Contacts of the helix formed by residues 155 - 178 (chain A) in PDB entry 3GD8
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 155 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A VAL* 3.8 6.5 - - - +
153A ASN 5.9 0.2 - - - +
154A LEU* 1.3 78.6 - - - +
156A ALA* 1.3 57.7 + - - +
157A GLY* 3.5 5.2 + - - -
158A HIS* 3.0 40.7 + - + +
159A GLY 2.9 23.7 + - - -
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Residues in contact with ALA 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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150A VAL* 4.7 8.9 - - - +
154A LEU 4.1 0.2 + - - -
155A THR* 1.3 72.2 - - - +
157A GLY* 1.3 56.7 + - - +
159A GLY* 3.3 1.5 + - - +
160A LEU* 2.8 30.7 + - - +
229A ASN* 3.8 13.9 - - - +
231A TRP* 4.5 7.0 - - + -
232A ILE* 4.0 16.6 - - + +
473A BOG 3.6 26.7 - - - +
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Residues in contact with GLY 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A THR* 3.2 7.1 + - - -
156A ALA* 1.3 78.3 - - - +
158A HIS* 1.3 60.1 + - - +
160A LEU* 3.3 12.5 + - - +
161A LEU* 3.1 25.6 + - - +
231A TRP* 5.8 1.8 - - - -
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Residues in contact with HIS 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 4.1 19.1 - - + +
155A THR* 3.0 32.8 + - + +
157A GLY* 1.3 74.4 - - - +
159A GLY* 1.3 60.3 + - - +
161A LEU* 3.2 19.2 + - + +
162A VAL* 3.0 33.7 + - + +
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Residues in contact with GLY 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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150A VAL* 4.6 3.1 - - - -
154A LEU* 3.9 5.9 - - - +
155A THR 2.9 14.0 + - - -
156A ALA 3.6 3.6 - - - -
158A HIS* 1.3 77.4 - - - +
160A LEU* 1.3 61.4 + - - +
162A VAL 3.3 0.9 + - - -
163A GLU* 3.0 28.9 + - - +
208A THR* 3.6 22.0 - - - +
232A ILE* 3.7 13.2 - - - -
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Residues in contact with LEU 160 (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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156A ALA 2.8 17.0 + - - +
157A GLY* 3.4 14.1 - - - +
158A HIS 3.3 0.2 - - - -
159A GLY* 1.3 73.3 - - - +
161A LEU* 1.3 57.6 + - - +
163A GLU* 3.3 4.7 + - - +
164A LEU* 2.8 34.4 + - + +
231A TRP* 4.2 20.4 - - + -
232A ILE* 3.8 24.6 - - + +
235A VAL* 3.9 16.2 - - + -
236A GLY* 3.2 36.1 - - - +
239A ILE* 5.5 4.3 - - + -
473A BOG 5.5 4.3 - - + -
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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
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157A GLY 3.1 13.0 + - - +
158A HIS* 3.2 22.2 + - + +
160A LEU* 1.3 74.9 - - - +
162A VAL* 1.3 66.6 + - + +
164A LEU* 3.3 17.8 + - + +
165A ILE* 3.0 53.6 + - + +
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Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 4.6 3.8 - - + -
158A HIS* 3.0 21.9 + - + +
159A GLY 3.3 4.2 + - - +
161A LEU* 1.3 76.5 - - + +
163A GLU* 1.3 64.1 + - - +
165A ILE* 3.2 6.3 + - - +
166A ILE* 3.0 24.9 + - + +
203A PHE* 4.0 21.3 - - + -
204A ALA* 3.6 31.2 - - + -
207A TYR* 4.4 24.2 - - + -
208A THR* 3.9 15.5 - - + +
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Residues in contact with GLU 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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159A GLY 3.0 20.4 + - - +
160A LEU* 3.7 3.8 - - - +
162A VAL* 1.3 73.3 - - - +
164A LEU* 1.3 64.2 + - - +
166A ILE* 3.6 7.2 - - - +
167A THR* 2.7 33.0 + - - -
208A THR* 2.7 29.0 + - - +
210A ALA* 3.5 1.0 - - - -
211A SER* 2.9 27.8 + - - -
212A MET* 2.8 29.1 + - - -
232A ILE* 4.5 4.9 - - + +
233A TYR* 3.6 19.4 - - + -
236A GLY* 4.2 3.8 - - - -
237A PRO* 3.9 17.8 - - + +
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Residues in contact with LEU 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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160A LEU* 2.8 22.1 + - + +
161A LEU* 3.4 17.3 - - + +
163A GLU* 1.3 76.2 - - - +
165A ILE* 1.3 70.2 + - + +
168A PHE* 2.8 37.7 + - + +
236A GLY* 3.4 15.8 + - - +
239A ILE* 3.7 26.2 - - + -
240A GLY* 3.5 22.6 - - - +
243A LEU* 4.3 14.1 - - + -
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Residues in contact with ILE 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* 3.0 45.6 + - + +
162A VAL* 3.9 5.2 - - - +
164A LEU* 1.3 85.7 - - + +
166A ILE* 1.3 66.8 + - + +
168A PHE* 3.3 8.7 + - + +
169A GLN* 3.1 25.3 + - + +
203A PHE* 5.8 6.3 - - + -
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Residues in contact with ILE 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 VAL* 3.0 22.0 + - + +
163A GLU* 3.6 18.2 - - - +
165A ILE* 1.3 77.7 - - + +
167A THR* 1.3 62.5 + - - +
169A GLN* 3.0 32.1 + - + +
170A LEU 3.3 2.6 + - - -
200A GLY* 4.1 22.7 - - - +
203A PHE* 3.6 32.3 - - + -
204A ALA* 3.7 21.5 - - + -
210A ALA* 3.8 13.9 - - - -
212A MET* 3.5 30.8 - - + +
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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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97A ASN* 5.4 0.4 - - - +
99A ALA* 4.2 2.9 - - + -
163A GLU 2.7 23.0 + - - -
164A LEU 4.0 2.0 - - - -
166A ILE* 1.3 74.5 - - - +
168A PHE* 1.3 66.9 + - - +
170A LEU* 3.2 6.8 + - + +
171A VAL* 2.9 39.3 + - + +
212A MET* 3.3 34.1 - - + +
237A PRO* 3.3 42.3 - - + +
240A GLY 4.5 0.4 - - - -
241A ALA* 4.1 2.7 - - + +
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Residues in contact with PHE 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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164A LEU* 2.8 23.9 + - + +
165A ILE* 3.4 12.1 - - + +
167A THR* 1.3 76.0 - - - +
169A GLN* 1.3 64.1 + - + +
172A PHE* 2.9 55.8 + + + +
240A GLY* 3.5 26.4 - - - +
243A LEU* 3.8 11.9 - - + -
244A ALA* 3.3 28.5 - - + +
247A LEU* 3.8 29.2 - - + -
252A PHE* 6.2 0.2 - + - -
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Residues in contact with GLN 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 ILE* 3.1 15.0 + - + +
166A ILE* 3.0 25.4 + - + +
168A PHE* 1.3 86.6 - - + +
170A LEU* 1.3 57.7 + - - +
172A PHE* 3.8 5.0 - - - +
173A THR* 2.8 35.9 + - - -
196A SER* 2.6 46.3 + - - -
199A ILE* 3.5 25.4 - - + +
200A GLY* 4.1 5.3 - - - +
212A MET* 3.5 9.1 - - - +
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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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97A ASN* 4.1 23.3 - - - +
100A VAL* 5.1 2.0 - - + -
166A ILE 3.3 9.4 + - - +
167A THR* 3.2 11.6 + - + +
169A GLN* 1.3 82.8 - - - +
171A VAL* 1.3 59.3 + - + +
173A THR* 3.2 5.0 + - - -
174A ILE* 3.0 40.5 + - + +
193A ILE* 3.9 17.5 - - + +
196A SER* 3.1 23.3 - - - +
197A VAL* 3.6 34.5 - - + +
212A MET* 4.0 23.1 - - + +
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Residues in contact with VAL 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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100A VAL* 4.2 24.0 - - + -
103A ALA* 4.0 5.8 - - + -
167A THR* 2.9 26.8 + - + +
170A LEU* 1.3 75.1 - - + +
172A PHE* 1.3 65.1 + - - +
174A ILE* 3.2 8.5 + - + +
175A PHE* 3.0 48.2 + - + -
241A ALA* 3.5 42.4 - - + +
244A ALA* 3.9 9.9 - - + -
245A GLY 4.1 0.2 - - - +
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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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168A PHE* 2.9 41.2 + + + +
169A GLN* 3.8 7.6 - - - +
171A VAL* 1.3 77.2 - - - +
173A THR* 1.3 56.4 + - - +
175A PHE* 3.3 5.1 + - - +
176A ALA* 2.9 38.9 + - + +
244A ALA* 3.6 17.3 - - + +
247A LEU* 4.4 3.6 - - + -
248A TYR* 3.6 41.3 - + + -
252A PHE* 3.7 37.0 - + + -
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Residues in contact with THR 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 GLN* 2.8 21.7 + - - -
170A LEU 3.2 8.9 + - - -
172A PHE* 1.3 77.0 - - - +
174A ILE* 1.3 55.9 + - - +
176A ALA* 3.9 4.2 - - - +
177A SER* 2.8 48.1 + - - +
192A ALA* 3.7 31.2 - - + +
193A ILE* 4.3 4.9 - - + -
196A SER* 3.5 16.0 + - - -
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Residues in contact with ILE 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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95A HIS 5.8 0.9 - - - +
100A VAL* 3.6 34.8 - - + -
104A MET* 4.0 25.6 - - + -
170A LEU* 3.0 29.3 + - + +
171A VAL* 3.5 10.8 - - + +
173A THR* 1.3 76.7 - - - +
175A PHE* 1.3 63.6 + - + +
177A SER* 4.6 0.2 - - - -
178A CYS* 3.1 38.6 + - + +
193A ILE* 3.9 35.4 - - + -
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Residues in contact with PHE 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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103A ALA* 4.1 10.5 - - + -
104A MET* 3.7 31.9 - - + -
107A THR* 3.6 25.4 - - - -
109A LYS* 3.6 13.9 - - + -
171A VAL* 3.0 46.7 + - + +
172A PHE* 3.9 2.5 - - - +
174A ILE* 1.3 76.7 - - + +
176A ALA* 1.3 62.9 + - - +
178A CYS* 3.9 2.3 - - - -
179A ASP* 3.2 25.1 + - - +
245A GLY* 3.9 19.3 - - - -
248A TYR* 3.8 23.2 - + + -
249A GLU* 3.4 37.1 - - + +
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Residues in contact with ALA 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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172A PHE* 2.9 26.0 + - + +
173A THR* 3.9 5.4 - - - +
175A PHE* 1.3 76.3 - - - +
177A SER* 1.3 60.7 - - - +
178A CYS 3.5 0.2 + - - -
179A ASP 3.6 2.1 + - - -
182A ARG* 3.0 44.4 + - - +
185A VAL* 4.1 0.2 - - - +
248A TYR* 3.6 24.6 - - + -
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Residues in contact with SER 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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173A THR* 2.8 35.2 + - - +
174A ILE* 3.9 4.3 - - - -
176A ALA* 1.3 77.6 - - - +
178A CYS* 1.3 60.5 + - - +
179A ASP 3.4 0.9 + - - +
182A ARG* 4.7 1.3 - - - +
185A VAL* 3.9 20.8 - - - +
189A ILE* 3.5 46.2 - - - +
192A ALA* 3.9 12.3 - - - +
193A ILE* 4.9 1.6 - - - -
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Residues in contact with CYS 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 ILE* 3.1 32.2 + - + +
175A PHE* 3.9 3.4 - - - +
176A ALA 3.3 0.2 - - - -
177A SER* 1.3 79.0 - - - +
179A ASP* 1.3 62.4 + - - +
180A SER* 3.1 9.9 + - - -
189A ILE* 4.1 23.6 - - - -
193A ILE* 4.8 3.8 - - - -
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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) + - + + + + + -
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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