Contacts of the helix formed by residues 92 - 117 (chain D) in PDB entry 3ECS
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 ILE 92 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D LEU* 3.3 33.9 - - + -
90D LYS 2.9 15.2 + - - +
91D LYS* 1.3 70.0 - - - +
93D MSE 1.3 66.1 + - - +
94D ILE 3.4 0.9 - - - -
95D GLU* 3.5 23.6 + - - +
96D ARG* 3.3 42.8 + - + +
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Residues in contact with MSE 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D LEU* 4.1 12.3 - - + -
43D GLN* 5.9 4.5 - - + +
46D ARG* 4.9 20.9 - - - -
76D ILE* 3.2 48.7 - - + +
77D SER* 4.1 15.0 - - - +
78D LEU* 4.2 20.6 - - + +
91D LYS* 2.9 25.8 - - + -
92D ILE* 1.3 84.2 - - + +
94D ILE* 1.3 55.6 + - - +
96D ARG* 3.1 3.5 + - - +
97D GLY 2.7 31.9 + - - -
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Residues in contact with ILE 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LEU* 4.2 5.7 - - + +
34D LEU* 3.8 22.2 - - + -
35D LYS* 3.7 52.0 - - + +
91D LYS* 3.6 35.0 + - + +
92D ILE 3.4 0.2 - - - -
93D MSE 1.3 75.3 - - - +
95D GLU* 1.3 62.4 + - - +
97D GLY* 3.2 1.3 + - - +
98D GLU* 3.0 30.3 + - - +
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Residues in contact with GLU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D ILE* 3.5 27.4 + - - +
93D MSE 3.2 0.6 - - - -
94D ILE* 1.3 74.9 - - - +
96D ARG* 1.3 67.2 + - + +
98D GLU* 3.2 13.3 + - - +
99D LEU* 3.1 19.7 + - + +
102D ARG* 5.0 3.1 + - - +
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Residues in contact with ARG 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D PHE* 3.6 34.0 + - + +
76D ILE* 2.9 18.6 + - - -
77D SER 2.6 33.7 + - - -
78D LEU* 3.4 24.6 - - - +
92D ILE* 3.3 29.2 + - + +
93D MSE 3.1 6.1 + - - +
95D GLU* 1.3 78.2 - - + +
97D GLY* 1.3 64.8 + - - +
99D LEU* 3.0 13.2 + - + +
100D PHE* 2.9 24.3 + - - +
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Residues in contact with GLY 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LEU* 4.4 7.2 - - - -
72D PHE* 3.6 28.9 - - - -
75D PHE* 5.6 0.2 - - - -
76D ILE* 4.0 6.9 - - - +
93D MSE 2.7 21.4 + - - -
94D ILE 3.5 2.9 - - - -
95D GLU 3.1 0.4 - - - -
96D ARG* 1.3 72.7 - - - +
98D GLU* 1.3 56.1 - - - +
100D PHE* 3.4 4.8 + - - +
101D LEU* 3.0 27.2 + - - +
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Residues in contact with GLU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LEU* 3.5 19.7 - - + -
35D LYS* 2.7 30.5 + - - -
94D ILE* 3.0 24.9 + - - +
95D GLU* 3.2 10.4 + - - +
97D GLY* 1.3 71.8 - - - +
99D LEU* 1.3 60.3 + - - +
101D LEU* 3.3 9.3 + - + +
102D ARG* 2.8 45.7 + - - +
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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
----------------------------------------------------------
75D PHE* 4.2 14.4 - - + -
95D GLU* 3.1 10.7 + - + +
96D ARG* 3.0 13.3 + - + +
98D GLU* 1.3 73.3 - - - +
100D PHE* 1.3 66.9 + - - +
102D ARG* 3.0 36.6 + - + +
103D ARG* 3.1 54.6 + - + +
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Residues in contact with PHE 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ILE* 3.4 33.7 - - + -
68D GLY 4.2 3.1 - - - -
71D LEU* 3.8 30.5 - - + -
72D PHE* 3.7 31.9 - + + -
75D PHE* 3.4 43.9 - + + -
96D ARG 2.9 6.1 + - - +
97D GLY* 3.5 7.9 - - - +
99D LEU* 1.3 76.6 - - - +
101D LEU* 1.3 63.2 + - - +
103D ARG* 3.1 16.9 + - - +
104D ILE* 3.2 41.7 + - + +
233D PHE* 5.1 7.6 - - + -
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Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D VAL* 4.6 3.1 - - + -
27D ILE* 3.3 33.0 - - + -
28D ARG* 2.8 59.5 + - + +
31D LEU* 3.6 29.2 - - + -
97D GLY 3.0 11.3 + - - +
98D GLU* 3.4 10.5 - - + +
100D PHE* 1.3 79.4 - - - +
102D ARG* 1.3 61.1 + - - +
103D ARG 3.5 0.2 + - - -
104D ILE* 3.5 15.9 - - + +
105D SER* 3.5 11.3 + - - -
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Residues in contact with ARG 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D GLU* 5.0 3.0 + - - +
98D GLU* 2.8 22.1 + - - +
99D LEU* 3.0 43.4 + - + +
101D LEU* 1.3 78.4 - - - +
103D ARG* 1.3 60.4 + - + +
105D SER* 2.8 19.6 + - - +
106D LEU* 4.0 13.9 + - - +
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Residues in contact with ARG 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D PHE* 4.1 20.5 - - - -
99D LEU* 3.1 53.3 + - + +
100D PHE* 3.1 8.0 + - - +
102D ARG* 1.3 75.7 - - + +
104D ILE* 1.3 58.4 + - + +
105D SER 3.0 4.7 - - - -
106D LEU* 2.8 36.6 + - + +
107D SER* 3.5 5.6 + - - -
110D LYS* 4.7 1.6 + - - -
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Residues in contact with ILE 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ALA 5.6 0.2 - - - -
24D VAL* 3.9 26.7 - - + +
27D ILE* 3.3 36.6 - - + -
100D PHE* 3.2 36.6 + - + +
101D LEU* 3.5 14.8 - - + +
103D ARG* 1.3 77.1 - - + +
105D SER* 1.3 63.3 + - - +
106D LEU 3.1 1.6 + - - -
107D SER* 3.4 24.3 - - - -
108D ARG* 4.5 1.9 + - - +
231D GLU* 5.3 0.5 - - - +
233D PHE* 3.7 33.8 - - + -
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Residues in contact with SER 105 (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 VAL* 5.7 7.6 - - - -
28D ARG* 4.8 13.7 - - - -
101D LEU 3.5 10.6 + - - -
102D ARG* 2.8 24.8 + - - +
104D ILE* 1.3 80.7 - - - +
106D LEU* 1.3 66.3 + - - +
108D ARG* 4.9 5.8 + - - +
109D ASN* 5.2 5.0 + - - +
136D ARG* 5.5 5.0 + - - -
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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
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102D ARG 4.0 14.1 - - - +
103D ARG* 2.8 18.5 + - + +
105D SER* 1.3 87.6 + - - +
107D SER* 1.3 63.7 + - - +
108D ARG 3.4 0.7 - - - -
109D ASN* 2.9 21.9 + - + +
110D LYS* 3.1 35.2 + - + +
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Residues in contact with SER 107 (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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103D ARG 3.5 2.8 + - - -
104D ILE* 3.4 25.4 + - - -
106D LEU* 1.3 77.5 - - - +
108D ARG* 1.3 65.9 + - - +
110D LYS* 2.9 17.9 + - - +
111D ILE* 3.1 15.3 + - - +
231D GLU* 4.1 13.1 - - - +
232D SER* 4.7 1.0 + - - -
233D PHE* 5.1 1.6 - - - -
287D ASP* 3.1 42.3 + - - +
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Residues in contact with ARG 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 ASP* 2.5 37.5 + - - +
20D MSE 3.9 2.0 - - - +
21D ALA* 3.2 27.5 - - - +
24D VAL* 5.9 0.6 - - - +
104D ILE 4.5 2.8 + - - +
105D SER 4.9 4.2 + - - +
106D LEU 3.2 1.4 + - - -
107D SER* 1.3 78.8 - - - +
109D ASN* 1.3 62.3 + - - +
111D ILE* 3.4 13.0 + - - +
112D ALA* 3.2 19.6 + - - +
132D ARG* 4.2 12.8 - - - +
133D VAL* 4.0 30.7 - - + +
136D ARG* 3.1 62.3 - - + +
137D VAL* 5.8 0.5 - - - +
231D GLU* 4.3 10.5 + - + +
504D SO4 5.3 0.2 + - - -
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Residues in contact with ASN 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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105D SER 5.4 0.4 + - - -
106D LEU* 2.9 13.3 + - + +
108D ARG* 1.3 74.8 - - - +
110D LYS* 1.3 66.9 + - + +
112D ALA* 3.2 12.1 + - - +
113D ASP* 3.1 29.3 + - - +
136D ARG* 2.5 40.8 + - - +
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Residues in contact with LYS 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B THR* 4.7 6.1 - - + +
120B LYS* 3.9 25.1 - - - +
146B LYS* 5.8 5.8 - - - +
103D ARG* 4.7 1.6 + - - +
106D LEU* 3.1 50.6 + - - +
107D SER* 2.9 9.1 + - - +
109D ASN* 1.3 77.6 - - + +
111D ILE* 1.3 62.4 + - - +
113D ASP* 3.4 7.5 + - - +
114D LEU* 3.0 31.9 + - + +
286D THR 5.2 0.2 - - - +
287D ASP* 3.9 35.6 - - + +
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Residues in contact with ILE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D SER 3.1 13.9 + - - +
108D ARG* 3.5 8.7 - - - +
110D LYS* 1.3 74.3 - - - +
112D ALA* 1.3 66.9 + - - +
114D LEU* 3.2 7.2 + - - +
115D CYS* 2.9 24.6 + - - +
133D VAL* 5.2 6.7 - - + -
137D VAL* 4.1 6.7 - - + -
229D VAL* 3.6 34.1 - - + -
230D ALA* 3.4 37.5 - - - +
231D GLU* 3.5 17.7 - - + +
285D PHE* 3.6 16.4 - - + +
286D THR 3.9 14.8 - - - -
287D ASP* 4.2 2.2 - - - +
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Residues in contact with ALA 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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108D ARG 3.2 9.9 + - - +
109D ASN* 3.2 22.0 + - - +
111D ILE* 1.3 81.6 - - - +
113D ASP* 1.3 63.3 + - - +
116D HIS* 3.2 28.2 + - - +
136D ARG* 3.8 16.8 - - + +
137D VAL* 4.0 13.8 - - - +
140D ALA* 3.8 21.1 - - + +
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Residues in contact with ASP 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ASP 4.8 1.2 - - - +
116B HIS* 3.2 23.9 - - + -
117B THR* 3.7 22.1 + - + +
144B ALA* 4.7 8.7 - - - +
146B LYS* 5.3 4.9 - - - -
109D ASN* 3.1 15.2 + - - +
110D LYS* 3.6 9.7 - - - +
111D ILE 3.2 0.2 - - - -
112D ALA* 1.3 78.6 - - - +
114D LEU* 1.3 61.1 + - - +
116D HIS* 3.0 28.7 + - - -
117D THR* 3.4 7.6 + - - -
140D ALA* 5.1 4.2 - - - +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B THR* 3.8 26.7 - - + -
118B PHE* 4.9 14.6 - - + -
110D LYS* 3.0 20.3 + - + +
111D ILE* 3.7 3.8 - - - +
113D ASP* 1.3 80.3 - - - +
115D CYS* 1.3 62.6 + - - +
117D THR* 3.6 14.8 - - - -
118D PHE* 3.8 11.4 - - - -
285D PHE* 3.9 11.9 - - + -
286D THR 3.2 31.6 - - - +
287D ASP* 5.2 2.0 - - - +
289D GLY* 4.1 18.6 - - - +
290D VAL* 3.9 17.3 - - + +
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Residues in contact with CYS 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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111D ILE 2.9 17.2 + - - +
114D LEU* 1.3 74.4 - - - +
116D HIS* 1.3 52.4 + - - +
117D THR 2.7 17.7 + - - -
118D PHE* 2.7 22.3 + - - +
119D ILE* 4.1 2.1 + - - +
137D VAL* 3.8 16.8 - - + -
194D ILE* 4.7 14.8 - - - -
227D TYR* 5.0 6.1 - - - -
229D VAL* 3.7 26.5 - - + -
285D PHE* 3.5 33.2 - - + -
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Residues in contact with HIS 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ASP* 2.4 34.1 + - - -
116B HIS* 5.1 3.8 - - - -
112D ALA 3.2 17.9 + - - +
113D ASP* 3.0 37.0 + - + -
115D CYS* 1.3 76.0 - - - +
117D THR* 1.3 67.7 + - - +
118D PHE 3.1 0.2 - - - -
119D ILE* 3.1 30.3 + - - +
137D VAL* 3.9 19.3 - - - +
140D ALA* 3.4 18.0 + - + +
141D ALA* 4.1 8.5 - - + +
144D ALA* 3.4 28.5 - - + +
146D LYS* 3.8 12.4 - - + +
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Residues in contact with THR 117 (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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110B LYS 5.4 0.7 - - - +
113B ASP* 3.8 20.9 + - + -
114B LEU* 3.1 41.8 - - + +
113D ASP 3.4 14.7 + - - -
114D LEU* 3.6 14.1 + - - -
115D CYS 2.7 4.8 + - - -
116D HIS* 1.3 84.9 + - - +
118D PHE* 1.3 64.9 + - + +
119D ILE 3.4 1.4 + - - +
146D LYS* 4.5 10.5 + - - +
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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
------------------------------------------------------------
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