Contacts of the helix formed by residues 134 - 157 (chain E) in PDB entry 5XRZ
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 SER 134 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E PHE* 3.7 1.8 - - - -
132E LEU* 3.6 2.0 - - - +
133E ALA* 1.3 77.8 - - - +
135E LYS* 1.3 64.6 + - - +
136E ALA* 3.8 2.9 + - - +
137E LEU* 3.7 34.2 + - - +
138E SER* 3.1 24.1 + - - -
130F GLU* 3.2 31.0 + - - -
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Residues in contact with LYS 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E VAL* 4.0 21.3 - - + +
103E PHE* 3.3 48.8 - - + -
105E VAL* 5.5 1.3 - - + -
134E SER* 1.3 72.5 + - - +
136E ALA* 1.3 58.3 + - - +
138E SER* 3.2 4.2 + - - -
139E LEU* 2.9 42.1 + - + +
95F PHE* 3.5 37.2 - - + +
97F ASP* 3.4 31.6 + - - +
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Residues in contact with ALA 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E SER* 3.3 6.5 + - - +
135E LYS* 1.3 78.5 - - - +
137E LEU* 1.3 59.0 + - - +
139E LEU 3.4 0.5 + - - -
140E GLU* 2.9 30.9 + - - +
95F PHE* 3.4 24.6 - - + -
105F VAL 4.6 0.7 - - - +
106F GLY* 4.4 2.9 - - - -
126F TYR* 3.7 12.6 - - + -
128F VAL* 3.6 37.2 - - + -
130F GLU* 5.1 2.7 - - + -
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Residues in contact with LEU 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E LEU* 3.8 34.1 - - + +
134E SER* 3.4 28.6 + - - +
135E LYS 3.3 0.4 - - - -
136E ALA* 1.3 83.0 - - + +
138E SER* 1.3 63.1 + - - +
140E GLU* 3.4 16.3 + - - +
141E LYS* 2.9 24.9 + - - +
58F GLY* 5.8 4.7 - - - +
128F VAL* 4.7 7.9 - - + -
130F GLU* 4.1 13.0 - - - +
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Residues in contact with SER 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E PHE* 3.7 17.3 + - - +
105E VAL* 3.8 19.7 - - - -
129E SER* 3.0 32.6 + - - -
132E LEU* 3.4 13.6 - - - +
134E SER 3.1 16.4 + - - -
135E LYS 3.6 4.7 - - - -
137E LEU* 1.3 77.0 - - - +
139E LEU* 1.3 57.8 + - - +
142E ALA* 2.9 30.9 + - - +
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Residues in contact with LEU 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E VAL* 4.5 16.6 - - + -
96E VAL* 3.9 16.2 - - + -
105E VAL* 3.6 26.0 - - + -
107E VAL* 4.7 1.8 - - + -
135E LYS* 2.9 23.2 + - + +
138E SER* 1.3 73.9 - - - +
140E GLU* 1.3 66.9 + - - +
142E ALA* 4.4 2.2 - - - +
143E ARG* 2.9 33.8 + - + +
94F ASP* 3.8 12.1 - - + +
95F PHE* 3.5 29.2 - - + -
126F TYR* 3.2 31.0 - - + +
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Residues in contact with GLU 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E ALA 2.9 15.9 + - - +
137E LEU* 3.6 16.4 - - - +
139E LEU* 1.3 75.7 - - - +
141E LYS* 1.3 63.5 + - - +
143E ARG* 4.1 0.8 - - - +
144E LYS* 2.7 69.6 + - + +
301E K 3.1 21.3 - - - -
126F TYR* 3.7 27.7 - - + +
128F VAL* 4.3 13.9 - - - +
19L C 5.1 2.0 - - - +
20L C 3.6 14.9 + - - +
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Residues in contact with LYS 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E VAL 3.3 19.3 + - - +
129E SER* 3.7 22.5 + - - +
130E GLU 5.1 2.0 - - - +
131E GLY 5.9 1.2 - - - +
132E LEU* 4.6 10.4 - - + +
137E LEU 2.9 18.1 + - - +
138E SER 3.7 3.4 - - - +
140E GLU* 1.3 77.8 - - - +
142E ALA* 1.3 62.7 + - - +
144E LYS* 4.2 1.9 - - - +
145E GLU* 2.9 42.3 + - - +
17L T 4.9 7.3 + - - +
18L T 3.5 33.6 - - - +
19L C 5.2 7.5 - - - +
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Residues in contact with ALA 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E VAL* 3.8 14.8 - - + +
107E VAL* 3.6 27.8 - - + +
127E GLY* 3.2 28.5 - - - +
128E VAL 4.0 2.7 - - - +
129E SER* 4.6 2.4 - - - +
138E SER 2.9 18.9 + - - +
139E LEU 3.3 1.3 + - - +
141E LYS* 1.3 76.8 - - - +
143E ARG* 1.3 57.2 + - - +
146E ALA* 2.9 27.2 + - - +
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Residues in contact with ARG 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E GLN* 2.5 52.4 + - - +
93E VAL* 3.8 23.8 - - - +
107E VAL* 3.9 19.1 - - + -
139E LEU* 2.9 24.2 + - + +
140E GLU* 4.2 2.7 - - - +
142E ALA* 1.3 75.8 - - - +
144E LYS* 1.3 63.8 + - + +
146E ALA* 3.2 3.1 + - - +
147E VAL* 3.0 21.2 + - - +
92F ASN* 5.0 5.5 - - - +
94F ASP* 2.8 27.8 + - - -
108F CYS* 2.8 40.9 - - - -
110F PHE* 4.2 6.8 - - - -
124F VAL* 4.6 11.4 - - + -
126F TYR* 4.1 15.7 - - + -
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Residues in contact with LYS 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E GLU* 2.7 50.5 + - + +
141E LYS 4.2 0.2 - - - +
143E ARG* 1.3 75.8 - - + +
145E GLU* 1.3 63.2 + - - +
147E VAL* 3.3 3.0 + - - -
148E THR* 3.0 28.0 + - - -
123F ASP* 5.2 0.7 - - - -
124F VAL* 4.7 9.0 - - + +
125F GLY* 4.2 2.5 - - - -
126F TYR* 3.9 15.0 - - + +
149F ASP* 2.6 24.5 + - - -
153F ARG* 3.4 28.8 + - - +
19L C 3.2 34.8 - - - +
20L C 2.3 29.0 + - - +
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Residues in contact with GLU 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D K 3.6 19.8 - - - -
55E ARG* 5.8 0.5 + - - -
126E TYR 3.7 8.7 - - - +
127E GLY* 3.9 3.6 - - - -
128E VAL* 3.5 35.9 + - - +
141E LYS* 2.9 33.1 + - + +
144E LYS* 1.3 76.6 - - - +
146E ALA* 1.3 58.0 + - - +
148E THR* 3.8 1.1 - - - -
149E ASP* 2.9 34.8 + - + +
17L T 4.6 13.0 + - - +
18L T 3.7 36.9 - - - +
19L C 4.3 1.4 - - - -
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Residues in contact with ALA 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E VAL* 3.6 17.0 - - + +
108E CYS 4.1 0.7 - - - -
109E ALA* 4.0 15.0 - - + +
125E GLY* 3.5 16.1 - - - +
126E TYR 3.4 13.6 + - - +
127E GLY 3.4 11.9 - - - +
142E ALA 2.9 18.6 + - - +
143E ARG 3.2 4.7 + - - +
145E GLU* 1.3 77.4 - - - +
147E VAL* 1.3 57.9 + - - +
150E GLY* 2.9 25.3 + - - -
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Residues in contact with VAL 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E HIS* 4.9 5.6 - - + -
88E ILE* 3.6 21.5 - - + -
91E GLN* 3.2 26.7 - - - +
109E ALA* 3.9 10.8 - - + -
111E VAL* 3.5 9.0 - - + +
143E ARG 3.0 11.7 + - - +
144E LYS 3.9 3.6 - - - +
146E ALA* 1.3 75.1 - - - +
148E THR* 1.3 59.7 + - - +
150E GLY 3.3 1.2 + - - -
151E LEU* 2.9 27.0 + - + +
122F GLU 4.7 1.8 - - - +
123F ASP* 3.4 35.2 - - - +
124F VAL* 3.5 18.4 - - + -
153F ARG* 4.5 0.4 - - - +
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Residues in contact with THR 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E GLY* 4.4 23.1 - - - -
72E ILE* 6.3 2.9 - - + -
144E LYS 3.0 12.7 + - - -
145E GLU 3.9 2.5 - - - -
147E VAL* 1.3 78.8 - - - +
149E ASP* 1.3 56.2 + - - +
151E LEU* 3.2 12.1 + - + +
152E LYS* 3.0 35.8 + - + +
123F ASP* 5.0 0.4 + - - -
153F ARG* 3.1 8.0 + - - -
18L T 3.8 16.4 - - - +
19L C 2.2 34.9 + - - +
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Residues in contact with ASP 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D GLU* 5.4 0.4 - - - -
144D LYS* 2.7 35.0 + - - -
301D K 4.3 1.9 - - - -
125E GLY* 3.6 3.1 - - - -
126E TYR 3.7 15.5 - - - +
145E GLU* 2.9 19.3 + - + +
146E ALA 3.8 2.0 - - - +
148E THR* 1.3 76.6 - - - +
150E GLY* 1.3 59.0 + - - +
152E LYS* 3.3 17.9 + - - +
153E ARG* 2.9 33.7 + - - +
16L T 3.4 16.0 - - - +
17L T 3.4 15.4 + - - -
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Residues in contact with GLY 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E VAL* 3.6 17.1 - - - +
123E ASP 4.2 3.1 - - - +
124E VAL 3.5 19.7 - - - -
125E GLY* 3.3 8.4 - - - -
146E ALA 2.9 12.1 + - - -
147E VAL 3.7 3.1 - - - -
149E ASP* 1.3 76.8 - - - +
151E LEU* 1.3 56.1 + - - +
153E ARG* 3.4 1.0 + - - +
154E ALA* 2.9 32.1 + - - +
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Residues in contact with LEU 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E ILE* 4.4 23.3 - - + -
84E TRP* 3.7 24.9 - - + -
86E HIS* 3.4 41.5 - - + +
111E VAL* 3.6 6.8 - - + +
113E VAL* 3.6 22.0 - - + -
147E VAL* 2.9 14.9 + - + +
148E THR* 3.2 13.2 + - + +
150E GLY* 1.3 75.8 - - - +
152E LYS* 1.3 58.4 + - + +
154E ALA* 3.3 1.4 + - - -
155E LEU* 2.9 38.2 + - + +
123F ASP* 5.6 2.0 - - - +
157F SER* 4.7 2.0 - - - +
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Residues in contact with LYS 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E ILE 3.6 18.4 + - - +
68E GLY* 4.0 16.8 - - - -
71E VAL* 4.2 23.2 - - + +
148E THR* 3.0 19.0 + - + +
149E ASP* 3.7 25.3 + - - +
151E LEU* 1.3 78.2 - - + +
153E ARG* 1.3 58.5 + - + +
155E LEU* 3.2 6.5 + - - +
156E ARG* 2.9 35.8 + - + +
162E LEU 4.7 1.4 - - - +
17L T 2.4 38.1 + - - -
18L T 2.5 26.5 + - - +
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Residues in contact with ARG 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D LYS* 3.7 38.6 + - - +
148D THR* 3.1 25.1 + - - +
123E ASP* 2.9 45.7 + - - +
124E VAL 3.2 20.0 + - - +
149E ASP* 2.9 20.9 + - - +
150E GLY 3.9 0.4 - - - +
152E LYS* 1.3 77.0 - - + +
154E ALA* 1.3 61.8 + - - +
156E ARG* 3.5 32.4 - - - +
157E SER* 3.9 5.5 + - - -
167E LEU* 5.6 0.2 - - - +
15L T 2.6 26.4 + - - -
16L T 3.2 32.0 + - - +
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Residues in contact with ALA 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D HIS* 5.8 0.2 - - - -
111E VAL 3.7 19.1 - - - +
113E VAL* 3.6 25.5 - - + +
121E HIS* 3.6 29.9 - - - +
123E ASP* 3.9 11.6 - - - +
150E GLY 2.9 18.6 + - - +
151E LEU* 3.8 0.7 - - - +
153E ARG* 1.3 77.2 - - - +
155E LEU* 1.3 62.4 + - - +
156E ARG 3.2 0.7 + - - -
157E SER* 3.6 10.9 + - - -
158E PHE* 4.6 1.4 - - - -
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Residues in contact with LEU 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E VAL* 3.8 31.4 - - + +
72E ILE* 5.2 1.1 - - + +
75E ALA* 4.0 25.4 - - + -
79E PHE* 4.5 2.5 - - + -
84E TRP* 4.2 11.4 - - + -
113E VAL* 3.8 29.6 - - + -
151E LEU* 2.9 40.5 + - + +
152E LYS* 3.2 4.0 + - - +
154E ALA* 1.3 75.4 - - - +
156E ARG* 1.3 65.9 + - - +
157E SER 3.2 0.6 + - - -
158E PHE* 3.3 27.5 + - + +
162E LEU* 3.3 25.5 - - + +
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Residues in contact with ARG 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ILE* 5.5 3.8 - - + -
65E TYR* 6.2 1.4 - - - +
152E LYS* 2.9 22.7 + - + +
153E ARG* 3.5 32.3 - - - +
154E ALA 3.2 0.2 - - - -
155E LEU* 1.3 77.8 - - - +
157E SER* 1.3 57.7 + - - +
158E PHE 2.8 8.0 + - - -
159E GLY 3.3 17.5 + - - +
162E LEU 3.8 7.8 + - - +
163E GLY* 3.6 28.4 + - - +
164E ASN* 3.4 17.7 - - - +
166E ILE* 3.5 24.5 - - - +
167E LEU* 3.4 27.5 - - - +
15L T 3.8 4.2 + - - -
16L T 2.3 45.1 + - - -
17L T 5.1 2.6 + - - -
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Residues in contact with SER 157 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ILE* 3.9 23.3 - - - +
76D ASN* 3.3 19.2 + - - +
84D TRP* 3.4 12.8 - - - -
86D HIS* 3.9 14.9 + - - -
151D LEU* 4.8 1.7 - - - +
121E HIS* 3.3 40.7 + - - -
123E ASP* 4.7 3.5 + - - -
153E ARG 3.9 10.6 + - - -
154E ALA 3.6 3.1 + - - -
155E LEU 3.2 1.6 - - - -
156E ARG* 1.3 74.8 - - - +
158E PHE* 1.3 55.5 + - - +
159E GLY 3.6 0.7 - - - -
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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