Contacts of the helix formed by residues 102 - 131 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LYS* 3.5 7.2 - - - +
101C TYR* 1.4 79.4 - - + +
103C ILE* 1.3 68.4 + - - +
104C HIS* 3.5 34.5 - - + +
105C ASP* 3.0 28.8 + - - +
106C HIS* 3.1 10.9 + - - -
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Residues in contact with ILE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 4.1 12.1 - - + -
44C LYS 3.1 20.8 + - - +
45C GLY* 3.6 20.4 - - - +
46C PRO* 5.8 0.9 - - + -
47C GLN* 3.5 24.2 - - + +
48C PHE* 3.4 35.9 - - - +
51C VAL* 4.3 18.6 - - + -
101C TYR 4.2 0.4 - - - -
102C LYS* 1.3 72.8 - - - +
104C HIS* 1.4 58.5 + - - +
106C HIS* 3.2 6.8 + - + +
107C LEU* 2.8 48.4 + - + +
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Residues in contact with HIS 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LYS* 3.5 37.7 - - + +
103C ILE* 1.4 79.3 - - - +
105C ASP* 1.4 73.3 + - - +
107C LEU* 3.8 11.2 - - + +
108C ASP* 3.0 42.3 + - - +
158C VAL* 5.5 5.7 - - + +
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Residues in contact with ASP 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C ILE* 3.7 33.4 - - + +
101C TYR 5.0 0.7 + - - -
102C LYS* 3.0 33.5 + - + +
104C HIS* 1.4 97.2 + - - +
106C HIS* 1.3 66.6 + - - +
108C ASP* 3.3 8.7 + - - +
109C ALA* 3.1 22.3 + - - +
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Residues in contact with HIS 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLN* 4.5 1.1 - - + -
39C ALA* 3.5 29.8 - - + +
42C ASN* 3.8 17.8 + - + -
43C LEU* 3.7 19.5 - - + -
51C VAL* 6.5 0.7 - - + -
55C LEU* 6.1 0.4 - - + -
96C TYR* 2.7 31.6 + + - +
97C PRO 5.0 0.9 - - - -
100C ILE* 2.9 40.2 + - + +
101C TYR* 3.4 27.5 - - - -
102C LYS 3.1 12.2 + - - -
103C ILE* 3.8 6.1 - - + +
105C ASP* 1.3 77.3 - - - +
107C LEU* 1.3 57.7 + - + +
109C ALA 3.2 0.7 + - - -
110C LEU* 2.8 38.0 + - + +
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Residues in contact with LEU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PRO* 6.4 0.4 - - + -
51C VAL* 4.5 17.3 - - + -
103C ILE* 2.8 37.9 + - + +
104C HIS* 3.8 7.9 - - + +
106C HIS* 1.3 75.5 - - + +
108C ASP* 1.3 57.5 + - - +
110C LEU* 3.8 5.9 - - + +
111C ILE* 2.8 38.6 + - + +
154C LEU* 3.8 35.2 - - + +
157C HIS* 3.8 33.4 - - + +
158C VAL* 3.8 20.6 - - + -
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Residues in contact with ASP 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C HIS* 3.0 32.2 + - - +
105C ASP* 3.7 8.9 - - - +
106C HIS 3.2 0.2 - - - -
107C LEU* 1.3 76.3 - - - +
109C ALA* 1.3 62.7 + - - +
111C ILE* 3.8 9.0 - - - +
112C GLU* 3.1 22.9 + - - +
158C VAL* 4.8 14.2 - - - +
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Residues in contact with ALA 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C TYR* 3.5 28.7 - - + +
97C PRO* 4.5 7.0 - - + -
100C ILE* 4.3 7.6 - - + -
105C ASP 3.1 16.8 + - - +
108C ASP* 1.3 77.9 - - - +
110C LEU* 1.3 62.9 + - - +
112C GLU* 3.5 3.3 + - - -
113C ARG* 2.9 44.4 + - - +
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Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C VAL* 3.5 31.0 - - + +
36C THR* 4.3 5.8 - - - -
39C ALA* 3.8 27.6 - - + -
51C VAL* 5.8 0.9 - - + -
55C LEU* 3.9 24.7 - - + -
96C TYR* 3.8 5.8 - - - +
106C HIS* 2.8 27.4 + - + +
107C LEU* 3.9 7.6 - - + +
109C ALA* 1.3 75.3 - - - +
111C ILE* 1.3 57.8 + - - +
113C ARG* 3.2 2.1 + - - -
114C TYR* 2.7 53.6 + - + +
154C LEU* 4.1 20.9 - - + -
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Residues in contact with ILE 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS* 3.6 30.8 - - + +
107C LEU* 2.8 26.8 + - + +
108C ASP* 3.8 8.3 - - - +
110C LEU* 1.3 76.1 - - - +
112C GLU* 1.3 63.6 + - - +
114C TYR* 4.6 1.1 - - - -
115C GLY* 2.8 22.3 + - - -
151C LEU* 4.0 2.8 - - + +
154C LEU* 3.6 44.0 - - + +
155C GLU* 3.9 20.9 - - + +
158C VAL* 3.8 26.0 - - + -
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Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS* 4.7 14.6 - - - +
94C LYS* 2.8 33.2 + - - +
108C ASP 3.1 13.4 + - - +
109C ALA* 3.7 8.5 - - - +
111C ILE* 1.3 77.6 - - - +
113C ARG* 1.3 78.3 + - - +
115C GLY* 3.9 0.9 - - - -
116C GLU* 3.0 44.3 + - - +
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Residues in contact with ARG 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.7 17.7 - - + -
35C VAL* 4.2 14.4 - - + -
93C LEU* 4.1 11.7 - - + -
94C LYS* 3.0 54.1 + - - +
95C ALA 3.0 17.0 + - - -
96C TYR* 3.8 26.5 - - - +
97C PRO* 4.0 4.8 - - - +
109C ALA* 2.9 42.5 + - - +
110C LEU* 3.2 3.9 + - - +
112C GLU* 1.3 92.7 + - - +
114C TYR* 1.3 60.6 + - - +
116C GLU* 3.3 6.4 + - - +
117C VAL* 3.0 34.1 + - - +
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Residues in contact with TYR 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.6 33.9 - - + -
36C THR* 2.7 29.2 + - + +
55C LEU* 5.5 0.7 - - + -
58C PHE* 3.3 34.1 - + + +
62C LEU* 3.5 9.2 - - + +
110C LEU* 2.7 43.8 + - + +
111C ILE 4.2 1.3 - - - +
113C ARG* 1.3 72.8 - - - +
115C GLY* 1.3 57.1 + - - +
117C VAL* 4.1 0.3 - - - +
118C ALA* 2.8 32.6 + - - +
147C LEU* 4.3 13.2 - - + +
150C SER* 3.9 30.5 - - - -
151C LEU* 4.2 13.5 - - + -
154C LEU* 3.6 21.8 - - + -
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Residues in contact with GLY 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS* 4.0 15.7 - - - -
111C ILE 2.8 18.6 + - - -
112C GLU 3.9 1.3 - - - -
114C TYR* 1.3 77.8 - - - +
116C GLU* 1.3 55.7 + - - +
118C ALA* 3.8 0.9 - - - +
119C ASN* 2.9 40.8 + - - -
151C LEU* 3.8 18.5 - - - +
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Residues in contact with GLU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LYS* 4.4 4.6 - - + +
93C LEU* 3.4 19.0 - - + +
94C LYS* 2.5 44.4 + - - -
112C GLU* 3.0 24.0 + - + +
113C ARG* 3.7 4.0 - - - +
114C TYR 3.3 0.2 - - - -
115C GLY* 1.3 73.7 - - - +
117C VAL* 1.3 60.2 + - - +
119C ASN* 3.4 6.1 + - - +
120C MET* 2.9 34.3 + - + +
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Residues in contact with VAL 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C SER* 4.0 25.6 - - - +
29C VAL* 4.1 24.0 - - + +
32C LEU* 4.0 20.0 - - + -
62C LEU* 5.5 0.2 - - + -
93C LEU* 3.9 18.2 - - + -
113C ARG 3.0 21.1 + - - +
114C TYR 4.1 0.4 - - - +
116C GLU* 1.3 74.8 - - - +
118C ALA* 1.3 67.3 + - - +
120C MET* 3.2 8.2 + - + +
121C ILE* 2.9 32.0 + - + +
147C LEU* 4.0 22.2 - - + -
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Residues in contact with ALA 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C TYR 2.8 19.4 + - - +
115C GLY 3.8 3.8 - - - +
117C VAL* 1.3 78.1 - - - +
119C ASN* 1.4 56.2 + - - +
121C ILE* 3.4 2.4 + - - +
122C ARG* 2.9 35.3 + - - +
144C SER* 5.1 2.5 + - - +
147C LEU* 4.0 29.7 - - + +
148C ASP* 3.6 22.8 - - - +
151C LEU* 4.4 10.1 - - + -
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Residues in contact with ASN 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS* 2.9 23.8 + - - +
8A ASN* 3.8 2.0 - - - -
9A ASP* 3.0 41.7 + - - +
115C GLY* 2.9 25.1 + - - +
116C GLU* 3.9 4.6 - - - +
118C ALA* 1.4 74.9 - - - +
120C MET* 1.3 63.9 + - - +
122C ARG* 2.8 29.3 + - - +
123C LYS* 3.1 22.5 + - - +
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Residues in contact with MET 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLU* 4.4 20.9 - - - +
25C SER* 3.8 30.1 - - - +
28C SER* 3.7 35.4 - - - +
92C LYS* 4.0 19.7 - - + -
93C LEU* 5.5 0.4 - - + -
116C GLU* 2.9 23.5 + - + +
117C VAL* 3.2 12.3 + - + +
119C ASN* 1.3 75.5 - - - +
121C ILE* 1.3 60.3 + - + +
123C LYS* 3.3 9.3 + - - +
124C ALA* 2.9 25.5 + - + +
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Residues in contact with ILE 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C SER* 3.6 30.1 - - - +
29C VAL* 4.4 14.6 - - + -
69C ILE* 4.5 4.7 - - + -
117C VAL* 2.9 25.3 + - + +
118C ALA 3.8 3.4 - - - +
120C MET* 1.3 77.0 - - + +
122C ARG* 1.3 64.6 + - - +
124C ALA* 3.1 4.4 + - - +
125C ILE* 3.1 21.8 + - - +
140C PHE* 3.2 41.7 - - + +
143C ALA* 4.1 6.1 - - + -
144C SER* 3.7 18.8 - - - +
147C LEU* 3.5 18.8 - - + -
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Residues in contact with ARG 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASN* 3.4 25.2 + - - +
9A ASP* 3.0 25.1 + - - -
10A LEU* 4.2 24.5 - - + +
11A PRO* 6.1 0.2 - - - -
72A ARG* 4.3 8.1 - - - +
133A ASP* 5.7 0.2 + - - -
134A PRO* 5.8 4.9 - - + +
135A THR* 4.8 3.0 + - - +
118C ALA* 2.9 21.1 + - - +
119C ASN* 2.8 23.9 + - - +
121C ILE* 1.3 77.3 - - - +
123C LYS* 1.3 61.3 + - - +
125C ILE* 3.4 27.6 + - + +
126C ASP* 3.6 12.6 + - - +
144C SER* 4.2 9.3 + - - +
148C ASP* 2.8 41.4 + - - -
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Residues in contact with LYS 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ASN 3.1 12.8 + - - +
120C MET* 3.6 10.3 - - - +
122C ARG* 1.3 78.7 - - - +
124C ALA* 1.3 58.8 + - - +
126C ASP* 3.1 11.1 + - + +
127C ASP* 2.7 57.2 + - - +
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Residues in contact with ALA 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ILE* 3.7 24.9 - - + -
25C SER* 4.2 4.0 - - - +
120C MET 2.9 14.7 + - - +
121C ILE* 3.1 10.5 + - - +
123C LYS* 1.3 75.1 - - - +
125C ILE* 1.3 65.5 + - - +
127C ASP* 4.4 3.8 - - - +
128C SER* 2.9 29.6 + - - -
140C PHE* 3.7 26.7 - - + -
----------------------------------------------------------
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Residues in contact with ILE 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PRO* 4.0 27.8 - - + -
135A THR* 3.5 24.5 - - - +
121C ILE 3.1 12.2 + - - +
122C ARG* 3.5 16.4 - - + +
123C LYS 3.2 0.2 - - - -
124C ALA* 1.3 75.1 - - - +
126C ASP* 1.3 60.6 + - - +
129C ASP* 2.9 30.3 + - + +
137C ALA* 3.6 15.2 - - + +
140C PHE* 3.7 21.1 - - + +
141C THR* 3.4 27.4 - - + +
144C SER* 3.8 17.0 - - - +
----------------------------------------------------------
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Residues in contact with ASP 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLY 5.1 5.0 - - - +
134A PRO* 3.6 26.5 - - - +
122C ARG* 3.6 12.5 + - - +
123C LYS* 3.1 10.9 + - + +
125C ILE* 1.3 83.1 - - - +
127C ASP* 1.3 60.6 + - - +
129C ASP* 3.4 4.0 + - - +
130C GLU* 2.9 50.1 + - - +
----------------------------------------------------------
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Residues in contact with ASP 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 5.2 0.9 - - - +
21C ILE* 3.7 23.1 - - + +
123C LYS* 2.7 57.6 + - - +
124C ALA* 4.2 4.2 + - - +
126C ASP* 1.3 80.9 - - - +
128C SER* 1.4 62.3 + - - +
130C GLU* 3.6 12.1 + - - +
131C ALA* 3.1 23.7 + - - +
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Residues in contact with SER 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C VAL* 4.2 8.3 - - - +
21C ILE* 4.1 12.2 - - - +
124C ALA 2.9 19.8 + - - -
125C ILE 3.7 3.1 - - - -
127C ASP* 1.4 76.6 - - - +
129C ASP* 1.3 62.7 + - - +
131C ALA* 3.2 9.4 + - - +
132C GLY 3.4 0.2 + - - -
133C ASP* 3.1 24.2 + - - +
136C THR* 3.5 10.0 - - - +
137C ALA* 3.8 24.0 - - - -
140C PHE* 3.4 19.3 - - - -
----------------------------------------------------------
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Residues in contact with ASP 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ILE* 2.9 21.3 + - + +
126C ASP* 3.8 4.7 - - - +
128C SER* 1.3 74.8 - - - +
130C GLU* 1.3 62.7 + - + +
132C GLY* 2.9 21.7 + - - -
133C ASP 4.4 3.4 - - - +
134C PRO* 3.9 24.9 - - - +
137C ALA* 3.9 11.0 - - + +
----------------------------------------------------------
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Residues in contact with GLU 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ASP* 2.9 36.6 + - - +
127C ASP* 4.0 12.2 - - - +
129C ASP* 1.3 81.4 - - + +
131C ALA* 1.3 60.0 + - - +
132C GLY* 3.2 1.3 + - - -
----------------------------------------------------------
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Residues in contact with ALA 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ALA* 3.3 24.9 - - - +
17C THR* 4.1 19.7 - - + -
18C VAL* 3.9 21.8 - - + -
127C ASP 3.1 17.5 + - - +
128C SER 3.6 6.3 - - - +
129C ASP 3.2 0.6 - - - -
130C GLU* 1.3 74.7 - - - +
132C GLY* 1.3 57.3 + - - +
----------------------------------------------------------
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il