Contacts of the helix formed by residues 138 - 168 (chain A) in PDB entry 6XPD
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 ARG 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLY 4.8 1.4 + - - -
136A TRP 3.5 0.4 - - - -
137A HIS* 1.3 74.2 - - - +
139A ALA* 1.3 62.0 + - - +
140A GLU 3.0 1.1 - - - -
141A ILE* 3.2 13.7 + - + +
142A LEU* 2.9 25.3 + - + +
273A LEU* 2.6 31.9 + - - +
274A LEU* 3.3 30.8 + - + +
276A GLU* 4.4 4.4 + - - +
306A TRP* 4.1 5.7 - - - -
307A SER 2.9 25.6 + - - -
308A LEU* 4.0 20.0 - - + +
309A THR* 4.0 9.9 - - - +
138B ARG* 5.8 0.2 - - - -
274B LEU 3.3 24.4 + - - +
275B MET* 4.1 17.1 + - + +
276B GLU* 2.6 42.5 + - - +
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A SER* 3.9 7.2 + - - +
123A LEU* 3.9 26.7 - - + -
124A SER 4.4 1.8 - - - +
136A TRP* 3.2 24.0 + - + +
137A HIS 2.6 5.7 + - - -
138A ARG* 1.3 74.5 - - - +
140A GLU* 1.3 60.8 + - - +
142A LEU* 3.3 8.6 + - - +
143A GLY* 2.9 21.5 + - - -
275B MET* 4.4 18.4 - - - -
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Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR* 5.5 0.3 - - - -
120A SER* 4.1 16.5 - - - +
121A LEU* 3.2 24.7 - - + +
124A SER* 2.9 33.7 + - - -
137A HIS 2.9 8.1 + - - +
139A ALA* 1.3 79.2 - - - +
141A ILE* 1.3 63.0 + - - +
143A GLY* 3.3 0.7 + - - -
144A ALA* 2.9 24.4 + - - +
211A ASN* 5.3 5.7 - - - +
212A ALA* 4.1 21.4 + - + +
213A SER* 4.8 12.3 - - - +
309A THR* 3.6 27.1 + - + -
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Residues in contact with ILE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ARG* 3.2 17.7 + - + +
140A GLU* 1.3 79.0 - - - +
142A LEU* 1.3 58.6 + - - +
144A ALA* 3.5 6.8 - - - +
145A LEU* 2.9 28.9 + - + +
212A ALA* 4.4 12.6 - - + -
270A PHE* 4.4 22.1 - - + +
273A LEU* 3.7 28.0 - - + -
274A LEU* 3.7 35.4 - - + -
308A LEU 4.8 0.7 - - - -
309A THR* 3.3 41.1 - - - +
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ARG* 2.9 17.7 + - + +
139A ALA* 3.6 6.3 - - - +
141A ILE* 1.3 76.6 - - - +
143A GLY* 1.3 63.2 + - - +
145A LEU* 3.3 6.9 + - + +
146A LEU* 2.9 24.4 + - - +
274A LEU* 4.3 18.2 - - + -
145B LEU* 5.1 7.6 - - + -
271B SER* 4.5 19.3 - - - +
274B LEU* 4.1 29.6 - - + -
275B MET* 3.8 32.3 - - + -
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Residues in contact with GLY 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.8 8.9 - - - +
117A SER* 6.0 1.3 - - - -
120A SER* 3.5 24.0 - - - -
139A ALA 2.9 11.7 + - - -
140A GLU 3.8 0.4 - - - -
142A LEU* 1.3 75.8 - - - +
144A ALA* 1.3 53.0 + - - +
146A LEU* 3.3 6.8 + - - +
147A SER* 2.7 38.6 + - - -
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Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER* 6.1 0.2 - - - -
120A SER* 5.3 0.2 - - - -
140A GLU 2.9 17.7 + - - +
141A ILE* 3.5 3.4 - - - +
143A GLY* 1.3 77.0 - - - +
145A LEU* 1.3 57.8 + - - +
147A SER* 3.2 4.6 + - - -
148A ILE* 2.9 34.0 + - - +
212A ALA 3.9 4.5 - - - +
213A SER* 5.4 0.9 - - - -
216A ALA* 3.5 24.2 - - + +
270A PHE* 3.4 31.6 - - + -
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Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE 2.9 16.3 + - - +
142A LEU* 3.8 7.6 - - + +
144A ALA* 1.3 76.0 - - - +
146A LEU* 1.3 58.6 + - - +
148A ILE* 3.3 3.6 + - + +
149A LEU* 2.9 45.2 + - + +
267A LEU* 3.6 30.3 - - + +
270A PHE* 3.8 33.2 - - + +
271A SER* 5.0 4.9 - - - +
274A LEU* 3.7 26.5 - - + -
142B LEU* 5.1 9.0 - - + -
145B LEU* 6.3 2.9 - - + -
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 4.7 21.8 - - + -
142A LEU 2.9 16.6 + - - +
143A GLY* 3.6 7.9 - - - +
145A LEU* 1.3 77.8 - - - +
147A SER* 1.3 62.7 + - - +
149A LEU* 3.3 8.1 + - + -
150A CYS* 2.9 42.4 + - - -
149B LEU* 4.4 28.7 - - + -
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Residues in contact with SER 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A SER* 4.8 10.9 + - - -
116A LEU* 3.5 19.2 - - - +
117A SER* 4.3 10.8 + - - -
143A GLY 2.7 23.0 + - - -
144A ALA* 3.6 7.0 - - - -
146A LEU* 1.3 75.2 - - - +
148A ILE* 1.3 63.5 + - - +
150A CYS* 3.2 10.0 + - - +
151A ILE* 2.9 27.9 + - - +
216A ALA* 5.1 7.2 - - - -
220A HIS* 4.0 14.5 + - - -
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Residues in contact with ILE 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ALA 2.9 22.8 + - - +
145A LEU* 3.8 5.2 - - + +
147A SER* 1.3 77.9 - - - +
149A LEU* 1.3 64.6 + - - +
151A ILE* 3.0 12.9 + - + +
152A TRP* 3.0 22.5 + - + -
216A ALA* 4.1 23.1 - - + +
219A VAL* 4.2 22.9 - - + -
220A HIS* 4.9 1.6 - - + +
263A THR* 3.9 21.1 - - + -
266A ILE* 4.3 20.6 - - + -
267A LEU* 3.7 34.1 - - + -
270A PHE* 5.8 0.2 - - + -
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Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 2.9 34.1 + - + +
146A LEU* 3.8 5.4 - - + +
148A ILE* 1.3 77.4 - - - +
150A CYS* 1.3 58.7 + - - +
152A TRP* 3.2 13.1 + - + +
153A VAL* 2.9 32.3 + - + +
267A LEU* 4.7 21.5 - - + -
146B LEU* 4.4 26.5 - - + -
149B LEU* 3.7 29.6 - - + -
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Residues in contact with CYS 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE* 6.6 0.2 - - + -
116A LEU* 6.1 3.8 - - - -
146A LEU* 2.9 39.4 + - - +
147A SER* 3.4 11.7 - - - +
148A ILE 3.1 0.2 - - - -
149A LEU* 1.3 75.7 - - - +
151A ILE* 1.3 61.1 + - - +
153A VAL* 3.7 8.2 - - - +
154A VAL* 2.9 37.9 + - + +
220A HIS* 5.4 5.2 - - + -
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Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A HIS* 6.0 3.1 - - + -
109A ILE* 6.1 0.9 - - + -
147A SER 2.9 10.3 + - - +
148A ILE* 3.0 15.7 + - + +
150A CYS* 1.3 76.7 - - - +
152A TRP* 1.3 65.8 + - + +
154A VAL* 3.9 7.6 - - + +
155A THR* 2.9 28.3 + - - +
219A VAL 5.3 1.3 - - - +
220A HIS* 3.1 59.6 - - + +
223A GLY* 5.7 1.8 - - - -
224A ASN* 4.5 6.1 - - - +
259A VAL* 4.1 21.3 - - + -
260A LEU* 5.6 1.3 - - + -
263A THR* 3.6 27.1 - - + +
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Residues in contact with TRP 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ILE* 3.0 31.0 + - + -
149A LEU* 3.2 17.5 + - + +
151A ILE* 1.3 77.6 - - + +
153A VAL* 1.3 59.1 + - + +
155A THR* 3.5 4.3 + - - -
156A GLY* 2.9 25.8 + - - -
260A LEU* 3.5 47.2 - - + +
263A THR* 3.2 37.0 + - + -
264A ILE* 4.0 24.2 - - + -
267A LEU* 3.5 18.3 - - + +
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Residues in contact with VAL 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LEU* 2.9 22.1 + - + +
150A CYS* 3.7 7.9 - - - +
151A ILE 3.2 0.2 - - - -
152A TRP* 1.3 78.3 - - + +
154A VAL* 1.3 63.1 + - + +
156A GLY* 3.2 2.7 + - - -
157A VAL* 2.9 37.0 + - + +
153B VAL* 4.0 36.6 - - + -
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Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A HIS* 3.9 28.7 - - + +
109A ILE* 4.3 31.9 - - + -
150A CYS* 2.9 23.0 + - + +
151A ILE* 4.0 8.7 - - + +
153A VAL* 1.3 80.4 - - + +
155A THR* 1.3 60.0 + - - +
157A VAL* 3.2 10.0 + - + +
158A LEU* 2.9 32.7 + - + +
220A HIS* 6.5 0.4 - - + -
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Residues in contact with THR 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 2.9 22.1 + - - +
152A TRP 3.9 2.7 - - - -
154A VAL* 1.3 77.6 - - - +
156A GLY* 1.3 66.7 + - - +
158A LEU* 3.2 8.6 + - + +
159A VAL* 2.9 25.6 + - + +
256A SER* 3.6 28.0 - - - +
259A VAL* 4.1 17.7 - - - +
260A LEU* 3.5 29.6 - - + -
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Residues in contact with GLY 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A TRP 2.9 15.9 + - - -
153A VAL* 3.2 3.8 + - - -
155A THR* 1.3 77.2 - - - +
157A VAL* 1.3 61.1 + - - +
159A VAL* 3.2 7.9 + - - +
160A TYR* 2.9 23.7 + - - +
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A VAL* 2.9 26.4 + - + +
154A VAL* 3.5 12.1 - - + +
156A GLY* 1.3 75.7 - - - +
158A LEU* 1.3 67.5 + - + +
160A TYR* 3.2 7.6 + - - +
161A LEU* 3.0 37.8 + - + +
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A HIS* 3.9 22.4 - - + +
154A VAL* 2.9 21.1 + - + +
155A THR* 3.2 8.7 + - + +
157A VAL* 1.3 79.1 - - + +
159A VAL* 1.3 58.3 + - + +
161A LEU* 3.3 16.1 + - + +
162A ALA* 2.9 28.4 + - - +
227A GLN* 3.5 39.3 - - - +
252A THR* 5.5 7.4 - - + +
256A SER* 5.5 2.2 - - - +
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Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A THR* 2.9 24.8 + - + +
156A GLY* 3.6 7.2 - - - +
158A LEU* 1.3 75.0 - - - +
160A TYR* 1.3 59.2 + - - +
162A ALA* 3.2 8.1 + - - +
163A CYS* 2.9 26.8 + - + +
252A THR* 4.9 3.8 - - - +
253A PHE* 4.0 24.5 - - + -
256A SER* 3.6 31.9 - - - +
257A ILE* 6.3 1.3 - - + -
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Residues in contact with TYR 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A GLY 2.9 13.3 + - - +
157A VAL* 3.2 8.9 + - - +
159A VAL* 1.3 78.5 - - - +
161A LEU* 1.3 70.2 + - + +
163A CYS* 3.2 17.8 + - + +
164A GLU* 2.9 39.1 + - + +
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A VAL* 3.0 32.8 + - + +
158A LEU* 3.7 15.5 - - + +
160A TYR* 1.3 90.1 - - + +
162A ALA* 1.3 57.6 + - - +
164A GLU* 3.3 25.7 + - - +
165A ARG* 2.9 37.0 + - + +
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Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU 2.9 14.9 + - - +
159A VAL* 3.2 9.4 + - - +
161A LEU* 1.3 74.1 - - - +
163A CYS* 1.3 65.7 + - - +
165A ARG* 3.2 16.1 + - - +
166A LEU* 2.9 22.2 + - - +
249A PRO* 4.3 10.3 - - + +
252A THR* 3.5 31.9 - - + +
253A PHE* 4.0 11.9 - - + -
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Residues in contact with CYS 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A VAL* 2.9 14.2 + - + +
160A TYR* 3.5 23.8 - - + +
162A ALA* 1.3 74.7 - - - +
164A GLU* 1.3 59.1 + - - +
166A LEU* 3.2 13.7 + - - +
167A LEU* 2.9 44.5 + - - +
253A PHE* 4.5 14.5 - - + -
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Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TYR* 2.9 25.1 + - + +
161A LEU* 3.4 31.9 - - - +
162A ALA 3.2 0.2 - - - -
163A CYS* 1.3 75.1 - - - +
165A ARG* 1.3 69.1 + - + +
167A LEU* 3.1 6.8 + - - +
168A TYR* 2.8 41.2 + - + +
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Residues in contact with ARG 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 2.9 20.7 + - + +
162A ALA* 3.5 14.0 - - - +
164A GLU* 1.3 78.0 - - + +
166A LEU* 1.3 62.6 + - - +
168A TYR* 3.1 23.6 - - - +
169A PRO* 3.4 5.5 - - - +
171A TYR* 3.7 43.2 + - + +
173A ILE* 6.3 0.8 - - - +
248A ASP* 3.4 39.7 + - - +
249A PRO* 3.8 18.6 - - + +
252A THR* 4.8 10.8 + - - +
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ALA 2.9 12.9 + - - +
163A CYS* 3.2 15.0 - - - +
164A GLU 3.1 0.2 - - - -
165A ARG* 1.3 76.7 - - - +
167A LEU* 1.3 91.1 + - + +
168A TYR 3.0 5.4 + - - -
169A PRO* 3.1 22.5 - - - +
246A ILE* 5.8 13.5 - - + +
249A PRO* 4.4 27.0 - - + +
250A ILE* 6.2 2.5 - - + -
253A PHE* 5.6 9.6 - - + -
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A CYS* 2.9 34.8 + - - +
164A GLU* 3.1 3.1 + - - -
166A LEU* 1.3 88.4 - - + +
168A TYR* 1.3 78.6 + - + +
169A PRO* 3.4 7.0 - - - +
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Residues in contact with TYR 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLU* 2.8 33.2 + - + +
165A ARG* 3.1 11.2 - - - +
166A LEU 3.0 0.2 + - - -
167A LEU* 1.3 97.5 - - + +
169A PRO* 1.3 58.5 - - - +
170A ASP* 2.7 23.2 + - + +
171A TYR* 3.4 9.7 - - - +
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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