 3.8 14.1 - - + +
55D ILE* 4.0 26.8 - - + +
56D SER 3.2 13.8 + - - +
57D SER* 3.2 11.4 + - - +
59D ALA* 1.3 76.0 - - - +
61D GLY* 1.3 58.0 + - - +
63D MET* 3.2 3.9 + - - +
64D ASN* 2.9 28.4 + - - +
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Residues in contact with GLY 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D SER 2.9 14.8 + - - -
58D LYS* 3.1 5.8 + - - -
60D MET* 1.3 77.7 - - - +
62D ILE* 1.3 55.2 + - - +
64D ASN* 3.3 11.3 + - - +
65D SER* 2.9 28.2 + - - -
100F GLY* 4.8 10.7 + - - -
102F GLY* 5.7 2.3 + - - -
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Residues in contact with ILE 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PRO* 3.7 33.7 - - + -
84C LEU* 3.9 17.5 - - + -
103C ILE* 4.0 30.7 - - + -
104C ALA* 4.2 10.3 - - + +
58D LYS* 2.9 23.0 + - + +
59D ALA* 3.1 10.1 + - - +
61D GLY* 1.3 71.3 - - - +
63D MET* 1.3 65.1 + - - +
65D SER* 3.3 9.1 + - - -
66D PHE* 2.9 27.5 + - + +
99F TYR* 4.4 9.3 - - + +
100F GLY* 3.8 21.8 - - - +
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Residues in contact with MET 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C THR* 3.9 33.0 - - + +
63C ILE* 3.8 37.0 - - + -
64C LEU* 4.8 13.0 - - + -
84C LEU* 4.3 15.9 - - + -
42D VAL* 4.5 25.4 - - + -
55D ILE* 4.8 2.7 - - + -
59D ALA 2.9 19.2 + - - +
60D MET* 3.2 9.4 + - - +
62D ILE* 1.3 78.8 - - - +
64D ASN* 1.3 57.1 + - - +
66D PHE* 3.2 19.1 + - + +
67D VAL* 2.9 35.6 + - + +
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Residues in contact with ASN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D GLU* 5.3 2.7 + - - +
37D SER* 3.9 28.9 + - - +
38D TYR* 3.5 24.3 + - + +
39D SER 5.8 0.2 - - - +
42D VAL* 5.6 0.4 - - - +
60D MET* 2.9 14.9 + - + +
61D GLY* 3.5 12.3 + - - +
62D ILE 3.2 0.2 - - - -
63D MET* 1.3 77.4 - - - +
65D SER* 1.3 63.0 + - - +
67D VAL* 3.3 6.7 + - - +
68D ASN* 2.9 50.8 + - - +
102F GLY* 5.6 2.6 - - - -
103F GLY* 4.9 11.7 - - - +
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Residues in contact with SER 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D GLY 2.9 13.5 + - - -
62D ILE 3.3 8.5 + - - -
64D ASN* 1.3 76.8 - - - +
66D PHE* 1.3 63.3 + - - +
68D ASN* 3.3 3.3 + - - +
69D ASP* 3.0 23.7 + - - +
98F LEU 4.2 0.9 + - - -
99F TYR* 3.0 32.6 - - - -
100F GLY 4.3 9.4 - - - -
102F GLY 5.5 0.9 - - - -
103F GLY* 2.5 36.8 + - - +
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Residues in contact with PHE 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 5.7 2.7 - - + -
59C LEU* 4.2 37.9 - - + -
60C THR* 5.0 2.2 - - + -
63C ILE* 4.9 14.1 - - + -
94C LEU* 5.4 2.9 - - + -
97C LEU* 4.3 8.5 - - + -
98C LEU* 4.1 24.2 - - + -
62D ILE* 2.9 16.0 + - + +
63D MET* 3.4 27.1 - - + +
65D SER* 1.3 76.8 - - - +
67D VAL* 1.3 71.1 + - + +
69D ASP* 3.2 3.1 + - - +
70D ILE* 3.0 56.2 + - + +
99F TYR* 3.8 29.1 - + + -
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 4.6 9.2 - - + -
56C LEU* 4.1 33.4 - - + +
60C THR* 4.2 24.7 - - + -
38D TYR* 3.9 37.0 - - + -
42D VAL* 5.4 1.8 - - + -
63D MET 2.9 21.7 + - - +
64D ASN* 3.6 6.1 - - - +
66D PHE* 1.3 82.5 - - + +
68D ASN* 1.3 63.3 + - - +
70D ILE* 3.3 2.0 + - - +
71D PHE* 2.9 24.3 + - + +
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Residues in contact with ASN 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 6.1 2.4 - - - +
36D GLU* 5.1 6.9 + - - -
38D TYR* 4.4 15.1 + - - -
64D ASN* 2.9 44.5 + - - +
65D SER* 3.6 5.4 - - - +
66D PHE 3.3 0.2 - - - -
67D VAL* 1.3 75.4 - - - +
69D ASP* 1.3 62.4 + - - +
71D PHE* 3.3 12.1 + - - +
72D GLU* 3.0 38.7 + - - +
103F GLY* 4.1 21.1 - - - +
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Residues in contact with ASP 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C VAL* 5.0 0.2 - - - +
65D SER 3.0 11.6 + - - +
66D PHE 3.2 3.8 + - - +
68D ASN* 1.3 77.3 - - - +
70D ILE* 1.3 66.0 + - + +
72D GLU* 3.3 9.0 + - - +
73D ARG* 3.0 60.4 + - - +
92F LYS* 6.3 4.3 - - - +
97F THR* 4.8 9.2 - - + +
99F TYR* 2.6 36.8 + - + +
103F GLY 5.2 0.4 + - - -
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Residues in contact with ILE 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C VAL* 5.6 0.4 - - + -
56C LEU* 4.2 15.5 - - + -
59C LEU* 4.5 12.6 - - + -
97C LEU* 4.2 25.1 - - + -
98C LEU* 5.1 1.6 - - + -
66D PHE* 3.0 51.0 + - + +
67D VAL 4.0 2.9 - - - +
69D ASP* 1.3 84.6 - - - +
71D PHE* 1.3 63.8 + - - +
73D ARG* 4.5 11.7 - - - +
74D ILE* 3.0 46.8 + - + +
102D LEU* 5.4 5.2 - - + -
103D LEU* 5.8 4.0 - - + -
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Residues in contact with PHE 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C VAL* 4.3 12.6 - - + -
34C LEU* 4.1 26.7 - - + -
35C LEU* 3.7 30.1 - - + -
40C TYR* 3.8 26.9 - + - -
52C LEU* 3.6 34.4 - - + +
56C LEU* 4.8 12.7 - - + +
38D TYR* 5.6 7.0 - - - +
67D VAL* 2.9 19.0 + - + +
68D ASN* 3.4 13.0 - - - +
69D ASP 3.2 0.2 - - - -
70D ILE* 1.3 78.2 - - - +
72D GLU* 1.3 67.0 + - + +
74D ILE* 3.9 2.6 - - - +
75D ALA* 2.9 29.7 + - + +
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Residues in contact with GLU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C TYR* 3.7 22.6 - - + +
68D ASN* 3.0 28.8 + - - +
69D ASP* 4.0 7.9 - - - +
71D PHE* 1.3 85.7 - - + +
73D ARG* 1.3 64.3 + - + +
75D ALA* 4.7 0.2 - - - -
76D GLY* 2.9 23.4 + - - -
92F LYS* 4.3 12.1 + - - +
80H ARG* 2.8 43.1 + - - +
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Residues in contact with ARG 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C LEU* 3.5 41.0 + - - +
98C LEU* 4.5 2.8 - - - +
101C VAL* 4.2 15.6 - - - +
69D ASP* 3.0 51.9 + - - +
70D ILE* 3.8 9.6 - - - +
72D GLU* 1.3 75.2 - - + +
74D ILE* 1.3 63.3 + - - +
76D GLY* 3.9 0.6 - - - -
77D GLU* 3.0 24.6 + - - +
80D ARG* 5.5 0.3 + - - -
102D LEU* 3.8 34.7 - - + +
97F THR* 5.7 2.0 + - - -
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Residues in contact with ILE 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU* 4.1 26.2 - - + -
55C VAL* 4.8 9.2 - - + -
70D ILE* 3.0 38.9 + - + +
71D PHE 4.0 1.6 - - - +
73D ARG* 1.3 76.9 - - - +
75D ALA* 1.3 63.9 + - - +
77D GLU* 3.3 5.2 + - - +
78D ALA* 2.9 22.2 + - - +
95D ILE* 4.2 31.4 - - + +
98D ALA* 4.2 15.8 - - + +
99D VAL* 4.5 18.8 - - + +
102D LEU* 4.3 15.3 - - + -
103D LEU* 5.8 4.3 - - + -
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Residues in contact with ALA 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU* 4.3 14.4 - - + -
40C TYR* 3.6 41.7 - - + +
52C LEU* 6.1 1.5 - - + +
71D PHE* 2.9 20.5 + - + +
72D GLU 4.1 0.4 - - - +
74D ILE* 1.3 77.3 - - - +
76D GLY* 1.3 57.9 + - - +
78D ALA* 3.3 6.7 + - - +
79D SER* 2.9 28.9 + - - -
90D ILE* 4.9 5.1 - - + +
95D ILE* 5.7 1.6 - - - -
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Residues in contact with GLY 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C TYR* 4.4 7.0 - - - -
72D GLU 2.9 17.6 + - - -
73D ARG 3.9 0.7 - - - -
75D ALA* 1.3 76.6 - - - +
77D GLU* 1.3 61.8 + - - +
79D SER* 3.2 9.0 + - - -
80D ARG* 3.0 31.7 + - - +
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Residues in contact with GLU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR* 3.0 22.3 + - - -
93B ARG* 3.3 28.0 + - - +
73D ARG 3.0 17.4 + - - +
74D ILE* 3.8 4.0 - - - +
76D GLY* 1.3 76.3 - - - +
78D ALA* 1.3 64.2 + - - +
80D ARG* 2.4 45.0 + - - +
81D LEU* 2.9 49.7 + - + +
98D ALA* 4.1 23.3 - - + +
101D LEU* 4.0 4.2 - - + +
102D LEU* 6.2 2.7 - - + -
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Residues in contact with ALA 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D ILE 2.9 17.9 + - - +
75D ALA 3.5 2.5 - - - +
77D GLU* 1.3 76.2 - - - +
79D SER* 1.3 63.2 + - - +
81D LEU* 3.3 7.5 + - - +
82D ALA* 3.0 24.8 + - - +
90D ILE* 3.3 35.4 - - + +
94D GLU* 4.3 18.3 - - + +
95D ILE* 4.3 9.4 - - + -
98D ALA* 4.4 4.2 - - + +
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Residues in contact with SER 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASN 5.3 0.7 + - - -
40C TYR* 3.6 27.3 + - - -
41C SER* 5.2 3.1 - - - -
75D ALA 2.9 13.6 + - - -
76D GLY* 3.3 12.6 - - - -
78D ALA* 1.3 76.1 - - - +
80D ARG* 1.3 64.4 + - - +
82D ALA* 3.3 6.5 + - - +
83D HIS* 3.0 48.5 + - - -
90D ILE* 5.0 0.8 - - - +
38G GLY 5.2 0.2 + - - -
39G ASN* 5.3 1.4 - - - +
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Residues in contact with ARG 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR* 4.1 6.9 + - - -
89B TYR* 5.6 2.2 + - - +
92B LYS* 5.1 17.7 - - - +
93B ARG* 4.4 11.5 - - - +
76D GLY 3.0 14.8 + - - +
77D GLU* 2.4 55.5 + - - +
79D SER* 1.3 77.2 - - - +
81D LEU* 1.3 62.7 + - - +
83D HIS* 3.2 7.4 + - - +
84D TYR* 2.9 63.7 + - + +
72H GLU* 5.4 9.6 - - - +
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Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR* 3.6 26.2 - - + -
76B HIS* 4.0 24.9 - - + +
77D GLU* 2.9 60.9 + - + +
78D ALA* 3.8 8.1 - - - +
80D ARG* 1.3 74.6 - - - +
82D ALA* 1.3 62.6 + - - +
84D TYR* 3.3 7.4 + - - +
85D ASN* 2.8 35.2 + - - +
94D GLU* 4.8 6.5 - - + +
97D THR* 3.4 34.5 - - + -
98D ALA* 5.4 1.8 - - - -
101D LEU* 4.4 2.9 - - + -
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Residues in contact with ALA 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B HIS* 5.8 0.7 - - - -
41C SER* 5.4 5.6 - - - +
78D ALA 3.0 17.8 + - - +
79D SER* 3.6 6.5 - - - +
81D LEU* 1.3 75.6 - - - +
83D HIS* 1.3 62.3 + - + +
85D ASN* 5.1 0.2 - - - -
86D LYS 3.3 2.6 + - - -
87D ARG* 2.8 56.7 + - + +
88D SER 5.4 0.7 - - - -
89D THR 4.4 14.8 - - - +
90D ILE* 5.4 2.0 - - + +
94D GLU* 4.9 7.1 - - + +
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Residues in contact with HIS 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C TYR 5.2 1.1 - - - -
79D SER* 3.0 38.9 + - - +
80D ARG* 3.2 9.2 + - - +
82D ALA* 1.3 78.4 - - + +
84D TYR* 1.3 68.7 + - + +
86D LYS* 3.2 23.8 + - - +
87D ARG 4.7 4.3 - - - +
37G LYS 5.7 0.4 - - - -
38G GLY* 3.3 44.5 + - - -
39G ASN* 3.9 14.1 + - + -
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Residues in contact with TYR 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR* 4.8 9.6 - + - -
89B TYR* 3.2 74.0 - + + +
92B LYS* 4.6 9.7 + - - +
80D ARG* 2.9 65.2 + - + +
81D LEU* 3.3 9.2 + - - +
83D HIS* 1.3 80.7 - - + +
85D ASN* 1.3 63.8 + - - +
86D LYS* 3.3 13.6 + - - +
72H GLU* 6.6 0.2 - - - -
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Residues in contact with ASN 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR* 5.3 5.1 + - - +
76B HIS* 3.7 26.0 + - + +
77B ALA* 3.3 26.8 - - - +
79B ARG* 4.0 9.4 + - - -
81D LEU* 2.8 32.2 + - - +
82D ALA* 4.3 1.8 - - - +
83D HIS 3.2 0.2 - - - -
84D TYR* 1.3 81.2 - - - +
86D LYS* 1.3 71.9 + - - +
87D ARG* 3.1 15.8 + - + +
----------------------------------------------------------
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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