Contacts of the helix formed by residues 154 - 176 (chain A) in PDB entry 1W4Z
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 ALA 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLY 3.8 7.0 - - - -
96A GLY* 4.2 0.4 - - - -
151A VAL* 2.9 36.6 + - + +
152A VAL 4.1 0.4 - - - +
153A HIS* 1.3 79.0 - - - +
155A ALA* 1.3 60.6 + - - +
156A PRO* 3.4 4.3 - - - -
157A TYR* 3.1 5.4 + - + -
158A SER* 2.8 26.9 + - - -
1265A FMT 3.8 26.7 - - - +
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLY 5.4 0.2 + - - -
99A THR* 3.5 25.7 + - + +
107A TRP* 4.1 2.4 - - + -
151A VAL 4.1 0.6 + - - -
153A HIS 3.8 1.4 - - - -
154A ALA* 1.3 77.8 - - - +
156A PRO* 1.3 65.6 - - + +
158A SER* 3.5 1.4 + - - -
159A ALA* 2.8 31.0 + - - +
167B PHE* 3.9 27.6 - - + -
170B ALA* 3.8 18.6 - - + +
171B LEU* 5.0 3.4 - - + +
174B GLU* 4.9 1.6 - - - +
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Residues in contact with PRO 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLY 3.9 13.9 - - - +
97A GLY 5.8 0.2 - - - +
99A THR* 5.4 0.2 - - - +
102A LEU* 3.6 39.5 - - + -
106A LEU* 5.3 1.3 - - + -
107A TRP* 3.5 33.4 - - + +
110A VAL* 3.5 23.0 - - + +
111A VAL* 4.5 2.6 - - + +
154A ALA* 3.4 2.9 - - - -
155A ALA* 1.3 97.6 - - + +
157A TYR* 1.3 54.1 + - - +
159A ALA* 3.8 0.3 - - - +
160A SER* 2.7 37.1 + - - -
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Residues in contact with TYR 157 (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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93A ARG 3.5 25.1 - - - -
94A PRO* 3.7 12.1 - - + -
95A GLY 3.6 16.6 + - - +
110A VAL* 3.8 4.0 - - - +
114A ASN* 3.9 3.4 - - - -
144A SER* 3.2 26.9 + - - -
146A GLY* 4.6 5.4 - - - -
151A VAL* 5.0 2.9 - - + -
154A ALA* 3.1 13.1 + - + +
156A PRO* 1.3 78.8 - - - +
158A SER* 1.3 67.8 + - - +
160A SER* 2.8 6.6 + - - -
161A LYS* 2.8 55.6 + - + +
1262A NAP 3.4 25.0 + - - -
1264A FMT 3.2 25.0 + - - -
1265A FMT 3.7 18.6 - - - +
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Residues in contact with SER 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLY 3.2 19.7 + - - +
149A GLN 3.4 4.5 + - - -
150A GLY* 4.4 0.2 - - - -
151A VAL* 3.1 33.1 + - - +
154A ALA 2.8 16.2 + - - -
155A ALA 3.9 3.1 - - - -
157A TYR* 1.3 75.4 - - - +
159A ALA* 1.3 59.0 + - - +
162A HIS* 2.9 37.4 + - - -
166B GLY* 4.0 16.6 - - - -
170B ALA* 4.0 7.2 - - - -
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Residues in contact with ALA 159 (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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107A TRP* 3.7 26.0 - - + -
111A VAL* 5.5 0.4 - - + -
155A ALA 2.8 22.7 + - - +
156A PRO 3.8 1.6 - - - +
158A SER* 1.3 73.5 - - - +
160A SER* 1.3 64.0 + - - +
163A GLY* 3.0 19.1 + - - -
115B LEU* 4.1 10.9 - - + +
163B GLY* 3.4 32.6 - - - +
166B GLY* 4.3 0.8 - - - -
167B PHE* 4.0 7.6 - - + +
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Residues in contact with SER 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A VAL* 3.7 10.9 - - - +
111A VAL* 4.2 14.8 - - - +
114A ASN* 3.1 36.7 + - - -
115A LEU* 3.9 14.5 - - - +
156A PRO 2.7 19.9 + - - -
157A TYR* 2.8 17.7 + - - -
159A ALA* 1.3 73.9 - - - +
161A LYS* 1.3 55.6 + - - +
163A GLY* 3.1 4.2 + - - -
164A VAL* 3.0 29.0 + - - +
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Residues in contact with LYS 161 (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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91A ALA 5.3 0.6 + - - -
92A GLY* 4.6 1.8 - - - -
114A ASN* 4.0 21.0 + - + +
142A ILE 3.2 16.1 + - - +
143A ALA* 3.4 24.6 + - - +
144A SER* 3.8 12.1 - - - +
146A GLY 4.1 0.7 - - - -
147A GLY* 3.6 21.9 - - - +
157A TYR* 2.8 44.8 + - + +
158A SER 4.0 0.9 - - - +
160A SER* 1.3 72.2 + - - +
162A HIS* 1.3 65.6 + - - +
164A VAL* 2.9 21.3 + - + +
165A VAL* 3.1 15.2 + - - +
1262A NAP 2.8 43.8 + - - -
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Residues in contact with HIS 162 (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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146A GLY 3.0 25.6 + - - -
147A GLY 3.2 31.0 + - - -
148A LYS* 3.3 21.9 + - - -
149A GLN 3.5 7.1 + - - -
158A SER* 2.9 21.5 + - - +
159A ALA 3.8 2.0 - - - +
161A LYS* 1.3 75.0 - - - +
163A GLY* 1.3 65.2 + - - +
165A VAL* 3.0 5.2 + - - +
166A GLY 2.8 18.5 + - - -
261A TYR* 4.9 1.6 - - - -
162B HIS* 3.3 31.9 + - + +
165B VAL* 4.4 4.6 - - + +
166B GLY* 3.4 27.2 + - - -
169B LYS* 3.7 22.0 - - + +
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Residues in contact with GLY 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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115A LEU* 3.5 15.7 - - - +
159A ALA 3.0 15.4 + - - -
160A SER 3.4 4.9 - - - -
161A LYS 3.1 0.4 - - - -
162A HIS* 1.3 78.1 - - - +
164A VAL* 1.3 55.6 + - - +
166A GLY* 3.1 1.2 + - - -
167A PHE* 2.8 31.2 + - - +
159B ALA* 3.3 27.8 - - - -
162B HIS* 4.2 0.2 - - - -
163B GLY 4.1 0.6 - - - +
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Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASN 3.1 28.3 - - - +
115A LEU* 4.2 8.3 - - + -
118A VAL* 4.0 15.0 - - + -
141A ASN* 3.8 31.0 - - + +
142A ILE 4.7 3.6 - - - +
143A ALA* 4.0 20.6 - - + -
160A SER 3.0 14.5 + - - +
161A LYS* 2.9 20.2 + - + +
163A GLY* 1.3 74.6 - - - +
165A VAL* 1.3 53.7 + - - +
167A PHE* 3.4 5.1 + - - +
168A THR* 2.7 37.8 + - - +
184A ALA* 5.0 0.2 - - + -
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Residues in contact with VAL 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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143A ALA* 4.0 18.8 - - + -
147A GLY 3.9 20.6 - - - +
148A LYS* 4.9 5.4 - - + -
161A LYS 3.1 10.9 + - - +
162A HIS* 3.0 8.4 + - - +
164A VAL* 1.3 74.7 - - - +
166A GLY* 1.3 66.9 + - - +
168A THR* 3.0 8.6 + - - -
169A LYS* 2.9 43.2 + - + +
184A ALA* 4.7 2.0 - - + -
186A CYS* 4.4 6.5 - - - -
251A ALA* 4.0 29.6 - - + -
162B HIS* 4.4 8.1 - - - +
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Residues in contact with GLY 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 HIS 2.8 11.3 + - - -
163A GLY 3.6 2.5 - - - -
165A VAL* 1.3 76.7 - - - +
167A PHE* 1.3 61.9 + - - +
169A LYS* 3.2 4.0 + - - +
170A ALA* 3.0 24.1 + - - +
150B GLY* 4.6 0.2 - - - -
158B SER* 3.9 11.1 - - - -
159B ALA 4.4 0.4 - - - -
162B HIS* 3.3 38.0 + - - -
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Residues in contact with PHE 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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115A LEU* 4.7 4.5 - - + -
118A VAL* 3.8 30.5 - - + -
119A PHE* 4.0 15.7 - + - -
122A THR* 4.1 14.6 - - + -
141A ASN* 4.3 9.4 - - - -
163A GLY 2.8 20.1 + - - +
164A VAL* 3.6 6.5 - - - +
166A GLY* 1.3 73.0 - - - +
168A THR* 1.3 59.3 + - - +
170A ALA* 3.9 1.2 - - - +
171A LEU* 2.9 56.9 + - + +
182A VAL* 5.7 0.4 - - + -
99B THR* 3.9 22.9 - - + -
107B TRP* 3.8 32.8 - + - -
155B ALA* 3.9 16.2 - - + -
159B ALA* 4.0 11.0 - - + +
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Residues in contact with THR 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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141A ASN* 2.9 21.0 + - - +
164A VAL 2.7 23.7 + - - -
165A VAL* 3.0 8.5 + - - -
167A PHE* 1.3 78.3 - - - +
169A LYS* 1.3 64.0 + - + +
172A GLY* 3.0 22.0 + - - -
182A VAL* 3.8 15.1 - - + +
183A ASN* 3.4 39.3 - - - +
184A ALA* 3.6 13.7 - - + +
249A ALA* 4.0 3.9 - - - -
250A GLN 4.0 6.7 - - - +
251A ALA* 6.0 0.4 - - + -
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Residues in contact with LYS 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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148A LYS* 6.3 0.4 - - - +
165A VAL* 2.9 37.2 + - + +
166A GLY 3.2 3.8 + - - +
168A THR* 1.3 78.1 - - + +
170A ALA* 1.3 63.8 + - - +
172A GLY* 3.2 1.4 + - - -
173A LEU* 3.0 29.4 + - + +
249A ALA* 3.5 29.9 - - + +
250A GLN* 5.2 0.9 - - - +
251A ALA* 4.8 12.4 - - + +
261A TYR* 5.7 4.6 - - - -
148B LYS 3.9 17.7 + - - +
149B GLN* 4.6 1.1 - - - -
150B GLY* 3.8 20.4 - - - +
162B HIS* 4.3 11.5 - - + -
261B TYR* 3.9 13.3 + - - -
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Residues in contact with ALA 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 GLY 3.0 16.0 + - - +
167A PHE 3.9 1.6 - - - +
169A LYS* 1.3 77.6 - - - +
171A LEU* 1.3 57.8 + - - +
173A LEU* 3.4 3.4 + - - +
174A GLU* 2.9 29.2 + - - +
150B GLY* 3.5 9.7 - - - -
151B VAL 3.7 29.8 - - - +
152B VAL* 4.4 4.3 - - - -
153B HIS 5.8 0.2 - - - -
155B ALA* 3.8 24.5 - - + +
158B SER* 3.9 4.0 - - - +
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Residues in contact with LEU 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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122A THR* 3.6 31.2 - - + -
126A LEU* 4.2 7.9 - - + -
139A ILE* 4.3 5.6 - - + -
167A PHE* 2.9 34.4 + - + +
168A THR 4.4 1.3 - - - +
170A ALA* 1.3 73.5 - - - +
172A GLY* 1.3 66.7 + - - +
174A GLU* 3.0 16.5 + - - +
175A LEU* 2.9 51.1 + - + +
182A VAL* 4.3 10.3 - - + -
99B THR* 3.5 33.2 - - + +
155B ALA* 5.0 1.2 - - + +
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Residues in contact with GLY 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 THR 3.0 19.5 + - - -
169A LYS 3.6 0.7 - - - -
171A LEU* 1.3 78.5 - - - +
173A LEU* 1.3 56.6 + - - +
175A LEU 3.2 1.6 + - - -
176A ALA* 2.9 29.7 + - - +
180A ILE 5.2 0.2 - - - +
182A VAL* 3.7 20.5 - - - +
248A THR* 4.0 12.6 + - - -
249A ALA* 4.1 10.1 - - - -
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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 LYS* 3.0 17.6 + - + +
170A ALA 3.9 2.5 - - - +
172A GLY* 1.3 75.5 - - - +
174A GLU* 1.3 63.2 + - - +
175A LEU 3.3 0.3 + - - -
176A ALA* 3.4 20.2 + - + +
177A ARG 5.2 0.2 + - - -
248A THR* 5.9 2.0 - - + -
249A ALA* 4.1 14.8 - - + +
149B GLN* 6.1 0.2 - - + -
150B GLY* 3.5 35.4 - - - +
152B VAL* 3.7 25.4 - - + +
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Residues in contact with GLU 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 ALA 2.9 16.2 + - - +
171A LEU* 3.0 16.8 + - - +
173A LEU* 1.3 79.5 - - - +
175A LEU* 1.3 69.2 + - + +
176A ALA 3.4 0.4 + - - -
177A ARG 5.3 0.5 + - - -
98B ALA* 3.5 10.6 - - - +
99B THR* 2.6 46.4 + - - -
100B ALA 4.8 0.7 + - - -
152B VAL* 3.9 20.1 - - + +
153B HIS* 3.9 34.6 + - + +
155B ALA* 4.9 1.9 - - - +
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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
----------------------------------------------------------
126A LEU* 4.0 15.9 - - + -
132A LEU* 4.0 26.7 - - + -
139A ILE* 4.5 0.4 - - + -
171A LEU* 2.9 44.6 + - + +
172A GLY 3.6 2.2 - - - +
174A GLU* 1.3 92.3 - - + +
176A ALA* 1.3 64.2 + - - +
177A ARG 3.2 2.7 - - - -
178A THR* 2.8 42.1 + - + +
180A ILE* 3.4 34.1 - - + +
182A VAL* 3.9 8.5 - - + -
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Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLY 2.9 14.9 + - - +
173A LEU* 3.4 20.3 + - + +
174A GLU 3.4 0.6 - - - -
175A LEU* 1.3 78.9 - - - +
177A ARG* 1.3 60.2 + - + +
178A THR 3.3 3.1 + - - -
179A GLY* 4.2 4.9 + - - -
180A ILE 4.7 4.8 - - - +
248A THR* 4.5 17.7 - - + +
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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