Contacts of the helix formed by residues 152 - 178 (chain A) in PDB entry 4KPD
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 TYR 152 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A PHE* 5.8 0.3 - - - -
84A ARG* 3.4 31.5 + - - -
147A CYS* 4.1 9.2 - - + -
150A GLN* 3.6 27.1 - - + -
151A PRO* 1.3 84.0 - - + +
153A TYR* 1.4 65.6 + - - +
154A LEU 3.4 2.2 - - - -
155A ASN* 3.3 14.3 + - + +
156A LEU* 3.0 47.9 + - + +
215A TYR* 3.5 28.7 - - + +
216A MET* 3.4 52.3 - - + +
218A GLY* 6.1 0.4 - - - -
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Residues in contact with TYR 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TYR 4.9 1.0 + - - -
143A LEU* 3.3 31.4 - - + -
144A LYS* 3.6 25.3 + - - +
147A CYS* 3.2 32.8 - - + +
148A ARG* 3.6 26.0 - - + +
150A GLN 3.2 12.2 + - - +
151A PRO 3.4 1.0 - - - -
152A TYR* 1.4 82.7 - - - +
154A LEU* 1.4 60.7 + - + +
156A LEU* 3.3 4.7 + - + +
157A ILE* 3.1 55.4 + - + +
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PRO 4.9 2.5 + - - +
152A TYR 3.4 0.4 - - - -
153A TYR* 1.4 79.2 - - + +
155A ASN* 1.4 65.9 + - - +
157A ILE* 3.3 19.3 + - + -
158A GLU* 3.0 50.0 + - + +
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Residues in contact with ASN 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PRO 5.0 4.0 + - - -
152A TYR* 3.3 19.8 + - - +
154A LEU* 1.4 76.7 - - - +
156A LEU* 1.4 57.5 + - - +
158A GLU* 3.6 11.3 + - - +
159A LEU* 2.9 31.0 + - - +
215A TYR* 3.8 45.2 + - + -
220A ASP* 4.2 15.0 + - - +
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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
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88A VAL* 3.8 26.0 - - + -
143A LEU* 4.1 18.8 - - + -
147A CYS* 4.5 4.3 - - + -
152A TYR* 3.0 44.0 + - + +
153A TYR* 3.7 6.5 - - + +
155A ASN* 1.4 72.9 - - - +
157A ILE* 1.3 66.6 + - - +
159A LEU* 3.3 5.1 + - + +
160A PHE* 2.9 35.1 + - + -
212A ALA* 3.8 41.7 - - + +
215A TYR* 4.2 13.0 - - + -
216A MET* 4.1 2.7 - - + -
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Residues in contact with ILE 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TYR* 4.0 15.3 - - + -
143A LEU* 4.3 17.0 - - + -
153A TYR* 3.1 62.7 + - + +
154A LEU* 3.3 20.8 + - + +
156A LEU* 1.3 76.2 - - - +
158A GLU* 1.4 57.9 + - + +
160A PHE* 3.3 2.3 + - - +
161A LEU* 2.9 52.5 + - + +
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Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 3.0 44.5 + - + +
155A ASN* 3.9 12.1 - - - +
157A ILE* 1.4 76.0 - - + +
159A LEU* 1.3 52.0 + - - +
161A LEU* 3.8 9.8 - - + +
162A GLN* 2.8 37.7 + - - +
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASN 2.9 19.1 + - - +
156A LEU* 3.3 8.3 + - + +
158A GLU* 1.3 75.5 - - - +
160A PHE* 1.4 54.7 + - + +
162A GLN* 4.2 4.0 - - + +
163A SER* 2.7 46.8 + - - +
207A TYR* 3.8 29.8 - - + +
208A LEU* 3.6 18.6 - - + -
211A ALA* 3.7 10.1 - - + -
212A ALA* 3.5 38.4 - - + +
215A TYR* 3.8 17.7 - - + -
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Residues in contact with PHE 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 4.0 17.7 - - + -
91A CYS* 3.7 38.1 - - + -
92A VAL* 3.6 28.9 - - + -
95A LEU* 4.4 11.2 - - + +
139A ILE* 3.7 15.3 - - + -
140A TYR* 3.4 21.3 - - + +
143A LEU* 4.0 19.1 - - + -
156A LEU* 2.9 33.0 + - + +
157A ILE 3.9 2.5 - - - +
159A LEU* 1.4 75.3 - - + +
161A LEU* 1.4 55.7 + - - +
163A SER* 3.9 2.3 - - - -
164A SER* 2.7 34.0 + - - -
208A LEU* 4.2 25.1 - - + -
212A ALA* 4.8 4.9 - - + -
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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
----------------------------------------------------------
136A GLU* 5.9 2.0 - - - +
140A TYR* 3.4 27.1 - - + +
157A ILE* 2.9 39.8 + - + +
158A GLU* 3.8 10.1 - - + +
159A LEU 3.3 0.2 - - - -
160A PHE* 1.4 73.0 - - - +
162A GLN* 1.3 64.0 + - - +
164A SER* 3.3 6.9 + - - +
165A TYR* 3.1 21.7 + - - +
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Residues in contact with GLN 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLU 2.8 20.7 + - - +
159A LEU* 4.2 5.6 - - + +
161A LEU* 1.3 72.3 - - - +
163A SER* 1.3 57.0 + - - +
165A TYR* 3.2 25.2 + - - +
166A GLN* 3.0 65.2 + - - +
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Residues in contact with SER 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 4.6 2.2 - - - -
159A LEU* 2.7 30.5 + - - +
160A PHE 3.9 3.6 - - - -
161A LEU 3.4 0.2 - - - -
162A GLN* 1.3 75.6 - - - +
164A SER* 1.4 53.3 + - - +
166A GLN* 3.6 13.8 + - - +
167A THR* 2.7 36.6 + - - -
203A PHE* 4.8 2.6 + - - +
204A PHE* 4.3 11.0 + - - +
207A TYR* 5.3 2.4 - - - -
208A LEU* 3.8 39.1 - - - +
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Residues in contact with SER 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 3.4 20.8 - - - +
99A PHE* 3.7 16.6 - - - -
136A GLU* 4.4 12.3 + - - -
140A TYR* 4.0 5.4 + - - -
160A PHE 2.7 21.3 + - - -
161A LEU* 3.5 9.6 - - - -
163A SER* 1.4 73.5 - - - +
165A TYR* 1.4 59.3 + - - +
167A THR* 3.3 2.4 + - - -
168A GLU* 3.0 44.3 + - - +
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Residues in contact with TYR 165 (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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161A LEU 3.1 13.1 + - - +
162A GLN* 3.7 32.5 - - - +
164A SER* 1.4 76.3 - - - +
166A GLN* 1.3 60.4 + - + +
168A GLU* 3.2 14.3 + - + +
169A ILE* 2.9 60.9 + - + +
199A TYR* 6.6 0.2 - + - -
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Residues in contact with GLN 166 (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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162A GLN* 3.0 52.2 + - - +
163A SER* 3.6 12.9 + - - +
165A TYR* 1.3 78.3 - - + +
167A THR* 1.4 57.6 + - - +
169A ILE* 3.4 2.4 + - - +
170A GLY 3.0 22.3 + - - -
199A TYR* 3.2 29.9 - - + +
203A PHE* 3.4 61.2 - - + +
207A TYR* 5.7 1.2 - - - -
229A LYS* 5.4 4.0 - - - +
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Residues in contact with THR 167 (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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99A PHE* 3.5 39.7 - - + -
163A SER 2.7 23.8 + - - -
165A TYR 3.3 0.2 - - - -
166A GLN* 1.4 74.5 - - - +
168A GLU* 1.3 53.3 + - - +
170A GLY* 3.1 2.6 + - - -
171A GLN* 2.7 39.4 + - + +
199A TYR 3.3 9.8 + - - -
200A LYS* 3.3 22.8 - - - +
204A PHE* 3.5 28.2 + - + +
405A RIS 4.1 6.5 - - + -
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Residues in contact with GLU 168 (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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98A PHE* 3.7 28.9 - - + -
99A PHE* 3.8 11.2 - - + -
136A GLU* 4.5 3.1 - - - +
164A SER* 3.0 30.5 + - - +
165A TYR* 3.6 13.7 - - + +
167A THR* 1.3 73.1 - - - +
169A ILE* 1.3 59.3 + - + +
171A GLN* 3.3 9.9 + - + +
172A THR* 2.9 32.4 + - - -
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Residues in contact with ILE 169 (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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165A TYR* 2.9 55.8 + - + +
166A GLN* 3.7 4.7 - - - +
167A THR 3.3 0.2 - - - -
168A GLU* 1.3 72.1 - - - +
170A GLY* 1.3 60.3 + - - +
172A THR* 3.2 16.2 + - + +
173A LEU* 3.0 33.5 + - + +
199A TYR* 4.0 26.0 - - + -
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Residues in contact with GLY 170 (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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166A GLN 3.0 11.1 + - - -
167A THR 3.1 4.2 + - - -
169A ILE* 1.3 75.9 - - - +
171A GLN* 1.3 50.6 + - - +
173A LEU* 3.1 8.5 + - - +
174A ASP* 2.8 33.8 + - - +
196A ILE* 4.0 4.6 - - - +
199A TYR* 3.4 22.7 - - - -
200A LYS* 3.5 16.3 - - - +
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Residues in contact with GLN 171 (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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99A PHE* 4.8 8.4 + - + -
103A ASP* 3.0 33.8 + - - +
106A MET* 4.2 17.1 - - + +
167A THR* 2.7 28.5 + - + +
168A GLU* 3.6 9.9 - - + +
170A GLY* 1.3 72.6 - - - +
172A THR* 1.4 54.9 + - - +
174A ASP* 3.3 6.4 + - - +
175A LEU* 2.9 46.6 + - + +
200A LYS* 3.8 15.3 - - - +
403A MG 4.1 3.9 - - - -
405A RIS 3.5 31.4 - - + -
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Residues in contact with THR 172 (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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168A GLU 2.9 16.2 + - - -
169A ILE* 3.2 20.8 + - + +
171A GLN* 1.4 73.5 - - - +
173A LEU* 1.4 57.4 + - + +
175A LEU* 3.3 8.5 + - - +
176A LEU* 2.9 54.5 + - + +
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Residues in contact with LEU 173 (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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169A ILE* 3.0 18.2 + - + +
170A GLY* 3.1 11.2 + - - +
172A THR* 1.4 74.1 - - + +
174A ASP* 1.3 62.0 + - - +
176A LEU* 3.5 12.1 + - + +
177A THR* 2.6 33.2 + - - -
192A ARG* 4.3 27.1 - - - +
195A SER* 3.9 20.0 - - - +
196A ILE* 3.9 34.8 - - + +
199A TYR* 5.2 6.3 - - + -
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Residues in contact with ASP 174 (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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170A GLY 2.8 13.8 + - - +
171A GLN* 3.5 14.2 - - - +
173A LEU* 1.3 75.3 - - - +
175A LEU* 1.3 69.5 + - - +
177A THR* 3.6 2.3 + - - -
178A ALA* 3.3 24.1 + - - +
196A ILE* 3.8 20.5 - - + +
200A LYS* 2.9 32.6 + - + +
266A LYS* 3.4 33.0 + - - +
267A CYS 5.7 0.7 + - - -
403A MG 3.9 10.7 - - - -
405A RIS 4.4 0.7 + - - -
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Residues in contact with LEU 175 (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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106A MET* 3.8 43.7 - - + +
107A ASP* 4.2 15.5 - - - +
171A GLN* 2.9 31.3 + - + +
172A THR* 3.9 6.3 - - - +
174A ASP* 1.3 86.8 - - - +
176A LEU* 1.4 62.2 + - - +
178A ALA* 3.3 22.6 + - + +
179A PRO* 3.9 2.9 - - - +
266A LYS* 4.8 4.7 - - - -
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A THR* 2.9 40.0 + - + +
173A LEU* 4.0 14.4 - - + +
174A ASP 3.5 0.2 - - - -
175A LEU* 1.4 77.0 - - + +
177A THR* 1.3 61.0 + - - +
179A PRO* 3.6 10.7 - - - +
187A ARG* 3.3 20.3 + - - +
192A ARG* 5.2 4.9 - - - +
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Residues in contact with THR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LEU 2.6 24.0 + - - -
174A ASP 4.1 3.6 - - - -
176A LEU* 1.3 74.3 - - - +
178A ALA* 1.3 57.2 + - - +
179A PRO* 3.3 7.8 - - - +
184A ASP* 2.8 29.9 - - - +
187A ARG* 4.0 10.1 - - + +
188A PHE* 3.3 21.3 - - + -
192A ARG* 3.0 39.0 + - + -
196A ILE* 3.8 6.2 - - - +
267A CYS* 3.8 24.2 - - + -
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Residues in contact with ALA 178 (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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174A ASP 3.3 16.3 + - - +
175A LEU* 3.3 12.0 + - - +
176A LEU 3.2 0.4 - - - -
177A THR* 1.3 79.5 - - - +
179A PRO* 1.4 64.6 - - - +
180A GLN* 3.4 2.6 + - - +
264A ASP 3.5 17.0 - - - +
265A ASN* 3.2 22.0 - - - +
266A LYS* 3.5 23.0 - - + -
267A CYS 4.9 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