Contacts of the helix formed by residues 134 - 157 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D PHE* 3.7 2.0 - - - -
132D LEU* 3.6 1.2 - - - +
133D ALA* 1.3 78.9 - - - +
135D LYS* 1.3 64.0 + - - +
136D ALA* 3.7 3.1 + - - +
137D LEU* 3.6 39.9 + - - +
138D SER* 3.0 25.1 + - - -
130E GLU* 3.3 25.0 + - - -
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Residues in contact with LYS 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D VAL* 4.2 20.6 - - + +
103D PHE* 3.3 46.9 - - + -
105D VAL* 5.6 1.8 - - + -
134D SER* 1.3 72.7 + - - +
136D ALA* 1.3 64.7 + - - +
138D SER* 3.2 4.4 + - - -
139D LEU* 2.9 33.4 + - + +
95E PHE* 3.6 37.6 - - + +
97E ASP* 3.4 28.8 + - - -
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Residues in contact with ALA 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D SER* 3.3 5.9 + - - +
135D LYS* 1.3 78.8 - - - +
137D LEU* 1.3 58.0 + - - +
140D GLU* 2.9 31.1 + - - +
95E PHE* 3.5 24.2 - - + -
105E VAL 4.7 1.1 - - - +
106E GLY* 4.6 2.7 - - - -
126E TYR* 3.8 12.4 - - + -
128E VAL* 3.7 38.1 - - + -
130E GLU* 5.1 3.1 - - + -
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D LEU* 4.0 32.3 - - + +
134D SER* 3.3 30.4 + - - +
135D LYS 3.3 0.4 - - - -
136D ALA* 1.3 82.2 - - + +
138D SER* 1.3 63.2 + - - +
140D GLU* 3.4 16.8 + - - +
141D LYS* 2.9 25.8 + - - +
58E GLY* 5.7 5.4 - - - +
128E VAL* 4.8 6.7 - - + -
130E GLU* 4.1 13.2 - - - +
16L T 5.7 5.2 - - - +
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Residues in contact with SER 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D PHE* 3.8 18.3 + - - +
105D VAL* 3.8 21.1 - - - -
129D SER* 3.1 32.2 + - - -
132D LEU* 3.8 11.7 - - - +
134D SER 3.0 14.5 + - - -
135D LYS 3.6 8.1 - - - -
137D LEU* 1.3 77.0 - - - +
139D LEU* 1.3 56.2 + - - +
141D LYS 3.4 0.2 + - - -
142D ALA* 2.9 30.4 + - - +
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Residues in contact with LEU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D VAL* 4.6 15.0 - - + -
96D VAL* 4.2 14.1 - - + -
105D VAL* 3.6 25.4 - - + -
107D VAL* 4.7 4.9 - - + -
135D LYS* 2.9 21.2 + - + +
136D ALA 3.9 0.2 - - - +
138D SER* 1.3 72.4 - - - +
140D GLU* 1.3 67.3 + - - +
142D ALA* 4.4 2.5 - - - +
143D ARG* 3.0 34.8 + - + +
94E ASP* 3.7 17.7 - - + +
95E PHE* 3.6 25.1 - - + -
126E TYR* 3.2 31.9 - - + +
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Residues in contact with GLU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ALA 2.9 17.5 + - - +
137D LEU* 3.6 16.3 - - - +
139D LEU* 1.3 77.2 - - - +
141D LYS* 1.3 63.0 + - - +
143D ARG* 4.6 0.6 - - - +
144D LYS* 3.2 54.8 + - + +
301D K 2.8 27.1 - - - -
126E TYR* 3.8 29.1 - - + +
128E VAL* 4.1 14.8 - - - +
16L T 3.5 17.4 - - - +
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Residues in contact with LYS 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D VAL 3.3 24.9 + - - +
129D SER* 3.8 17.3 + - - +
130D GLU 5.4 0.8 - - - +
132D LEU* 4.9 10.4 - - + +
137D LEU 2.9 17.8 + - - +
138D SER 3.7 3.6 - - - +
140D GLU* 1.3 78.1 - - - +
142D ALA* 1.3 63.3 + - - +
144D LYS* 4.1 2.0 - - - +
145D GLU* 2.9 39.6 + - + +
13L T 5.5 3.9 + - - -
14L T 3.4 31.4 - - - +
15L T 5.0 13.9 - - + +
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Residues in contact with ALA 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D VAL* 4.0 13.9 - - + +
107D VAL* 3.7 26.6 - - + +
127D GLY* 3.3 27.9 - - - +
128D VAL 4.2 3.4 - - - +
129D SER 4.7 2.2 - - - +
138D SER 2.9 18.8 + - - +
139D LEU 3.2 2.2 + - - +
141D LYS* 1.3 77.2 - - - +
143D ARG* 1.3 58.2 + - - +
146D ALA* 2.9 27.0 + - - +
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Residues in contact with ARG 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D GLN* 2.4 56.3 + - - +
93D VAL* 3.8 23.7 - - - +
107D VAL* 3.9 17.3 - - + -
139D LEU* 3.0 21.4 + - + +
140D GLU* 4.6 1.8 - - - +
142D ALA* 1.3 76.5 - - - +
144D LYS* 1.3 64.4 + - + +
146D ALA* 3.2 1.0 + - - +
147D VAL* 3.0 21.2 + - - +
92E ASN* 5.0 5.3 - - - +
94E ASP* 2.8 27.9 + - - -
108E CYS* 2.7 47.1 - - - -
110E PHE* 4.4 5.1 - - - -
124E VAL* 4.4 11.2 - - + -
126E TYR* 4.2 9.2 - - + -
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Residues in contact with LYS 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D GLU* 3.2 50.4 + - + +
141D LYS* 4.2 2.2 - - - +
142D ALA 3.4 0.2 - - - -
143D ARG* 1.3 77.2 - - + +
145D GLU* 1.3 62.4 + - - +
147D VAL* 3.3 3.4 + - - +
148D THR* 2.9 30.1 + - - -
124E VAL* 4.7 11.0 - - + -
125E GLY* 4.3 2.7 - - - -
126E TYR* 4.0 14.8 - - - +
149E ASP* 2.7 30.9 + - - -
153E ARG* 3.7 37.2 + - - +
14L T 5.5 0.4 - - - +
15L T 4.3 12.8 - - - +
16L T 3.3 20.4 + - - +
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Residues in contact with GLU 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C K 4.2 13.3 - - - -
126D TYR 3.8 9.6 - - - +
127D GLY* 3.8 2.5 - - - -
128D VAL* 3.5 26.3 + - - +
141D LYS* 2.9 47.1 + - + +
142D ALA 3.8 2.9 - - - +
144D LYS* 1.3 76.8 - - - +
146D ALA* 1.3 57.2 + - - +
148D THR* 3.9 1.2 - - - -
149D ASP* 2.9 35.2 + - + +
13L T 5.2 9.1 - - - +
14L T 4.2 37.9 + - - +
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Residues in contact with ALA 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D VAL* 3.6 17.5 - - + +
108D CYS 4.0 0.7 - - - -
109D ALA* 3.9 14.7 - - + +
125D GLY* 3.4 17.8 - - - +
126D TYR 3.4 11.7 - - - -
127D GLY* 3.4 13.2 - - - +
142D ALA 2.9 19.1 + - - +
143D ARG 3.2 4.7 + - - +
145D GLU* 1.3 77.3 - - - +
147D VAL* 1.3 57.0 + - - +
150D GLY* 2.9 25.1 + - - -
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Residues in contact with VAL 147 (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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86D HIS* 5.0 5.2 - - + +
88D ILE* 3.6 24.7 - - + -
91D GLN* 3.3 27.1 - - - +
109D ALA* 3.7 12.6 - - + -
111D VAL* 3.4 9.1 - - + +
143D ARG 3.0 10.8 + - - +
144D LYS 3.9 2.5 - - - +
146D ALA* 1.3 75.1 - - - +
148D THR* 1.3 59.9 + - - +
150D GLY 3.3 0.9 + - - -
151D LEU* 2.9 26.9 + - + +
122E GLU 4.8 1.6 - - - +
123E ASP* 3.7 31.2 - - - +
124E VAL* 3.5 18.8 - - + -
153E ARG* 4.7 0.2 - - - +
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Residues in contact with THR 148 (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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68D GLY* 4.4 19.3 - - - -
72D ILE* 6.3 3.1 - - + -
144D LYS 2.9 18.0 + - - -
145D GLU* 3.9 4.3 - - - -
147D VAL* 1.3 77.5 - - - +
149D ASP* 1.3 57.5 + - - +
151D LEU* 3.2 12.1 + - + +
152D LYS* 2.9 33.4 + - + +
123E ASP* 5.0 0.7 + - - -
153E ARG* 3.1 10.6 + - - -
14L T 4.7 10.5 - - - +
15L T 3.1 33.1 + - - +
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Residues in contact with ASP 149 (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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140C GLU* 5.3 1.4 - - - +
144C LYS* 2.9 35.9 + - - -
125D GLY* 3.6 3.6 - - - -
126D TYR 3.8 15.0 - - - +
145D GLU* 2.9 20.8 + - + +
146D ALA 3.8 2.2 - - - +
148D THR* 1.3 77.0 - - - +
150D GLY* 1.3 56.6 + - - +
152D LYS* 3.3 29.9 + - - +
153D ARG* 2.9 30.1 + - - +
12L T 3.6 10.4 + - - +
13L T 4.2 5.9 + - - -
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Residues in contact with GLY 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D VAL* 3.5 16.8 - - - +
123D ASP 4.1 2.6 - - - +
124D VAL 3.5 19.1 - - - -
125D GLY* 3.3 9.1 - - - -
146D ALA 2.9 12.9 + - - -
147D VAL 3.7 3.4 - - - -
149D ASP* 1.3 73.9 - - - +
151D LEU* 1.3 59.0 + - - +
153D ARG* 3.4 1.0 + - - +
154D ALA* 2.9 31.9 + - - +
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Residues in contact with LEU 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ILE* 4.4 21.8 - - + -
84D TRP* 3.8 18.4 - - + -
86D HIS* 3.6 47.1 - - + +
111D VAL* 3.5 10.0 - - + +
113D VAL* 3.7 13.7 - - + -
147D VAL* 2.9 15.5 + - + +
148D THR* 3.5 14.4 - - + +
150D GLY* 1.3 75.1 - - - +
152D LYS* 1.3 59.0 + - + +
154D ALA* 3.3 1.5 + - - -
155D LEU* 2.9 43.3 + - + +
123E ASP* 5.7 2.5 - - - +
157E SER* 4.8 2.0 - - - +
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Residues in contact with LYS 152 (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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65D TYR* 5.3 0.8 - - - +
66D ILE* 3.7 22.4 + - + +
68D GLY* 4.4 9.4 - - - +
71D VAL* 4.2 25.7 - - + +
148D THR* 2.9 21.2 + - + +
149D ASP* 3.3 32.9 + - - +
151D LEU* 1.3 76.2 - - + +
153D ARG* 1.3 58.8 + - + +
155D LEU* 3.3 5.6 + - - +
156D ARG* 2.9 40.4 + - + +
162D LEU 4.7 1.6 - - - +
13L T 3.0 24.7 + - - -
14L T 2.9 25.4 + - - +
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Residues in contact with ARG 153 (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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144C LYS* 3.7 29.2 + - - +
147C VAL* 4.6 1.2 - - - +
148C THR* 3.2 10.9 + - - -
123D ASP* 2.9 49.0 + - - +
124D VAL 3.2 24.1 + - - +
149D ASP* 2.9 15.8 + - - +
150D GLY 3.9 0.7 - - - +
152D LYS* 1.3 77.6 - - + +
154D ALA* 1.3 60.4 + - - +
156D ARG* 3.4 31.9 - - - +
157D SER* 3.8 7.6 + - - -
11L T 3.0 38.7 + - - -
12L T 2.9 43.1 + - - +
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Residues in contact with ALA 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D VAL 3.7 19.5 - - - +
113D VAL* 3.6 24.8 - - + +
121D HIS* 3.7 28.3 + - - +
122D GLU 4.9 0.7 - - - -
123D ASP* 3.9 10.5 - - - +
150D GLY 2.9 19.1 + - - +
151D LEU 3.8 0.9 - - - +
153D ARG* 1.3 75.9 - - - +
155D LEU* 1.3 63.6 + - - +
156D ARG 3.2 0.6 + - - -
157D SER* 3.6 11.0 + - - -
158D PHE* 4.6 2.4 - - - -
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Residues in contact with LEU 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D VAL* 3.8 32.8 - - + +
72D ILE* 5.2 1.1 - - + +
75D ALA* 4.0 25.4 - - + -
79D PHE* 4.8 2.5 - - + -
84D TRP* 4.1 11.7 - - + -
113D VAL* 3.8 24.0 - - + -
151D LEU* 2.9 43.9 + - + +
152D LYS 3.9 3.4 - - - +
154D ALA* 1.3 74.1 - - - +
156D ARG* 1.3 65.5 + - - +
157D SER 3.2 0.6 + - - -
158D PHE* 3.4 25.3 + - + +
162D LEU* 3.3 27.0 - - + +
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Residues in contact with ARG 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ILE* 5.2 4.3 - - + -
152D LYS* 2.9 25.3 + - + +
153D ARG* 3.4 31.6 - - - +
154D ALA 3.2 0.4 - - - -
155D LEU* 1.3 76.9 - - - +
157D SER* 1.3 53.3 + - - +
158D PHE 2.8 12.0 + - - -
159D GLY 3.3 18.2 + - - +
162D LEU 3.7 8.0 + - - +
163D GLY* 3.5 28.6 + - - +
164D ASN* 3.5 18.0 - - - +
166D ILE* 3.4 25.2 - - - +
167D LEU* 3.6 24.1 - - - +
12L T 2.4 48.4 + - - -
13L T 5.6 1.0 + - - -
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Residues in contact with SER 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ILE* 4.1 24.5 - - - +
76C ASN* 3.3 17.9 + - - +
84C TRP* 3.7 9.3 - - - -
86C HIS* 3.9 16.8 + - - -
151C LEU* 5.0 0.5 - - - +
121D HIS* 3.4 40.6 - - - -
123D ASP* 4.7 2.8 + - - -
153D ARG 3.8 12.1 + - - -
154D ALA* 3.6 5.1 + - - -
155D LEU 3.2 1.8 - - - -
156D ARG* 1.3 73.6 - - - +
158D PHE* 1.3 56.2 + - - +
159D GLY 3.6 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