Contacts of the helix formed by residues 162 - 184 (chain A) in PDB entry 4DHZ
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 ASP 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A THR 3.2 13.5 + - - +
159A ILE* 3.3 10.2 + - - +
161A ASN* 1.3 73.8 - - - +
163A ASP* 1.3 59.9 + - - +
164A GLY* 3.1 7.7 + - - -
165A SER* 3.1 31.0 + - - -
166A ALA* 2.8 32.4 + - - +
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Residues in contact with ASP 163 (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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38A ALA* 5.6 0.9 - - - +
43A LEU* 4.0 18.0 - - + +
83A ARG* 3.5 24.0 + - - -
161A ASN 3.2 6.2 + - - +
162A ASP* 1.3 74.4 + - - +
164A GLY* 1.3 64.2 + - - +
167A ASN* 3.0 38.2 + - - +
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Residues in contact with GLY 164 (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 ASP* 3.1 10.1 + - - -
163A ASP* 1.3 80.6 - - - +
165A SER* 1.3 61.9 + - - +
167A ASN* 4.3 1.6 - - - +
168A TYR* 3.5 22.2 + - - +
64F MET* 4.9 1.7 - - - +
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Residues in contact with SER 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PHE* 3.9 18.5 - - - -
159A ILE* 3.6 34.1 - - - +
162A ASP* 3.1 16.5 + - - -
164A GLY* 1.3 72.9 - - - +
166A ALA* 1.3 65.4 + - - +
168A TYR* 3.0 16.7 + - - +
169A ILE* 3.1 18.5 + - - +
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Residues in contact with ALA 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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43A LEU* 3.9 8.7 - - + -
91A ARG* 3.5 18.3 + - - +
94A LEU* 5.2 2.1 - - - +
159A ILE 3.7 3.3 + - - -
160A LEU* 3.5 35.0 - - + +
162A ASP 2.8 21.7 + - - +
163A ASP 4.2 0.2 - - - +
165A SER* 1.3 73.7 - - - +
167A ASN* 1.3 58.6 + - - +
169A ILE* 3.4 9.6 + - - +
170A LEU* 2.9 26.0 + - - +
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Residues in contact with ASN 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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43A LEU* 4.8 2.7 - - - +
87A ASN* 4.4 0.2 + - - -
91A ARG* 2.8 33.1 + - - -
163A ASP* 3.0 31.6 + - - +
164A GLY 4.4 0.4 - - - +
166A ALA* 1.3 73.2 - - - +
168A TYR* 1.3 63.5 + - - +
170A LEU* 3.7 6.9 - - - +
171A MET* 3.1 18.0 + - - +
209A MET* 3.9 14.6 - - + +
210A TRP* 3.9 19.9 - - - -
61F GLU* 6.4 0.4 - - - +
64F MET* 3.4 37.4 - - + +
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Residues in contact with TYR 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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131A THR 5.3 0.9 + - - -
134A ASP* 3.3 23.2 + - - +
135A PHE* 3.1 45.4 - + - +
138A PHE* 3.5 44.4 - + + -
164A GLY 3.5 12.9 + - - +
165A SER* 3.0 10.8 + - - +
167A ASN* 1.3 75.7 - - - +
169A ILE* 1.3 64.3 + - - +
171A MET* 3.2 17.8 + - - +
172A PHE* 3.7 4.0 + - - +
5F PRO* 6.2 2.2 - - + -
6F ARG* 4.7 8.7 - - + -
7F ARG* 3.4 38.7 + - + +
63F PRO* 4.3 11.7 - - + -
64F MET* 3.7 15.7 - - + +
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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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94A LEU* 4.4 16.6 - - + -
135A PHE 6.0 0.2 - - - -
138A PHE* 3.9 19.3 - - + -
139A PHE* 3.6 34.5 - - + -
142A PHE* 4.0 40.2 - - + -
159A ILE* 4.3 13.0 - - + -
160A LEU* 4.5 10.3 - - + -
165A SER 3.1 14.5 + - - +
166A ALA* 3.6 7.9 - - - +
168A TYR* 1.3 75.0 - - - +
170A LEU* 1.3 62.3 + - - +
172A PHE* 3.1 21.1 + - - +
173A PHE* 3.4 11.8 - - + -
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Residues in contact with LEU 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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87A ASN* 3.8 7.9 - - + -
90A TYR* 3.8 19.1 - - + -
91A ARG* 3.6 63.0 - - + +
94A LEU* 4.1 14.8 - - + -
166A ALA 2.9 15.6 + - - +
167A ASN* 3.8 8.7 - - - +
168A TYR 3.2 0.4 - - - -
169A ILE* 1.3 77.2 - - - +
171A MET* 1.3 63.3 + - - +
173A PHE* 2.9 15.5 + - + +
174A ARG* 3.1 38.7 + - + +
209A MET* 4.1 12.1 - - + -
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Residues in contact with MET 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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135A PHE* 3.9 27.4 - - + -
167A ASN 3.1 14.7 + - - +
168A TYR 3.4 11.7 - - - +
169A ILE 3.2 0.6 - - - -
170A LEU* 1.3 78.1 - - - +
172A PHE* 1.3 55.5 + - - +
174A ARG* 3.2 13.2 + - + +
175A LEU* 2.8 64.6 + - + +
207A GLU 3.6 24.5 - - - +
209A MET* 4.0 13.5 - - - +
64F MET* 4.3 2.7 - - - -
96F SER* 4.8 1.6 - - - +
97F PRO* 3.7 39.0 - - + -
98F ALA* 4.4 5.6 - - + +
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Residues in contact with PHE 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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111A PHE* 4.9 4.5 - + - -
115A SER* 4.1 19.3 - - - -
118A TRP* 4.2 16.6 - + + -
122A LEU* 5.2 0.4 - - + -
135A PHE* 4.8 7.5 - - + +
136A CYS* 3.6 42.4 - - + -
139A PHE* 3.4 48.2 - + + -
168A TYR 3.7 4.2 + - - +
169A ILE 3.1 12.9 + - - +
170A LEU 3.1 0.4 - - - -
171A MET* 1.3 78.4 - - - +
173A PHE* 1.3 71.5 + + - +
175A LEU* 3.1 12.5 + - + +
176A ILE* 2.9 55.9 + - + +
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Residues in contact with PHE 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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90A TYR* 4.4 13.5 - - + +
93A ILE* 4.9 3.4 - - + -
94A LEU* 4.0 25.8 - - + -
97A LEU* 3.6 29.8 - - + -
98A ILE* 5.3 3.8 - - + -
111A PHE* 4.4 10.8 - + - -
139A PHE* 3.6 40.6 - + - -
169A ILE* 3.4 22.7 - - + -
170A LEU* 2.9 10.1 + - - +
172A PHE* 1.3 80.6 - + - +
174A ARG* 1.3 58.7 + - - +
176A ILE* 4.0 11.9 - - + -
177A THR* 2.6 35.3 + - - -
221A LEU* 3.5 25.8 - - + +
225A ALA* 5.5 0.2 - - + -
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Residues in contact with ARG 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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86A GLY 3.3 8.1 + - - -
87A ASN* 2.8 26.4 + - - -
90A TYR* 3.4 33.4 + - + -
170A LEU* 3.1 27.5 + - + +
171A MET* 3.5 15.0 - - - +
173A PHE* 1.3 78.5 - - - +
175A LEU* 1.3 62.0 + - - +
177A THR* 3.5 3.3 + - - -
178A SER* 3.1 18.5 + - - -
205A GLU 4.1 3.2 + - - -
206A ILE* 3.1 39.2 + - - +
207A GLU* 4.1 6.2 - - - +
208A PRO 3.1 25.4 + - - -
209A MET* 3.8 18.3 - - - -
211A LYS 2.9 32.1 + - - +
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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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122A LEU* 4.5 16.6 - - + -
127A PHE* 3.7 29.7 - - + -
132A CYS* 4.0 25.4 - - + +
135A PHE* 3.7 35.4 - - + -
171A MET* 2.8 32.9 + - + +
172A PHE* 3.1 11.4 + - + +
174A ARG* 1.3 74.7 - - - +
176A ILE* 1.3 61.0 + - - +
178A SER* 3.0 5.9 + - - -
179A ALA* 2.7 28.6 + - - +
207A GLU* 4.7 11.2 - - + -
98F ALA* 4.9 5.2 - - + -
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Residues in contact with ILE 176 (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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111A PHE* 5.5 4.0 - - + -
118A TRP* 3.7 44.8 - - + +
122A LEU* 5.4 3.1 - - + -
172A PHE* 2.9 45.0 + - + +
173A PHE* 3.6 22.9 - - + +
175A LEU* 1.3 69.5 - - + +
177A THR* 1.3 60.7 + - - +
179A ALA* 3.5 6.7 - - + +
180A PHE* 2.7 37.7 + - - +
221A LEU* 4.1 14.4 - - + -
224A ALA* 4.0 27.8 - - + +
225A ALA* 4.3 6.1 - - + +
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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
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90A TYR* 3.4 9.6 - - - +
173A PHE 2.6 24.2 + - - -
174A ARG 3.6 5.6 - - - -
176A ILE* 1.3 79.1 - - - +
178A SER* 1.3 63.4 + - - +
180A PHE* 3.7 1.1 + - - -
181A LEU* 3.4 20.3 + - - +
206A ILE* 3.9 15.9 - - + -
217A ALA* 3.4 37.9 - - + +
220A SER* 3.8 16.1 - - - -
221A LEU* 3.3 22.6 - - + +
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Residues in contact with SER 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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127A PHE* 4.1 5.6 - - - -
174A ARG 3.1 12.7 + - - -
175A LEU 3.0 9.4 + - - -
177A THR* 1.3 74.6 - - - +
179A ALA* 1.3 67.5 + - - +
181A LEU* 3.0 14.2 + - - +
182A LYS* 3.1 18.4 + - - +
202A CYS* 3.2 25.7 - - - +
206A ILE* 3.9 7.6 - - - +
207A GLU* 2.9 36.5 + - - +
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Residues in contact with ALA 179 (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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118A TRP* 3.8 19.5 - - + -
122A LEU* 3.6 23.1 - - + -
125A LEU* 3.8 15.9 - - + +
127A PHE* 3.7 9.9 - - - -
175A LEU 2.7 19.0 + - - +
176A ILE* 3.5 6.3 - - - +
178A SER* 1.3 71.7 - - - +
180A PHE* 1.3 57.4 + - - +
181A LEU 3.2 0.3 + - - -
182A LYS* 3.2 4.3 + - - +
183A GLN* 2.9 30.7 + - - +
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Residues in contact with PHE 180 (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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118A TRP* 4.3 9.8 - + + -
176A ILE 2.7 19.7 + - - +
177A THR 4.0 3.8 - - - +
179A ALA* 1.3 73.3 - - - +
181A LEU* 1.3 62.3 + - - +
183A GLN* 3.5 14.1 - - - +
184A ASN* 3.2 33.8 + - - +
188A TYR* 3.9 29.2 - + - -
219A ASN* 5.1 0.2 - - - -
220A SER* 3.7 29.2 - - - +
223A LYS* 3.6 27.4 - - + -
224A ALA* 3.6 36.8 - - + -
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Residues in contact with LEU 181 (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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177A THR 3.4 6.0 + - - +
178A SER 3.0 9.9 + - - +
180A PHE* 1.3 77.8 - - - +
182A LYS* 1.3 65.7 + - - +
184A ASN 3.0 13.7 + - - +
185A SER* 3.1 14.9 + - - -
188A TYR* 3.8 36.5 - - + +
192A ILE* 5.8 1.1 - - + -
198A VAL* 3.9 11.1 - - + +
201A TYR* 4.5 4.0 - - + -
202A CYS* 3.8 15.7 - - - -
206A ILE* 3.4 33.2 - - + -
216A LEU* 4.2 24.5 - - + -
220A SER* 3.4 24.2 - - - +
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Residues in contact with LYS 182 (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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125A LEU* 4.4 21.8 + - + +
126A GLY 6.2 0.2 - - - -
127A PHE* 3.2 37.5 - - + -
178A SER* 3.1 21.6 + - - +
179A ALA 3.7 4.5 - - - +
181A LEU* 1.3 74.1 - - - +
183A GLN* 1.3 62.6 - - - +
184A ASN 3.0 1.2 + - - -
185A SER* 3.2 18.9 + - - -
198A VAL* 4.1 13.2 - - + -
199A ALA* 4.7 15.5 - - + +
202A CYS* 4.0 16.4 - - - -
203A GLU* 5.2 5.9 + - - +
207A GLU* 2.9 23.0 + - - -
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Residues in contact with GLN 183 (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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118A TRP* 3.8 29.1 - - - -
121A THR* 3.5 25.5 - - - +
125A LEU* 4.3 14.9 - - + +
179A ALA 2.9 14.2 + - - +
180A PHE* 3.5 16.2 - - - +
181A LEU 3.2 0.2 - - - -
182A LYS* 1.3 75.7 - - - +
184A ASN* 1.3 72.4 + - - +
185A SER 3.7 0.2 - - - -
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Residues in contact with ASN 184 (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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180A PHE* 3.2 34.2 + - - +
181A LEU 3.0 5.5 + - - +
182A LYS 3.0 0.8 - - - -
183A GLN* 1.3 98.6 - - - +
185A SER* 1.3 62.8 + - - +
186A GLU* 3.5 3.8 - - - -
187A GLU* 3.2 27.8 + - - +
188A TYR* 3.2 33.6 + - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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