Contacts of the helix formed by residues 102 - 131 (chain D) in PDB entry 1O9R
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 LYS 102 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D LYS 3.5 3.8 - - - -
101D TYR* 1.3 77.9 - - - +
103D ILE* 1.3 66.2 + - - +
104D HIS* 3.6 27.6 - - + +
105D ASP* 3.0 31.2 + - - +
106D HIS* 3.1 11.3 + - - -
160F GLU* 3.3 33.8 - - + +
161F LYS 5.8 0.7 - - - +
162F SER* 3.4 24.4 + - - +
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Residues in contact with ILE 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU* 3.9 22.7 - - + -
44D LYS 3.1 13.9 + - - +
45D GLY* 3.7 11.2 - - - +
47D GLN* 3.6 29.4 - - + +
48D PHE* 3.4 34.8 - - - +
51D VAL* 4.3 17.9 - - + -
101D TYR 4.2 0.4 - - - -
102D LYS* 1.3 70.7 - - - +
104D HIS* 1.4 60.1 + - - +
106D HIS* 3.1 4.4 + - + +
107D LEU* 2.8 47.7 + - + +
162F SER* 3.1 12.8 + - - +
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Residues in contact with HIS 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D LYS* 3.2 22.7 - - + +
103D ILE* 1.4 73.6 - - - +
105D ASP* 1.3 75.2 + - - +
107D LEU* 3.4 11.7 + - + +
108D ASP* 3.0 42.0 + - - +
158D VAL* 5.4 4.7 - - + +
162F SER* 2.8 50.4 + - - +
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Residues in contact with ASP 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ILE* 3.6 38.1 - - + +
101D TYR 4.9 0.5 + - - -
102D LYS* 3.0 31.2 + - + +
104D HIS* 1.3 99.5 + - - +
106D HIS* 1.3 65.5 + - - +
108D ASP* 3.4 7.8 + - - +
109D ALA* 3.1 18.5 + - - +
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Residues in contact with HIS 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D GLN* 4.5 1.8 - - + -
39D ALA* 3.5 29.9 - - + +
42D ASN* 3.8 16.0 + - + -
43D LEU* 3.6 18.8 - - + -
51D VAL* 6.5 0.7 - - + -
96D TYR* 2.8 30.8 + + - +
97D PRO 5.1 0.9 - - - -
100D ILE* 2.9 40.4 + - + +
101D TYR* 3.4 26.9 - - - -
102D LYS 3.1 11.9 + - - -
103D ILE* 3.7 5.8 - - - +
105D ASP* 1.3 77.9 - - - +
107D LEU* 1.4 57.7 + - + +
109D ALA 3.2 0.9 + - - -
110D LEU* 2.8 38.8 + - + +
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Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PRO* 6.4 0.2 - - + -
51D VAL* 4.5 17.7 - - + -
103D ILE* 2.8 43.1 + - + +
104D HIS* 3.7 8.3 - - + +
105D ASP 3.3 0.2 - - - -
106D HIS* 1.4 72.6 - - - +
108D ASP* 1.3 57.8 + - - +
110D LEU* 3.7 5.1 - - + +
111D ILE* 2.8 38.3 + - + +
154D LEU* 3.8 34.5 - - + +
157D HIS* 3.7 35.4 - - + +
158D VAL* 4.0 19.7 - - + -
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Residues in contact with ASP 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D HIS* 3.0 33.5 + - - +
105D ASP* 3.8 8.4 - - - +
106D HIS 3.3 0.2 - - - -
107D LEU* 1.3 76.7 - - - +
109D ALA* 1.3 63.6 + - - +
111D ILE* 3.4 8.4 + - - +
112D GLU* 3.1 23.6 + - - +
158D VAL* 4.4 17.2 - - - +
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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
----------------------------------------------------------
96D TYR* 3.4 29.6 - - + +
97D PRO* 4.5 7.2 - - + -
100D ILE* 4.3 7.4 - - + -
105D ASP 3.1 14.6 + - - +
108D ASP* 1.3 79.3 - - - +
110D LEU* 1.3 63.2 + - - +
112D GLU* 3.5 3.3 + - - +
113D ARG* 2.9 44.2 + - - +
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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
----------------------------------------------------------
35D VAL* 3.7 28.3 - - + +
36D THR* 4.4 6.1 - - - -
39D ALA* 3.9 25.6 - - + -
51D VAL* 5.7 0.9 - - + -
55D LEU* 3.9 24.5 - - + -
96D TYR* 3.9 6.1 - - - +
106D HIS* 2.8 31.0 + - + +
107D LEU* 3.8 7.9 - - + +
109D ALA* 1.3 72.1 - - - +
111D ILE* 1.3 60.1 + - - +
113D ARG* 3.2 2.8 + - - +
114D TYR* 2.8 53.7 + - + +
154D LEU* 4.0 20.2 - - + -
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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
----------------------------------------------------------
7B LYS* 3.8 29.9 - - + +
107D LEU* 2.8 30.3 + - + +
108D ASP* 3.8 8.7 - - - +
110D LEU* 1.3 71.2 - - - +
112D GLU* 1.3 64.0 + - - +
115D GLY* 2.9 21.8 + - - -
151D LEU* 4.0 4.2 - - + +
154D LEU* 3.6 37.5 - - + +
155D GLU* 3.9 20.4 - - + +
158D VAL* 3.7 33.4 - - + -
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Residues in contact with GLU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LYS* 4.6 15.1 - - - +
94D LYS* 4.2 16.6 - - - +
108D ASP 3.1 13.4 + - - +
109D ALA* 3.7 8.2 - - - +
110D LEU 3.2 0.4 - - - -
111D ILE* 1.3 75.9 - - - +
113D ARG* 1.3 88.0 + - - +
115D GLY* 3.9 0.7 - - - -
116D GLU* 3.1 54.4 + - - +
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Residues in contact with ARG 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 3.7 19.3 - - + -
35D VAL* 4.1 14.6 - - + +
93D LEU* 4.1 19.0 - - + +
94D LYS* 3.0 34.9 + - - +
95D ALA 3.0 16.8 + - - -
96D TYR* 3.7 27.8 - - - +
97D PRO* 4.0 5.4 - - - +
109D ALA* 2.9 42.7 + - - +
110D LEU* 3.2 3.8 + - - +
112D GLU* 1.3 101.7 + - + +
114D TYR* 1.3 59.6 + - - +
116D GLU* 3.2 10.9 + - - +
117D VAL* 2.9 34.5 + - - +
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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
----------------------------------------------------------
32D LEU* 3.7 32.8 - - + -
36D THR* 2.7 29.4 + - - +
55D LEU* 5.6 0.2 - - + -
58D PHE* 3.2 34.0 - + + +
62D LEU* 3.5 9.2 - - + +
110D LEU* 2.8 43.2 + - + +
111D ILE 4.3 1.8 - - - +
113D ARG* 1.3 74.1 - - - +
115D GLY* 1.3 58.9 + - - +
117D VAL* 4.1 0.3 - - - +
118D ALA* 2.8 33.9 + - - +
147D LEU* 4.3 13.7 - - + +
150D SER* 3.9 30.1 - - - -
151D LEU* 4.3 13.0 - - + +
154D LEU* 3.7 20.4 - - + -
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Residues in contact with GLY 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LYS* 4.0 15.9 - - - -
111D ILE 2.9 17.9 + - - -
112D GLU 3.9 1.1 - - - -
114D TYR* 1.3 77.8 - - - +
116D GLU* 1.3 63.1 + - - +
118D ALA* 3.8 0.5 - - - +
119D ASN* 3.0 34.1 + - - -
151D LEU* 3.9 19.2 - - - +
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Residues in contact with GLU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D LYS* 4.5 6.1 - - + +
93D LEU* 3.5 29.7 - - + +
94D LYS* 4.9 3.4 + - - +
112D GLU* 3.1 40.0 + - - +
113D ARG* 3.2 8.5 + - - +
115D GLY* 1.3 77.2 - - - +
117D VAL* 1.3 60.4 + - - +
119D ASN* 3.3 6.2 + - - +
120D MET* 2.9 38.2 + - + +
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Residues in contact with VAL 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D SER* 3.8 28.5 - - - +
29D VAL* 4.1 23.6 - - + +
32D LEU* 3.9 20.0 - - + -
93D LEU* 3.9 15.9 - - + -
113D ARG 2.9 20.5 + - - +
114D TYR 4.1 0.9 - - - +
116D GLU* 1.3 75.4 - - - +
118D ALA* 1.3 65.9 + - - +
120D MET* 3.2 7.7 + - + +
121D ILE* 2.9 27.0 + - + +
147D LEU* 3.9 23.1 - - + -
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Residues in contact with ALA 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D TYR 2.8 23.6 + - - +
115D GLY 3.8 2.9 - - - +
117D VAL* 1.3 71.8 - - - +
119D ASN* 1.4 58.9 + - - +
121D ILE* 3.4 2.3 + - - +
122D ARG* 3.0 36.5 + - - +
144D SER* 5.1 1.9 + - - -
147D LEU* 4.0 26.6 - - + +
148D ASP* 3.5 21.1 - - - +
151D LEU* 4.4 12.6 - - + -
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Residues in contact with ASN 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LYS* 3.0 22.6 + - - +
8B ASN* 3.7 2.1 - - - -
9B ASP* 3.0 41.4 + - - +
115D GLY 3.0 23.9 + - - +
116D GLU* 3.9 5.5 - - - +
118D ALA* 1.4 75.4 - - - +
120D MET* 1.3 63.3 + - - +
122D ARG* 2.9 29.6 + - - +
123D LYS* 3.1 22.0 + - - +
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Residues in contact with MET 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLU* 4.3 17.7 - - + +
25D SER* 3.9 29.5 + - - +
28D SER* 3.7 35.9 - - - +
92D LYS* 4.2 18.6 - - + -
93D LEU* 5.5 1.1 - - - -
116D GLU* 2.9 26.0 + - + +
117D VAL* 3.7 11.2 - - + +
119D ASN* 1.3 76.3 - - - +
121D ILE* 1.3 62.2 + - + +
123D LYS* 3.3 8.6 + - - +
124D ALA* 2.9 27.6 + - - +
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Residues in contact with ILE 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D SER* 3.5 32.8 - - - +
29D VAL* 4.4 9.4 - - + -
69D ILE* 4.4 10.5 - - + -
117D VAL* 2.9 24.4 + - + +
118D ALA 3.8 3.6 - - - +
120D MET* 1.3 78.7 - - + +
122D ARG* 1.4 60.5 + - - +
124D ALA* 3.1 5.0 + - - +
125D ILE* 3.1 22.2 + - - +
140D PHE* 3.3 39.2 - - + +
143D ALA* 4.0 7.0 - - + -
144D SER* 3.7 19.3 - - - +
147D LEU* 3.5 17.3 - - + -
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Residues in contact with ARG 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASN* 3.4 25.0 - - - +
9B ASP* 2.9 25.3 + - - -
10B LEU* 4.1 25.0 - - + +
72B ARG* 4.4 7.1 - - - +
133B ASP* 5.6 0.4 + - - -
134B PRO* 5.7 5.2 - - + +
135B THR* 4.9 3.8 + - - +
118D ALA* 3.0 21.4 + - - +
119D ASN* 2.9 23.9 + - - +
121D ILE* 1.4 75.6 - - - +
123D LYS* 1.3 63.1 + - - +
125D ILE* 3.4 27.1 + - + +
126D ASP* 3.8 11.0 + - - +
144D SER* 4.2 9.1 + - - +
148D ASP* 2.8 42.0 + - - -
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Residues in contact with LYS 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLU* 6.0 0.4 + - - -
119D ASN 3.1 10.6 + - - +
120D MET* 3.3 10.1 + - - +
122D ARG* 1.3 79.6 - - - +
124D ALA* 1.3 58.7 + - - +
126D ASP* 3.1 11.3 + - + +
127D ASP* 2.9 48.7 + - - +
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Residues in contact with ALA 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ILE* 3.7 21.3 - - + -
25D SER* 4.2 3.8 - - - +
120D MET 2.9 13.9 + - - +
121D ILE* 3.1 10.9 + - - +
123D LYS* 1.3 73.4 - - - +
125D ILE* 1.3 65.7 + - - +
127D ASP* 4.4 3.6 - - - +
128D SER* 2.8 31.0 + - - -
140D PHE* 3.7 31.9 - - + -
----------------------------------------------------------
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Residues in contact with ILE 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PRO* 4.0 27.6 - - + -
135B THR* 3.6 24.7 - - - +
121D ILE 3.1 13.1 + - - +
122D ARG* 3.5 15.0 - - + +
123D LYS 3.2 0.2 - - - -
124D ALA* 1.3 76.5 - - - +
126D ASP* 1.3 61.2 - - - +
129D ASP* 3.0 28.9 + - + +
137D ALA* 3.6 15.1 - - + +
140D PHE* 3.6 21.3 - - + +
141D THR* 3.5 32.3 - - + +
144D SER* 3.9 10.1 - - - +
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Residues in contact with ASP 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLY 5.2 4.5 - - - +
134B PRO* 3.6 26.8 - - - +
122D ARG* 3.8 10.7 + - - +
123D LYS* 3.1 10.4 + - + +
125D ILE* 1.3 78.1 - - - +
127D ASP* 1.3 66.6 - - - +
129D ASP* 3.4 5.2 + - - +
130D GLU* 2.9 50.8 + - - +
----------------------------------------------------------
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Residues in contact with ASP 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D THR* 5.2 0.9 - - - +
21D ILE* 3.8 22.9 - - + +
123D LYS* 2.9 50.8 + - - +
124D ALA* 4.2 3.4 + - - +
126D ASP* 1.3 81.8 - - - +
128D SER* 1.4 59.5 + - - +
130D GLU* 3.5 13.8 + - - +
131D ALA* 3.2 23.6 + - - +
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Residues in contact with SER 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D VAL* 4.2 12.3 - - - +
21D ILE* 4.2 8.7 - - - +
124D ALA 2.8 23.4 + - - -
125D ILE 3.8 2.7 - - - -
127D ASP* 1.4 74.1 - - - +
129D ASP* 1.3 65.0 + - - +
131D ALA* 3.3 9.2 + - - +
132D GLY 3.5 0.3 + - - -
133D ASP* 3.1 23.4 + - - +
136D THR* 3.6 10.7 - - - +
137D ALA* 3.9 22.0 - - - -
140D PHE* 3.3 20.8 - - - -
----------------------------------------------------------
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Residues in contact with ASP 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D ILE* 3.0 18.1 + - + +
126D ASP* 3.7 6.5 - - - +
128D SER* 1.3 76.5 - - - +
130D GLU* 1.3 63.1 - - + +
132D GLY* 2.9 22.3 + - - -
133D ASP 3.8 3.3 + - - +
134D PRO* 3.6 27.4 - - - +
137D ALA* 3.9 10.9 - - + +
----------------------------------------------------------
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Residues in contact with GLU 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ASP* 2.9 38.1 + - - +
127D ASP* 4.0 13.8 - - - +
129D ASP* 1.3 80.9 - - + +
131D ALA* 1.3 58.9 + - - +
132D GLY 3.5 0.9 + - - -
----------------------------------------------------------
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Residues in contact with ALA 131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ALA* 3.5 23.9 - - - +
17D THR* 4.1 20.0 - - + -
18D VAL* 3.9 20.9 - - + -
127D ASP 3.2 16.7 + - - +
128D SER 3.7 6.1 - - - +
129D ASP 3.1 0.4 - - - -
130D GLU* 1.3 77.8 - - - +
132D GLY* 1.3 57.8 + - - +
133D ASP 3.5 0.4 - - - -
----------------------------------------------------------
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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