Contacts of the helix formed by residues 95 - 119 (chain D) in PDB entry 5DIR
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 GLU 95 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ARG* 4.8 9.2 + - - -
91D LEU* 3.7 24.0 - - + +
92D LYS* 3.3 37.6 + - + +
93D LYS 3.3 0.8 + - - -
94D GLY* 1.3 78.7 - - - +
96D THR* 1.3 58.4 + - - +
97D TRP* 3.3 3.4 - - - -
98D LEU* 3.3 28.9 + - + +
99D ALA* 2.9 26.3 + - - +
156D ASP* 4.7 7.2 - - - +
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Residues in contact with THR 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D TRP* 3.5 32.3 - - + +
93D LYS* 5.7 0.4 - - - -
94D GLY* 3.2 24.1 + - - +
95D GLU* 1.3 74.4 - - - +
97D TRP* 1.3 69.7 + - - +
99D ALA* 3.1 9.0 + - - +
100D ILE* 3.0 33.1 + - - +
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Residues in contact with TRP 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D GLU 3.3 0.8 - - - -
96D THR* 1.3 83.5 + - - +
98D LEU* 1.3 62.2 + - - +
100D ILE* 3.6 6.6 + - + -
101D ALA* 3.5 4.9 + - - +
152D MET* 2.9 87.9 - - + +
155D LEU* 3.9 22.2 - - + -
156D ASP* 4.0 23.1 - - + -
159D ARG* 3.8 37.6 - - - +
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Residues in contact with LEU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C ARG* 5.3 5.2 - - - +
87D TRP* 4.4 19.7 - - + +
91D LEU* 3.9 20.4 - - + -
95D GLU* 3.3 38.0 + - + +
96D THR 3.2 0.2 - - - -
97D TRP* 1.3 80.4 - - - +
99D ALA* 1.3 63.3 + - - +
101D ALA* 3.2 12.5 + - + +
102D LEU* 3.3 30.6 + - + +
153D LEU* 4.9 11.7 - - + +
156D ASP* 3.3 43.3 + - + +
157D MET* 6.5 0.4 - - + -
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Residues in contact with ALA 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D TRP* 3.9 34.2 - - + +
88D LEU* 3.8 11.6 - - + +
91D LEU* 3.9 17.5 - - + -
95D GLU 2.9 14.1 + - - +
96D THR* 3.4 14.6 - - - +
98D LEU* 1.3 77.8 - - - +
100D ILE* 1.3 61.5 + - - +
102D LEU 3.4 1.6 + - - -
103D ALA* 3.1 23.5 + - - +
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Residues in contact with ILE 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D TRP* 4.3 14.4 - - + -
15D ILE* 3.9 29.6 - - + -
96D THR* 3.0 23.7 + - - +
97D TRP* 3.8 11.9 - - + +
98D LEU 3.3 0.2 - - - -
99D ALA* 1.3 74.4 - - - +
101D ALA* 1.3 58.5 + - - +
103D ALA* 3.3 2.5 + - - +
104D LEU* 2.9 45.4 + - + +
152D MET* 3.8 16.6 - - + -
201D OLC 4.3 16.2 - - + -
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Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D TRP 3.5 6.5 + - - +
98D LEU* 3.2 13.5 + - + +
100D ILE* 1.3 80.3 - - - +
102D LEU* 1.3 65.2 + - + +
104D LEU* 3.5 0.8 + - - -
105D VAL* 3.2 28.6 + - - +
149D GLY* 3.5 19.2 - - - +
152D MET* 3.5 33.6 - - + +
153D LEU* 3.9 11.0 - - + +
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Residues in contact with LEU 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D LEU* 3.7 28.7 - - + +
87D TRP* 3.9 30.7 - - + +
88D LEU* 4.1 36.1 - - + +
91D LEU* 4.5 7.9 - - + -
98D LEU* 3.3 27.9 + - + +
99D ALA 3.9 5.4 - - - +
100D ILE 3.3 0.6 - - - -
101D ALA* 1.3 75.7 - - + +
103D ALA* 1.3 54.6 - - - +
105D VAL* 3.1 5.0 + - - +
106D LEU* 2.8 36.8 + - - +
153D LEU* 4.0 26.0 - - + -
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Residues in contact with ALA 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D TRP* 3.8 22.7 - - + +
15D ILE* 3.8 16.3 - - + +
16D THR* 3.0 27.6 + - - +
88D LEU* 4.8 7.7 - - + +
99D ALA 3.1 15.1 + - - +
100D ILE* 3.7 5.8 - - - +
102D LEU* 1.3 77.7 - - - +
104D LEU* 1.3 58.1 + - - +
106D LEU* 4.3 1.6 - - - -
107D GLY* 2.9 26.5 + - - -
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Residues in contact with LEU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ILE* 3.8 16.2 - - + -
19D VAL* 3.9 16.4 - - + -
100D ILE* 2.9 27.4 + - + +
101D ALA 3.6 4.7 - - - +
102D LEU 3.2 0.2 - - - -
103D ALA* 1.3 77.8 - - - +
105D VAL* 1.3 57.2 + - - +
107D GLY* 3.5 0.5 + - - -
108D GLY* 3.0 24.3 + - - -
145D ALA* 3.4 31.3 - - + +
148D VAL* 3.7 30.5 - - + -
149D GLY* 4.1 4.5 - - - +
152D MET* 3.9 16.4 - - - -
201D OLC 3.8 31.0 - - + -
202D OLC 5.1 0.2 - - + -
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Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D VAL* 6.0 0.2 - - + -
84D LEU* 3.6 23.6 - - + -
101D ALA 3.2 15.4 + - - +
102D LEU* 3.1 8.8 + - - +
104D LEU* 1.3 75.7 - - - +
106D LEU* 1.3 58.4 + - - +
109D ALA* 2.8 27.9 + - - +
146D ILE* 3.8 25.7 - - + +
149D GLY* 3.8 22.4 - - - +
150D ALA* 4.0 2.7 - - + +
153D LEU* 5.9 5.8 - - + -
201G MLE 4.0 21.8 - - + -
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU* 4.0 15.3 - - + -
16D THR* 3.7 25.6 - - + +
81D SER* 3.5 48.0 - - - +
84D LEU* 4.2 12.3 - - + +
85D VAL* 3.8 24.2 - - + +
88D LEU* 5.0 5.8 - - + -
102D LEU 2.8 16.6 + - - +
103D ALA* 3.7 4.3 - - - +
105D VAL* 1.3 78.2 - - - +
107D GLY* 1.3 56.1 + - - +
109D ALA* 3.3 3.7 + - - +
110D LEU* 2.9 44.4 + - + +
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Residues in contact with GLY 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D THR* 3.6 28.0 - - - +
19D VAL* 3.7 12.2 - - - +
20D PHE* 3.8 12.4 - - - +
103D ALA 2.9 16.1 + - - -
104D LEU 3.9 0.7 - - - -
106D LEU* 1.3 76.6 - - - +
108D GLY* 1.3 57.9 + - - +
110D LEU* 3.6 1.4 + - - -
111D GLY* 3.1 23.4 + - - -
142D ALA* 5.1 0.2 - - - +
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Residues in contact with GLY 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL* 3.7 4.9 - - - +
104D LEU 3.0 11.7 + - - -
107D GLY* 1.3 74.8 - - - +
109D ALA* 1.3 62.9 + - - +
111D GLY 3.2 8.8 + - - -
112D ASN* 3.2 12.0 + - - -
142D ALA* 3.2 39.2 - - - +
146D ILE* 3.5 14.5 - - - +
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Residues in contact with ALA 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D ALA* 4.3 5.1 - - + +
80D VAL* 4.8 2.5 - - + -
81D SER* 3.9 15.9 - - - +
84D LEU* 5.6 0.7 - - + -
105D VAL* 2.8 21.0 + - + +
106D LEU* 3.3 6.0 + - - +
108D GLY* 1.3 77.4 - - - +
110D LEU* 1.3 57.9 + - - +
112D ASN* 3.4 2.4 + - - +
113D LEU* 2.9 27.9 + - - +
146D ILE* 3.6 7.5 - - - +
201G MLE 3.8 33.3 - - + +
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Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D THR* 4.4 12.1 - - + -
20D PHE* 3.3 25.6 - - + -
81D SER* 3.5 26.7 - - - +
106D LEU* 2.9 35.6 + - + +
107D GLY* 4.1 2.0 - - - +
109D ALA* 1.3 74.3 - - - +
111D GLY* 1.3 59.9 + - - +
113D LEU* 3.6 23.0 - - + +
114D TYR* 2.9 26.0 + - - +
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Residues in contact with GLY 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D PHE* 3.5 10.7 - - - -
23D ASP* 3.4 22.4 - - - -
24D GLN* 2.5 29.9 + - - -
27D LYS* 3.4 3.7 + - - -
107D GLY 3.1 13.9 + - - -
108D GLY 3.2 5.3 + - - -
110D LEU* 1.3 79.2 - - - +
112D ASN* 1.3 59.0 + - - +
115D ASP 3.5 6.9 + - - -
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Residues in contact with ASN 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D LYS* 3.0 22.5 + - - +
108D GLY 3.2 8.2 + - - +
109D ALA 4.1 2.0 - - - +
111D GLY* 1.3 73.7 - - - +
113D LEU* 1.3 60.6 + - - +
115D ASP* 3.2 6.3 + - - +
116D ARG* 2.9 43.5 + - - +
122D VAL* 3.4 11.9 - - + +
140D ASN* 3.2 11.3 + - - -
142D ALA* 3.3 12.8 - - - +
143D ASP* 2.9 24.7 + - - -
146D ILE* 4.3 2.4 - - - +
201G MLE 2.8 29.1 + - - +
202G IIL 3.9 0.2 - - - -
203G SER 3.7 3.6 - - - +
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Residues in contact with LEU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D ALA* 3.7 35.2 - - + +
77D ALA* 4.1 12.8 - - + +
78D ILE* 3.8 21.8 - - + +
109D ALA 2.9 18.4 + - - +
110D LEU* 3.3 27.8 + - + +
112D ASN* 1.3 74.0 - - - +
114D TYR* 1.3 66.2 + - - +
116D ARG* 3.2 6.9 + - + +
117D MET* 3.0 54.2 + - + +
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Residues in contact with TYR 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D PHE* 3.8 24.5 - + + -
24D GLN* 3.5 33.4 - - + +
110D LEU 2.9 17.3 + - - +
112D ASN 3.4 0.2 - - - -
113D LEU* 1.3 75.7 - - - +
115D ASP* 1.3 62.9 + - - +
117D MET* 4.5 10.3 - - + -
118D VAL* 2.9 65.8 + - + +
119D LEU* 5.7 3.4 - - + -
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Residues in contact with ASP 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D GLN* 3.4 17.3 - - - +
27D LYS* 2.6 41.5 + - - +
111D GLY 3.5 3.0 + - - -
112D ASN 3.2 9.6 + - - +
113D LEU 3.1 0.6 - - - -
114D TYR* 1.3 82.5 - - - +
116D ARG* 1.3 50.6 + - - +
119D LEU* 2.7 64.2 + - - +
121D HIS 3.3 15.0 - - - +
122D VAL* 3.9 6.8 - - - +
123D VAL* 3.5 11.4 + - - +
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Residues in contact with ARG 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D ASN 5.9 0.2 + - - -
56D GLY* 5.5 0.6 - - - -
70D ARG* 2.8 52.7 + - + +
71D TRP* 5.1 0.3 - - - -
73D PHE* 3.4 37.8 + - - +
74D ALA* 4.3 9.0 - - + +
77D ALA* 5.7 1.8 - - - +
112D ASN* 2.9 35.7 + - - +
113D LEU* 3.2 7.9 + - - +
115D ASP* 1.3 74.5 - - - +
117D MET* 1.3 57.8 + - - +
119D LEU 2.9 5.6 - - - +
121D HIS* 4.3 8.1 - - - +
122D VAL* 3.6 17.1 - - + +
201G MLE 3.5 27.4 + - - -
202G IIL 2.6 27.3 + - - -
203G SER* 3.5 17.8 + - - +
205G 5BV 3.8 10.7 + - - -
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Residues in contact with MET 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ARG* 2.9 22.7 + - - +
71D TRP* 4.0 29.7 - - + -
74D ALA* 4.5 3.6 - - + -
78D ILE* 4.8 11.4 - - - -
113D LEU* 3.0 52.7 + - + +
114D TYR* 4.2 8.1 - - + +
116D ARG* 1.3 77.3 - - - +
118D VAL* 1.3 66.2 + - + +
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Residues in contact with VAL 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ARG* 4.3 2.9 + - - -
114D TYR* 2.9 60.8 + - + +
117D MET* 1.3 82.9 - - + +
119D LEU* 1.3 74.1 + - + +
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Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D GLN* 4.0 17.0 - - - +
70D ARG* 3.6 4.3 + - - -
114D TYR* 5.7 3.4 - - + -
115D ASP* 2.7 45.9 + - - +
116D ARG 2.9 15.8 - - - +
118D VAL* 1.3 90.7 - - + +
120D GLY* 1.3 59.3 + - - +
121D HIS* 3.0 23.7 + - + +
123D VAL* 3.7 25.6 - - + -
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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