Contacts of the helix formed by residues 138 - 169 (chain A) in PDB entry 5CXV
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 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 4.3 2.2 - - - -
135A ALA 4.4 6.5 - - - +
136A LYS* 2.9 21.2 + - - +
137A ARG* 1.3 79.2 - - - +
139A PRO* 1.3 70.5 - - + +
140A ARG* 3.3 32.1 + - - +
141A ARG* 3.2 23.2 + - - +
142A ALA* 3.0 22.9 + - - +
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Residues in contact with PRO 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 4.0 17.9 - - + -
62A TYR* 3.4 36.1 - - + +
137A ARG 4.3 0.7 - - - +
138A THR* 1.3 86.7 - - + +
140A ARG* 1.3 69.1 + - + +
142A ALA* 4.4 0.9 - - + -
143A ALA* 2.9 31.7 + - - +
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A THR* 3.1 33.9 + - - +
139A PRO* 1.3 91.6 - - + +
141A ARG* 1.3 58.6 + - - +
143A ALA* 3.2 5.6 + - - +
144A LEU* 2.9 29.6 + - - +
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Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TYR* 5.6 5.8 - - - -
136A LYS* 3.4 56.5 + - - +
137A ARG* 5.3 2.2 - - - +
138A THR* 3.2 17.2 + - - +
140A ARG* 1.3 78.8 - - - +
142A ALA* 1.3 65.0 + - - +
144A LEU* 3.2 9.9 + - + +
145A MET* 3.0 52.8 + - + +
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 3.7 26.7 - - + -
62A TYR* 3.9 14.4 - - + -
63A PHE* 4.5 16.6 - - + -
137A ARG* 6.4 0.2 - - - -
138A THR 3.0 15.9 + - - +
139A PRO 3.8 3.8 - - - +
141A ARG* 1.3 78.7 - - - +
143A ALA* 1.3 56.2 + - - +
145A MET* 3.9 4.9 - - - +
146A ILE* 2.9 36.8 + - - +
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TYR* 4.4 7.5 - - + -
139A PRO 2.9 19.2 + - - +
140A ARG* 3.6 5.6 - - - +
142A ALA* 1.3 76.2 - - - +
144A LEU* 1.3 62.3 + - - +
146A ILE* 3.9 2.5 - - - +
147A GLY* 2.9 22.5 + - - -
502A Y01 4.0 30.8 - - + +
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG 2.9 16.9 + - - +
141A ARG* 3.2 10.5 + - + +
143A ALA* 1.3 77.0 - - - +
145A MET* 1.3 62.4 + - + +
147A GLY* 3.4 0.9 + - - -
148A LEU* 2.9 57.7 + - + +
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Residues in contact with MET 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PHE* 5.8 7.2 - - + -
118A LEU* 3.5 30.7 - - + +
133A TYR* 4.7 15.3 - - + +
141A ARG* 3.0 49.0 + - + +
142A ALA* 4.2 4.7 - - - +
144A LEU* 1.3 78.9 - - + +
146A ILE* 1.3 60.4 + - - +
148A LEU* 4.0 7.5 - - + +
149A ALA* 2.9 28.9 + - - +
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Residues in contact with ILE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TYR* 3.6 45.1 - - + +
63A PHE* 3.9 27.1 - - + +
66A SER* 3.4 29.8 - - - +
115A ASN* 5.0 1.8 - - - +
118A LEU* 3.9 8.1 - - + -
142A ALA* 2.9 24.2 + - + +
143A ALA* 3.9 5.2 - - - +
145A MET* 1.3 76.4 - - - +
147A GLY* 1.3 62.5 + - - +
149A ALA* 3.1 5.5 + - - +
150A TRP* 3.0 27.1 + - + -
502A Y01 4.2 21.8 - - + -
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Residues in contact with GLY 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ALA 2.9 17.1 + - - -
144A LEU 3.8 1.6 - - - -
146A ILE* 1.3 77.8 - - - +
148A LEU* 1.3 59.1 + - - +
150A TRP* 3.3 4.5 + - - +
151A LEU* 2.9 26.3 + - - +
502A Y01 4.1 19.3 - - - +
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Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 2.9 45.3 + - + +
145A MET* 4.0 7.2 - - + +
146A ILE 3.2 0.2 - - - -
147A GLY* 1.3 75.2 - - - +
149A ALA* 1.3 61.6 + - - +
151A LEU* 3.5 29.4 - - + +
152A VAL* 2.9 35.6 + - + +
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A MET* 4.1 28.2 - - + +
115A ASN* 4.1 13.5 - - - +
118A LEU* 4.1 13.9 - - + -
145A MET 2.9 14.8 + - - +
146A ILE 3.1 9.4 + - - +
148A LEU* 1.3 77.0 - - - +
150A TRP* 1.3 60.9 + - - +
152A VAL* 3.3 4.2 + - - +
153A SER* 2.9 29.1 + - - -
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Residues in contact with TRP 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 2.6 33.5 + - - -
69A CYS* 4.1 1.1 - - + -
70A ALA* 3.6 41.3 - - + -
73A ILE* 3.8 16.8 - - + -
107A VAL* 4.6 9.4 - - + -
108A ALA* 4.4 8.5 - - - -
111A ALA* 3.8 22.7 - - + -
115A ASN* 3.9 8.8 + - - +
146A ILE* 3.0 21.6 + - + -
147A GLY 3.6 7.9 - - - +
149A ALA* 1.3 75.4 - - - +
151A LEU* 1.3 63.6 + - - +
153A SER* 3.3 6.4 + - - -
154A PHE* 3.0 24.1 + - - +
502A Y01 3.5 74.6 - - + +
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLY 2.9 16.5 + - - +
148A LEU* 3.5 29.6 - - + +
149A ALA 3.3 0.2 - - - -
150A TRP* 1.3 76.5 - - - +
152A VAL* 1.3 63.7 + - + +
154A PHE* 3.3 9.4 + - + +
155A VAL* 2.9 46.0 + - + +
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Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A MET* 3.9 21.1 - - + -
148A LEU* 2.9 20.5 + - + +
149A ALA* 3.9 4.3 - - - +
151A LEU* 1.3 79.0 - - + +
153A SER* 1.3 61.6 + - - +
155A VAL* 4.1 6.4 - - + +
156A LEU* 2.9 48.9 + - + +
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Residues in contact with SER 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A VAL* 3.6 26.5 - - - -
110A GLN* 3.5 20.8 + - - +
111A ALA* 3.2 26.6 + - - -
114A MET* 4.1 4.2 - - - +
149A ALA 2.9 15.9 + - - -
150A TRP* 3.5 7.4 - - - -
152A VAL* 1.3 75.2 - - - +
154A PHE* 1.3 63.9 + - - +
156A LEU* 3.1 4.7 + - - +
157A TRP* 3.0 25.8 + - - +
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Residues in contact with PHE 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A VAL* 3.7 17.4 - - + +
150A TRP 3.0 17.1 + - - +
151A LEU* 3.7 10.3 - - + +
153A SER* 1.3 75.6 - - - +
155A VAL* 1.3 70.1 + - + +
158A ALA* 2.9 54.3 + - + -
159A PRO* 3.3 12.7 - - + +
162A LEU* 5.9 2.7 - - + -
502A Y01 3.7 27.4 - - + -
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 2.9 38.3 + - + +
152A VAL* 4.1 6.5 - - + +
154A PHE* 1.3 82.9 - - + +
156A LEU* 1.3 66.2 + - + +
159A PRO* 3.3 25.8 - - + +
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Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLN* 4.2 23.8 - - + +
114A MET* 4.9 5.8 - - + -
152A VAL* 2.9 42.1 + - + +
153A SER 3.1 4.2 + - - +
155A VAL* 1.3 82.4 - - + +
157A TRP* 1.3 73.7 + - + +
160A ALA* 5.0 8.0 - - - +
182A PHE* 5.7 1.0 - - - -
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Residues in contact with TRP 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 3.5 44.0 - + + -
107A VAL* 3.9 13.0 - - + -
110A GLN* 3.3 44.4 + - + +
153A SER 3.0 14.3 + - - +
156A LEU* 1.3 90.9 - - + +
158A ALA* 1.3 66.6 + - - +
159A PRO* 3.6 1.3 - - - -
160A ALA* 3.8 3.0 + - - +
161A ILE* 3.2 40.2 + - + +
180A ILE* 4.6 1.8 - - + -
182A PHE* 3.7 28.7 - + - -
183A LEU* 4.5 6.5 - - + -
192A THR* 4.4 12.8 - - - -
196A ALA* 4.5 7.9 - - + -
501A 0HK 3.6 40.0 - - + +
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Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA* 4.4 14.6 - - + -
107A VAL* 4.0 7.3 - - + +
154A PHE* 2.9 53.0 + - + +
157A TRP* 1.3 73.5 - - - +
159A PRO* 1.3 66.1 - - + +
161A ILE* 3.2 1.2 + - - -
162A LEU* 3.0 40.2 + - + +
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Residues in contact with PRO 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A PHE* 3.3 13.7 - - + +
155A VAL* 3.3 32.3 - - + +
157A TRP 3.8 0.9 - - - -
158A ALA* 1.3 90.3 - - + +
160A ALA* 1.3 56.6 + - - +
163A PHE* 2.9 52.5 + - + +
164A TRP 4.0 0.5 + - - -
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Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU 5.0 6.7 - - - +
157A TRP 3.8 5.0 + - - +
158A ALA 3.3 0.4 - - - -
159A PRO* 1.3 78.3 - - - +
161A ILE* 1.3 65.5 + - - +
164A TRP* 3.1 37.6 + - + +
182A PHE* 3.6 33.9 - - + -
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Residues in contact with ILE 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASP* 3.7 25.5 - - - +
102A LEU* 3.7 29.6 - - + +
103A ALA* 3.7 26.7 - - + +
106A TYR* 3.9 14.8 - - + -
157A TRP* 3.2 25.9 + - + +
158A ALA 3.2 2.7 + - - +
160A ALA* 1.3 78.4 - - - +
162A LEU* 1.3 62.2 + - + +
164A TRP* 4.9 1.4 + - - +
165A GLN* 4.8 2.9 + - - -
180A ILE* 3.9 35.5 - - + +
181A GLN 5.9 1.4 + - - -
182A PHE* 4.0 12.6 - - + -
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 5.8 2.7 - - + -
99A ASP* 3.3 47.8 - - + +
100A LEU* 4.0 16.6 - - + +
103A ALA* 3.8 12.3 - - + -
154A PHE* 5.9 2.5 - - + -
158A ALA* 3.0 31.1 + - + +
161A ILE* 1.3 79.6 - - + +
163A PHE* 1.3 83.9 + - + +
164A TRP 3.6 0.4 - - - -
165A GLN* 3.7 21.5 + - - +
166A TYR* 3.7 10.2 - - - -
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Residues in contact with PHE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ALA 5.7 0.2 - - - -
159A PRO* 2.9 34.3 + - + +
162A LEU* 1.3 99.5 - - + +
164A TRP* 1.3 66.5 + - - +
165A GLN 3.1 2.7 - - - -
166A TYR* 3.1 25.7 + + + +
167A LEU* 3.0 27.4 + - + +
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Residues in contact with TRP 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PRO 4.0 1.4 + - - -
160A ALA* 3.1 32.7 + - + +
161A ILE 5.3 1.1 - - - +
162A LEU 3.6 0.8 - - - -
163A PHE* 1.3 76.8 - - - +
165A GLN* 1.3 57.8 + - - +
167A LEU* 3.8 18.7 - - + +
168A VAL* 2.9 50.0 + - + +
181A GLN* 4.0 21.6 + - + +
182A PHE* 3.5 48.6 - + + +
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Residues in contact with GLN 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A THR* 5.7 1.6 - - - -
99A ASP* 3.1 29.6 + - - +
161A ILE 4.8 3.4 + - - -
162A LEU 3.7 12.6 + - - +
164A TRP* 1.3 79.4 - - - +
166A TYR* 1.3 83.5 + - + +
168A VAL 3.5 0.2 + - - -
169A GLY* 2.9 24.3 + - - -
170A GLU 3.3 22.3 + - - +
171A ARG* 3.2 28.6 + - - +
181A GLN* 3.6 20.9 + - - +
503A EDO 2.9 28.0 + - - -
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Residues in contact with TYR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 6.0 1.6 - - - +
99A ASP* 6.0 0.2 - - - -
162A LEU 3.7 18.8 - - - -
163A PHE* 3.1 25.4 + + + +
165A GLN* 1.3 95.3 + - + +
167A LEU* 1.3 65.1 + - - +
169A GLY* 3.6 9.8 + - - +
503A EDO 3.7 32.5 + - - -
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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 PHE* 3.0 19.3 + - + +
164A TRP* 3.8 22.4 - - + +
165A GLN 3.3 0.2 - - - -
166A TYR* 1.3 78.9 - - - +
168A VAL* 1.3 62.8 + - + +
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TRP* 2.9 51.8 + - + +
165A GLN 4.0 1.8 - - - +
167A LEU* 1.3 79.9 - - + +
169A GLY* 1.3 57.6 + - - +
170A GLU* 4.0 26.5 - - + +
172A THR* 5.8 0.7 - - - +
181A GLN* 4.4 6.7 - - - +
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Residues in contact with GLY 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLN 2.9 9.9 + - - -
166A TYR 3.6 8.2 + - - -
167A LEU 3.4 1.2 - - - -
168A VAL* 1.3 78.6 - - - +
170A GLU* 1.3 62.5 + - - +
503A EDO 3.3 16.3 + - - -
----------------------------------------------------------
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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