Contacts of the helix formed by residues 92 - 119 (chain D) in PDB entry 1IES
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 THR 92 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE* 3.9 10.7 - - - -
44D LEU* 3.8 5.0 - - - +
47D VAL* 3.8 34.7 - - + +
91D THR* 1.3 69.9 - - - +
93D LEU* 1.3 52.7 + - - +
95D ALA* 3.2 1.7 + - + +
96D MET* 2.7 42.3 + - + +
151D ILE* 3.6 24.9 - - + -
163D GLU* 2.8 37.4 + - - +
166D PHE* 4.3 15.0 - - + -
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Residues in contact with LEU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D THR* 3.1 8.5 + - - +
92D THR* 1.3 76.5 - - - +
94D ASP* 1.3 68.0 + - - +
96D MET* 3.9 0.3 - - - +
97D LYS* 3.0 45.0 + - + +
148D LEU* 3.5 28.0 - - + -
151D ILE* 4.2 25.8 - - + +
152D GLN* 3.8 32.8 - - + +
155D VAL* 4.6 20.2 - - + -
163D GLU* 5.6 0.8 - - - +
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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
----------------------------------------------------------
89D TRP 3.5 16.8 - - - +
90D GLY* 3.8 6.0 - - - -
91D THR* 2.8 30.0 + - - +
93D LEU* 1.3 83.8 - - - +
95D ALA* 1.4 55.6 + - - +
97D LYS* 3.3 12.7 + - - +
98D ALA* 3.0 29.0 + - - +
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Residues in contact with ALA 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LEU* 3.8 20.1 - - + +
37D PHE* 3.5 30.3 - - + -
51D PHE* 3.8 12.5 - - + -
89D TRP* 3.9 6.1 + - - +
91D THR 2.8 17.6 + - - +
92D THR* 3.4 7.4 - - - +
94D ASP* 1.4 71.1 - - - +
96D MET* 1.3 63.2 + - - +
98D ALA* 3.2 7.1 + - - +
99D ALA* 2.9 22.0 + - - +
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Residues in contact with MET 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D VAL* 5.5 0.4 - - + -
50D PHE* 3.6 39.7 - - + -
51D PHE* 4.2 9.6 - - + -
92D THR* 2.7 30.4 + - + +
93D LEU 3.9 0.4 - - - +
95D ALA* 1.3 71.6 - - - +
97D LYS* 1.3 58.7 + - - +
99D ALA* 3.2 4.4 + - - +
100D ILE* 2.8 31.7 + - - +
144D MET* 4.6 12.4 - - + +
147D HIS* 3.9 30.7 - - + -
148D LEU* 3.6 23.1 - - + +
151D ILE* 3.4 23.8 - - + -
166D PHE* 4.6 5.6 - - + -
171D LEU* 5.0 3.6 - - + -
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Residues in contact with LYS 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D LEU* 3.0 37.7 + - + +
94D ASP* 3.5 12.0 + - - +
96D MET* 1.3 76.4 - - - +
98D ALA* 1.3 62.3 + - - +
100D ILE* 3.2 10.4 - - + +
101D VAL* 3.2 30.3 + - + +
148D LEU* 3.6 15.5 - - + -
152D GLN* 3.7 26.6 - - - +
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Residues in contact with ALA 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LEU* 5.3 3.8 - - + -
86D GLN* 5.3 4.0 - - - +
89D TRP* 4.3 28.9 - - + -
94D ASP 3.0 13.7 + - - +
95D ALA 3.2 9.2 + - - +
97D LYS* 1.3 74.6 - - - +
99D ALA* 1.3 58.7 - - - +
101D VAL* 3.4 9.2 - - - +
102D LEU* 3.0 27.0 + - - +
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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
----------------------------------------------------------
30D TYR* 3.7 21.1 - - + +
33D LEU* 5.0 2.9 - - + +
51D PHE* 3.7 23.3 - - + -
95D ALA 2.9 12.7 + - - +
96D MET* 3.2 10.3 + - - +
98D ALA* 1.3 73.6 - - - +
100D ILE* 1.3 62.8 + - - +
102D LEU* 2.8 9.1 + - - +
103D GLU* 2.8 28.8 + - - +
144D MET* 3.9 13.0 - - + -
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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
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96D MET 2.8 17.7 + - - +
97D LYS* 3.2 14.8 - - + +
99D ALA* 1.3 71.4 - - - +
101D VAL* 1.3 63.2 + - + +
103D GLU* 3.4 2.7 + - - +
104D LYS* 2.9 44.1 + - + +
141D ILE* 4.1 10.1 - - + -
144D MET* 4.0 18.8 - - + -
145D GLY* 4.1 10.5 - - - +
148D LEU* 4.0 27.4 - - + -
3F GLN* 4.3 16.6 - - + +
4F ILE* 4.1 25.8 - - + -
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Residues in contact with VAL 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LYS* 3.2 16.6 + - + +
98D ALA* 3.4 11.2 - - - +
100D ILE* 1.3 80.0 - - + +
102D LEU* 1.3 64.2 + - - +
104D LYS* 3.3 8.4 + - - +
105D SER* 3.0 23.9 + - - -
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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
----------------------------------------------------------
25D ARG* 5.5 7.0 - - - +
26D ALA* 4.1 25.8 - - + +
29D THR* 3.7 30.3 - - + +
30D TYR* 3.7 33.9 - - + +
33D LEU* 5.5 0.4 - - + -
98D ALA 3.0 13.3 + - - +
99D ALA* 2.8 11.0 + - - +
101D VAL* 1.3 77.2 - - - +
103D GLU* 1.3 61.8 + - - +
105D SER* 2.8 28.3 + - - +
106D LEU* 3.1 12.6 + - + +
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Residues in contact with GLU 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 2.6 31.2 + - - +
58D LYS* 2.8 37.5 + - - -
99D ALA 2.8 14.2 + - - +
100D ILE* 3.8 7.0 - - - +
102D LEU* 1.3 72.6 - - - +
104D LYS* 1.3 54.4 + - - +
106D LEU* 3.1 10.5 + - - +
107D ASN* 2.7 35.5 + - - +
137D GLU* 2.7 29.8 - - - +
140D LEU* 3.5 15.9 - - + +
141D ILE* 3.8 15.0 - - + -
144D MET* 3.9 16.4 - - - -
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Residues in contact with LYS 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ILE* 2.9 36.7 + - + +
101D VAL* 3.4 8.9 - - - +
103D GLU* 1.3 75.8 - - - +
105D SER* 1.3 56.7 + - - +
107D ASN* 3.3 1.0 + - - -
108D GLN* 2.9 14.6 + - - +
141D ILE* 4.2 10.1 - - + -
3F GLN 3.1 29.3 + - - -
4F ILE* 3.9 18.6 - - - +
5F ARG 4.7 7.2 + - - -
6F GLN* 2.9 46.5 + - + +
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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
----------------------------------------------------------
22D LEU* 4.9 3.2 - - - +
101D VAL* 3.0 13.4 + - - -
102D LEU* 2.8 28.7 + - - +
104D LYS* 1.3 71.3 - - - +
106D LEU* 1.3 63.3 + - - +
108D GLN* 3.3 7.9 + - - +
109D ALA* 2.9 27.9 + - - +
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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
----------------------------------------------------------
19D LEU* 4.8 0.3 - - - +
22D LEU* 4.0 42.0 - - + +
23D TYR* 4.1 21.3 - - + +
26D ALA* 3.9 22.9 - - + -
58D LYS* 3.9 18.2 - - + +
102D LEU* 3.1 12.2 + - + +
103D GLU* 3.4 29.6 - - - +
105D SER* 1.3 83.2 + - - +
107D ASN* 1.3 63.8 + - - +
109D ALA* 3.1 8.3 + - - +
110D LEU* 3.0 26.7 + - - +
137D GLU* 4.7 4.3 - - - +
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Residues in contact with ASN 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 GLU 2.7 19.1 + - - +
104D LYS 3.5 0.4 - - - +
106D LEU* 1.3 74.0 - - - +
108D GLN* 1.3 62.4 + - - +
110D LEU* 3.2 11.6 + - - +
111D LEU* 2.9 37.3 + - - +
134D LEU* 4.5 8.1 + - - +
137D GLU* 3.3 33.5 - - + +
138D VAL* 4.7 10.3 - - - +
141D ILE* 4.0 8.5 - - + +
6F GLN* 3.0 31.5 - - - +
72F ARG* 5.8 1.0 + - - -
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Residues in contact with GLN 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D LYS 2.9 13.7 + - - +
105D SER* 3.6 11.0 - - - +
107D ASN* 1.3 75.0 - - - +
109D ALA* 1.3 53.9 + - - +
111D LEU* 3.2 21.3 + - - +
112D ASP* 2.8 65.6 + - - +
6F GLN* 3.6 19.0 + - - +
7F ASN* 5.6 1.4 - - - +
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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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19D LEU* 3.5 24.4 - - + +
22D LEU* 3.6 21.5 - - + -
105D SER 2.9 10.4 + - - +
106D LEU 3.3 9.0 - - - +
108D GLN* 1.3 75.7 - - - +
110D LEU* 1.3 55.6 + - - +
112D ASP* 3.4 8.2 + - - +
113D LEU* 2.9 28.4 + - - +
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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
----------------------------------------------------------
19D LEU* 3.6 24.5 - - + -
23D TYR* 3.7 23.6 - - + +
106D LEU 3.0 16.8 + - - +
107D ASN* 3.5 8.7 - - - +
109D ALA* 1.3 71.5 - - - +
111D LEU* 1.3 58.2 + - - +
113D LEU* 3.2 5.8 + - - +
114D HIS* 2.7 36.8 + - - +
129D LEU* 4.1 11.9 - - + +
133D PHE* 3.7 38.6 - - + +
134D LEU* 3.7 16.4 - - + -
137D GLU* 4.0 25.4 - - + -
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Residues in contact with LEU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D ASN* 2.9 33.0 + - - +
108D GLN* 3.3 30.5 - - - +
110D LEU* 1.3 77.6 - - - +
112D ASP* 1.3 61.3 + - - +
114D HIS* 3.5 5.3 + - - +
115D ALA* 3.1 21.3 + - - +
134D LEU* 4.3 15.3 - - + -
6F GLN* 4.7 5.6 - - + +
7F ASN* 3.7 37.7 - - + +
123F PRO* 3.7 27.3 - - + +
124F HIS* 5.7 1.6 - - + +
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Residues in contact with ASP 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D GLN* 2.8 54.6 + - - +
109D ALA* 3.6 8.1 - - - +
111D LEU* 1.3 72.2 - - - +
113D LEU* 1.3 61.4 + - - +
115D ALA* 3.0 9.5 + - - +
116D LEU* 3.0 20.5 + - - +
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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
----------------------------------------------------------
12D VAL* 4.3 7.6 - - + -
15D ALA* 3.7 27.8 - - + +
16D VAL* 4.2 21.5 - - + +
19D LEU* 3.6 28.7 - - + -
65D LEU* 5.2 1.3 - - + -
109D ALA 2.9 17.9 + - - +
110D LEU* 3.7 4.5 - - - +
112D ASP* 1.3 74.2 - - - +
114D HIS* 1.3 63.6 + - - +
116D LEU* 3.1 15.6 + - + +
117D GLY* 2.9 20.1 + - - -
125D LEU* 3.7 18.0 - - + +
129D LEU* 3.7 22.7 - - + -
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Residues in contact with HIS 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D LEU 2.7 21.8 + - - +
111D LEU* 3.5 9.2 - - - +
113D LEU* 1.3 74.0 - - - +
115D ALA* 1.3 57.3 + - - +
117D GLY* 3.3 2.6 + - - -
118D SER* 2.9 32.6 + - - -
126D CYS* 3.7 32.8 - - + +
129D LEU* 3.7 14.0 - - + +
130D GLU* 2.8 32.7 + - + +
134D LEU* 3.9 15.5 - - + -
123F PRO* 3.5 33.6 - - + +
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Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D LEU 3.1 12.7 + - - +
112D ASP* 3.0 13.7 + - - +
114D HIS* 1.3 73.6 + - - +
116D LEU* 1.3 65.7 + - - +
118D SER* 3.1 10.2 + - - -
119D ALA* 2.9 23.8 + - - +
121F ALA* 6.3 2.7 - - + -
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D GLU* 3.8 43.1 - - + +
12D VAL* 3.9 8.5 - - + -
15D ALA* 3.8 19.3 - - + -
18D ARG* 5.6 2.2 - - - +
112D ASP 3.0 10.9 + - - +
113D LEU* 3.3 11.7 - - + +
115D ALA* 1.3 75.7 - - - +
117D GLY* 1.3 52.0 + - - +
119D ALA* 3.0 9.5 + - + +
120D GLN* 2.8 63.7 + - + +
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Residues in contact with GLY 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D VAL* 4.5 4.0 - - - +
113D LEU 2.9 10.5 + - - -
114D HIS 3.6 2.9 - - - -
116D LEU* 1.3 75.2 - - - +
118D SER* 1.3 53.6 + - - +
120D GLN* 3.6 0.6 + - - -
121D ALA 3.1 6.9 + - - -
122D ASP* 2.7 37.3 + - - +
125D LEU* 3.5 26.6 - - - +
126D CYS* 3.6 8.7 - - - -
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Residues in contact with SER 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D HIS* 2.9 25.8 + - - -
115D ALA* 3.1 14.4 + - - -
117D GLY* 1.3 73.9 - - - +
119D ALA* 1.3 61.3 + - - +
121D ALA* 3.2 13.2 + - - +
122D ASP 4.8 0.2 - - - +
126D CYS* 3.4 11.5 - - - -
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Residues in contact with ALA 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D ALA 2.9 13.6 + - - +
116D LEU* 3.4 13.5 - - + +
118D SER* 1.3 75.8 - - - +
120D GLN* 1.3 67.6 + - + +
121D ALA* 3.2 2.9 + - - +
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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