Contacts of the helix formed by residues 79 - 111 (chain D) in PDB entry 5C5B
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 ASP 79 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C LYS* 3.4 37.7 + - - +
68D TYR* 5.6 0.4 + - - -
77D LYS 3.6 2.3 + - - -
78D GLY* 1.3 73.9 - - - +
80D GLU* 1.3 75.9 + - - +
81D GLU* 3.0 33.0 + - - +
82D VAL* 3.2 34.4 - - + +
83D ILE* 3.4 11.3 + - - +
232D MET* 5.1 1.7 - - - +
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Residues in contact with GLU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D GLY 3.4 4.6 + - - +
79D ASP* 1.3 76.0 + - - +
81D GLU* 1.3 59.6 + - + +
83D ILE* 4.1 21.1 - - + +
84D SER* 2.5 53.3 + - - -
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Residues in contact with GLU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ASP* 3.0 20.4 + - - +
80D GLU* 1.3 78.5 - - + +
82D VAL* 1.3 56.5 + - - +
84D SER* 3.9 4.0 - - - -
85D THR* 2.6 39.5 + - - +
232D MET* 3.7 25.8 - - + +
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Residues in contact with VAL 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C LYS* 3.7 33.2 - - + -
196C LEU* 5.1 7.6 - - + -
197C LEU* 4.3 18.4 - - + -
68D TYR* 4.4 21.5 - - + +
79D ASP* 3.2 28.9 - - + +
81D GLU* 1.3 75.7 - - - +
83D ILE* 1.3 62.8 - - - +
85D THR* 4.1 5.4 - - - -
86D LEU* 2.9 39.7 + - + +
232D MET* 3.9 17.9 - - + -
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Residues in contact with ILE 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D TYR* 3.9 27.4 - - + -
69D GLU* 4.8 27.4 - - + +
73D PHE* 4.7 11.7 - - + -
78D GLY* 4.3 13.2 - - - +
79D ASP 3.4 18.7 + - - +
80D GLU* 4.0 23.3 - - + +
81D GLU 3.2 0.4 - - - -
82D VAL* 1.3 82.7 - - - +
84D SER* 1.3 58.3 + - - +
86D LEU* 3.4 6.9 + - - +
87D HIS* 2.9 28.7 + - + +
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Residues in contact with SER 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D GLU* 2.5 44.1 + - - -
81D GLU* 3.9 5.6 - - - -
82D VAL 3.4 0.2 - - - -
83D ILE* 1.3 75.9 - - - +
85D THR* 1.3 59.4 + - - +
87D HIS* 3.2 7.3 + - - +
88D TYR* 2.9 29.9 + - - +
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Residues in contact with THR 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C LEU* 3.8 21.5 - - + +
81D GLU 2.6 26.5 + - - -
82D VAL* 3.7 5.0 - - - -
84D SER* 1.3 75.5 - - - +
86D LEU* 1.3 58.0 + - - +
88D TYR* 3.2 7.7 + - - +
89D PHE* 2.9 59.0 + - + +
225D PHE* 4.9 7.1 - - + -
229D VAL* 4.2 17.3 - - + +
232D MET* 4.4 11.3 - - - -
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Residues in contact with LEU 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C TYR* 4.2 3.8 - - - +
196C LEU* 4.0 26.7 - - + +
197C LEU* 4.1 20.9 - - + -
200C LEU* 4.0 24.0 - - + -
65D LEU* 3.9 20.6 - - + +
68D TYR* 3.6 44.6 - - + -
82D VAL* 2.9 23.7 + - + +
83D ILE* 3.7 4.9 - - - +
84D SER 3.3 0.2 - - - -
85D THR* 1.3 77.3 - - + +
87D HIS* 1.3 57.4 + - - +
89D PHE* 3.8 6.0 - - - +
90D SER* 2.9 28.8 + - - -
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Residues in contact with HIS 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D LEU 5.7 0.4 - - - -
66D LEU* 3.5 26.6 - - + +
69D GLU* 5.3 8.2 + - - -
83D ILE* 2.9 16.7 + - + +
84D SER* 3.2 11.6 + - - +
86D LEU* 1.3 73.9 - - - +
88D TYR* 1.3 64.7 + - - +
90D SER* 2.5 24.4 + - - -
91D LYS* 2.9 36.4 + - + +
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Residues in contact with TYR 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D SER 2.9 13.6 + - - +
85D THR* 3.5 8.5 - - - +
87D HIS* 1.3 76.5 - - - +
89D PHE* 1.3 60.3 + + - +
91D LYS* 3.0 15.1 + - + +
92D VAL* 3.0 46.9 + - + +
222D MET* 4.2 17.5 - - + +
225D PHE* 3.3 57.8 - + + +
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Residues in contact with PHE 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C LEU* 4.8 4.3 - - + -
200C LEU* 3.6 35.4 - - + -
201C LEU* 4.6 5.2 - - - -
204C MET* 3.8 28.9 - - + +
65D LEU* 3.9 13.7 - - + -
85D THR* 2.9 41.9 + - + +
86D LEU* 3.8 5.6 - - + +
88D TYR* 1.3 81.6 - + - +
90D SER* 1.3 57.3 + - - +
92D VAL* 3.2 6.3 + - + +
93D VAL* 2.9 34.0 + - - +
222D MET* 5.7 1.3 - - - -
225D PHE* 4.1 12.6 - + - -
226D LEU* 3.7 32.3 - - + -
229D VAL* 4.3 16.8 - - + -
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Residues in contact with SER 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D SER* 3.2 11.7 + - - -
65D LEU* 3.9 18.3 - - - +
66D LEU* 3.3 37.0 - - - +
86D LEU 2.9 15.4 + - - -
87D HIS* 2.5 19.9 + - - -
89D PHE* 1.3 75.7 - - - +
91D LYS* 1.3 60.0 + - - +
93D VAL* 3.4 2.3 + - - +
94D ASP* 2.9 35.1 + - - +
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Residues in contact with LYS 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D HIS* 2.9 39.1 + - + +
88D TYR* 3.2 14.1 - - + +
90D SER* 1.3 82.1 + - - +
92D VAL* 1.3 66.4 + - + +
94D ASP* 3.1 16.1 + - + +
95D GLU* 3.0 32.0 + - - +
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Residues in contact with VAL 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C MET* 3.7 28.3 - - + -
88D TYR* 3.0 34.0 + - + +
89D PHE* 3.5 9.2 - - + +
91D LYS* 1.3 75.4 - - + +
93D VAL* 1.3 58.4 + - - +
95D GLU* 3.1 16.8 + - - +
96D LEU* 2.9 25.6 + - + +
217D MET* 3.5 18.9 - - + +
218D PHE* 3.9 11.2 - - + -
222D MET* 4.1 27.6 - - + -
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Residues in contact with VAL 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C TYR* 4.3 5.8 - - + +
204C MET* 3.7 17.9 - - + -
58D THR* 3.1 37.5 - - + +
61D LEU* 3.9 24.9 - - + -
62D SER* 3.6 16.6 - - - +
65D LEU* 4.5 5.8 - - + -
89D PHE 2.9 22.3 + - - +
90D SER* 3.6 5.2 - - - +
92D VAL* 1.3 75.8 - - - +
94D ASP* 1.3 57.9 + - - +
96D LEU* 3.7 7.5 - - - +
97D ASN* 2.9 27.9 + - - +
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Residues in contact with ASP 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D GLN* 5.6 1.6 - - - -
62D SER* 2.8 24.3 + - - -
66D LEU* 5.0 6.1 - - - +
90D SER* 2.9 24.5 + - - +
91D LYS* 3.1 20.3 + - + +
93D VAL* 1.3 77.4 - - - +
95D GLU* 1.3 57.3 + - + +
97D ASN* 3.3 12.2 + - - +
98D LEU* 2.9 33.4 + - + +
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Residues in contact with GLU 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D LYS* 3.0 22.0 + - - +
92D VAL* 3.3 17.3 + - - +
94D ASP* 1.3 75.9 - - + +
96D LEU* 1.3 61.1 + - - +
98D LEU* 3.0 27.7 + - + +
99D LEU* 3.0 15.6 + - - +
217D MET* 3.5 33.2 - - - +
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Residues in contact with LEU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C TYR* 3.5 25.6 - - + +
207C GLN* 3.4 30.1 - - + +
211C PHE* 3.9 29.6 - - + -
58D THR* 4.9 3.6 - - + -
92D VAL* 2.9 15.4 + - + +
93D VAL* 3.7 7.6 - - - +
95D GLU* 1.3 76.4 - - - +
97D ASN* 1.3 56.8 + - - +
99D LEU* 3.2 16.7 + - + +
100D HIS* 2.9 54.0 + - + +
217D MET* 3.7 8.6 - - + -
218D PHE* 4.2 11.7 - - + -
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Residues in contact with ASN 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D CYS* 3.0 29.6 - - - +
58D THR* 3.1 18.8 + - - +
59D GLN* 3.8 16.1 + - - +
93D VAL 2.9 15.1 + - - +
94D ASP* 3.3 15.8 + - - +
95D GLU 3.2 0.2 - - - -
96D LEU* 1.3 76.5 - - - +
98D LEU* 1.3 62.5 + - - +
100D HIS* 3.3 4.4 + - - +
101D THR* 2.7 47.1 + - - -
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Residues in contact with LEU 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D ASP* 2.9 20.0 + - + +
95D GLU* 3.0 19.3 + - + +
97D ASN* 1.3 83.2 - - - +
99D LEU* 1.3 64.6 + - + +
101D THR* 3.2 9.3 + - + +
102D GLU* 3.0 25.9 + - - +
213D LYS* 6.3 0.2 - - - -
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Residues in contact with LEU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C PHE* 4.5 1.6 - - + -
95D GLU 3.0 14.0 + - - +
96D LEU* 3.2 20.2 - - + +
98D LEU* 1.3 77.0 - - + +
100D HIS* 1.3 56.6 - - - +
102D GLU* 3.2 7.4 + - + +
103D LEU* 3.0 27.0 + - - +
210D PHE* 3.9 23.4 - - + +
213D LYS* 3.6 45.5 - - + +
214D GLY* 3.5 32.5 - - - +
217D MET* 3.9 20.6 - - + -
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Residues in contact with HIS 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C GLN* 5.7 2.2 + - - -
54C LEU* 4.9 6.1 - - + -
100C HIS* 5.9 2.5 - + - -
207C GLN* 5.2 3.6 + - - -
210C PHE* 6.0 1.6 - + - -
51D GLN* 2.8 27.1 + - - +
54D MET* 3.4 31.3 - - + +
55D CYS* 3.4 24.7 - - - -
58D THR* 4.4 7.6 - - + +
96D LEU* 2.9 50.1 + - + +
97D ASN* 3.7 4.7 - - - +
99D LEU* 1.3 77.0 - - - +
101D THR* 1.3 57.5 + - - +
103D LEU* 3.3 4.7 + - - +
104D ALA* 2.9 24.9 + - - +
210D PHE* 3.3 29.9 - + - -
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Residues in contact with THR 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D CYS* 3.4 17.0 - - - +
97D ASN* 2.7 35.8 + - - -
98D LEU* 3.5 9.6 - - + +
100D HIS* 1.3 77.0 - - - +
102D GLU* 1.3 57.9 + - + +
104D ALA* 3.1 4.6 + - + +
105D LYS* 2.9 29.1 + - + +
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Residues in contact with GLU 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D LEU 3.0 13.8 + - - +
99D LEU* 3.7 9.2 - - + +
101D THR* 1.3 77.0 - - + +
103D LEU* 1.3 58.0 + - - +
105D LYS* 3.3 11.8 + - - +
106D GLN* 2.9 47.4 + - - +
213D LYS* 4.9 15.9 - - - +
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Residues in contact with LEU 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C HIS* 6.4 1.1 - - + -
51D GLN* 3.4 34.8 - - + +
99D LEU 3.0 14.0 + - - +
100D HIS 3.5 7.6 - - - +
101D THR 3.2 0.2 - - - -
102D GLU* 1.3 77.5 - - - +
104D ALA* 1.3 57.0 + - - +
106D GLN* 3.1 4.4 + - - +
107D LEU* 2.9 42.2 + - + +
206D GLY* 3.5 35.2 - - - +
207D GLN* 3.6 23.8 - - - +
210D PHE* 3.6 35.2 - - + -
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Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D TYR* 3.4 26.6 - - + -
51D GLN* 3.9 21.5 - - + +
52D ASN* 4.5 8.3 - - - +
55D CYS* 4.2 11.2 - - - -
100D HIS 2.9 14.5 + - - +
101D THR* 3.1 10.5 + - + +
103D LEU* 1.3 77.2 - - - +
105D LYS* 1.3 56.7 + - - +
107D LEU* 3.3 2.8 + - - +
108D ALA 2.9 23.9 + - - -
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Residues in contact with LYS 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D TYR* 5.3 0.4 - - - -
101D THR* 2.9 17.0 + - + +
102D GLU* 3.8 15.9 - - - +
103D LEU 3.3 0.2 - - - -
104D ALA* 1.3 77.3 - - - +
106D GLN* 1.3 59.5 + - - +
108D ALA* 3.8 5.8 - - - +
109D ASP* 2.9 41.6 + - - +
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Residues in contact with GLN 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D GLU* 2.9 30.3 + - - +
103D LEU* 3.1 11.2 + - + +
105D LYS* 1.3 76.1 - - - +
107D LEU* 1.3 59.7 + - + +
109D ASP* 4.9 4.2 - - - +
110D THR* 2.5 61.4 + - - +
202D GLY* 4.5 2.4 + - - +
205D HIS* 4.9 6.3 - - - +
206D GLY* 4.1 32.2 - - - +
209D ASN* 5.1 8.9 - - + +
----------------------------------------------------------
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Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D VAL* 3.9 21.5 - - + -
48D TYR* 4.3 11.7 - - + -
51D GLN* 3.9 36.3 - - + +
103D LEU* 2.9 33.3 + - + +
104D ALA* 3.6 5.6 - - - +
106D GLN* 1.3 77.2 - - + +
108D ALA* 1.3 58.7 + - - +
111D MET* 3.2 33.3 + - + +
112D VAL* 3.0 30.5 + - - +
202D GLY 5.7 0.2 - - - +
203D PHE* 3.8 30.1 - - + -
206D GLY* 5.8 0.2 - - - -
207D GLN* 4.6 1.8 - - - +
----------------------------------------------------------
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Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D TYR* 3.7 25.1 - - + +
104D ALA 2.9 16.1 + - - +
105D LYS* 3.8 7.4 - - - +
107D LEU* 1.3 77.3 - - - +
109D ASP* 1.3 62.9 + - - +
112D VAL* 3.9 8.2 - - - +
113D LEU* 3.2 31.9 + - - +
----------------------------------------------------------
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Residues in contact with ASP 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D LYS* 2.9 22.9 + - - +
106D GLN* 4.8 3.9 - - - +
108D ALA* 1.3 83.1 - - - +
110D THR* 1.3 67.1 + - + +
113D LEU* 3.4 23.0 - - + +
114D PRO* 3.3 19.1 - - - +
----------------------------------------------------------
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Residues in contact with THR 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D GLN* 2.5 46.3 + - - +
109D ASP* 1.3 81.3 - - + +
111D MET* 1.3 57.7 + - - +
114D PRO* 3.6 11.9 - - - +
198D GLU* 3.4 25.2 - - - +
199D PRO* 3.5 1.7 - - - +
202D GLY* 3.3 32.4 + - - -
----------------------------------------------------------
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Residues in contact with MET 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C PHE* 5.9 0.7 - - - -
44D MET* 3.6 39.7 - - - +
47D VAL* 4.0 21.3 - - + -
48D TYR 5.0 0.2 - - - +
107D LEU* 3.2 40.7 + - + +
109D ASP 3.5 1.0 - - - -
110D THR* 1.3 80.9 + - - +
112D VAL* 1.3 75.8 + - + +
113D LEU 3.4 0.4 - - - -
114D PRO* 3.2 8.2 - - - +
115D ILE* 3.4 19.1 - - - +
199D PRO* 3.5 24.4 - - + +
203D PHE* 3.6 36.3 - - + +
----------------------------------------------------------
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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).
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