Contacts of the helix formed by residues 162 - 185 (chain A) in PDB entry 1S9J
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 PRO 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ARG 4.1 3.8 - - - +
161A ILE* 1.3 92.0 - - + +
163A GLU* 1.3 64.5 + - - +
164A GLN* 4.1 9.9 - - + +
165A ILE* 3.2 16.2 + - + +
166A LEU* 3.1 19.2 + - - +
374A TRP* 3.4 37.7 - - + +
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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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161A ILE 3.6 1.9 + - - -
162A PRO* 1.3 71.2 - - - +
164A GLN* 1.3 65.3 + - + +
166A LEU* 3.4 12.2 + - - +
167A GLY* 3.1 18.2 + - - -
329A VAL 4.2 2.9 - - - +
330A PHE* 3.5 25.7 - - + -
331A SER* 2.7 46.8 + - - -
334A PHE* 3.2 33.2 - - + +
360A PHE* 4.2 8.2 - - + -
363A ARG* 3.6 15.6 + - - +
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Residues in contact with GLN 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PRO* 3.2 6.7 - - + -
163A GLU* 1.3 80.8 - - + +
165A ILE* 1.3 64.1 + - + +
167A GLY* 3.2 10.2 + - - +
168A LYS* 3.5 9.2 + - - +
363A ARG* 4.4 9.2 + - - +
364A SER* 5.4 0.9 - - - -
367A GLU* 3.0 43.9 + - - +
368A GLU 5.4 1.8 + - - -
369A VAL* 4.3 28.3 - - + +
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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
----------------------------------------------------------
151A LEU* 6.5 0.2 - - + -
161A ILE* 3.5 20.2 - - + -
162A PRO* 3.2 31.7 + - + +
164A GLN* 1.3 73.8 - - + +
166A LEU* 1.3 59.6 + - - +
167A GLY 3.1 4.3 - - - -
168A LYS* 3.2 7.9 + - - +
169A VAL* 3.1 22.8 + - + +
369A VAL* 3.7 27.1 - - + -
371A PHE* 3.5 37.0 - - + -
374A TRP* 3.9 33.9 - - + -
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ILE* 3.7 28.3 - - + +
162A PRO 3.1 11.9 + - - +
163A GLU* 3.4 7.2 + - - +
165A ILE* 1.3 71.4 - - - +
167A GLY* 1.3 55.4 + - - +
169A VAL* 3.7 11.4 - - + +
170A SER* 2.7 36.4 + - - -
253A LEU* 3.9 16.6 - - + +
256A MET* 3.7 35.4 - - + -
257A ALA* 3.6 40.8 - - + +
334A PHE* 4.1 15.3 - - + -
360A PHE* 4.3 2.0 - - - -
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Residues in contact with GLY 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLU 3.1 10.2 + - - -
164A GLN* 3.2 6.2 + - - -
165A ILE 3.1 1.0 - - - -
166A LEU* 1.3 78.4 - - - +
168A LYS* 1.3 60.8 + - - +
170A SER* 3.3 4.9 + - - -
171A ILE* 3.2 25.6 + - - +
360A PHE* 3.5 14.7 - - - -
361A ILE* 4.7 0.5 - - - +
364A SER* 3.5 27.8 - - - -
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Residues in contact with LYS 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 GLN 3.5 8.4 + - - +
165A ILE* 3.2 10.8 + - - +
167A GLY* 1.3 72.4 - - - +
169A VAL* 1.3 64.1 + - - +
171A ILE* 3.5 15.5 + - + +
172A ALA* 3.3 16.8 + - - +
202A GLY* 4.4 16.1 + - - -
204A ILE* 3.8 17.5 - - + +
364A SER* 4.6 4.7 + - - +
369A VAL* 3.8 26.5 + - + +
371A PHE* 3.4 34.2 - - + +
372A ALA 5.2 0.4 - - - +
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Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 3.8 33.4 - - + -
161A ILE* 5.8 0.7 - - + -
165A ILE* 3.1 23.6 + - + +
166A LEU* 3.7 17.5 - - + +
167A GLY 3.2 0.2 - - - -
168A LYS* 1.3 75.2 - - - +
170A SER* 1.3 65.7 + - - +
172A ALA* 3.1 5.4 + - - +
173A VAL* 3.0 34.7 + - + +
196A ILE* 4.7 4.7 - - + -
204A ILE* 4.0 20.2 - - + -
253A LEU* 4.6 5.8 - - + -
256A MET* 4.6 13.2 - - + -
371A PHE* 4.7 3.6 - - + -
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Residues in contact with SER 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU 2.7 23.3 + - - -
167A GLY 3.3 5.8 + - - -
169A VAL* 1.3 78.3 - - - +
171A ILE* 1.3 61.1 + - - +
173A VAL* 3.4 5.5 + - - +
174A ILE* 3.1 33.0 + - - +
249A MET* 5.1 3.4 - - - -
253A LEU* 3.3 25.4 - - - +
337A PHE* 4.1 12.3 - - - -
360A PHE* 3.8 9.1 - - - -
361A ILE* 3.8 17.0 - - - -
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Residues in contact with ILE 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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125A TYR* 5.0 4.5 - - + +
167A GLY 3.2 18.3 + - - +
168A LYS* 3.7 14.8 - - + +
169A VAL 3.2 0.4 - - - -
170A SER* 1.3 75.4 - - - +
172A ALA* 1.3 64.5 + - - +
174A ILE* 4.0 3.8 - - - +
175A LYS* 3.1 54.0 + - + +
356A MET* 6.3 1.8 - - - -
361A ILE* 3.8 27.4 - - + +
364A SER* 3.7 25.1 - - - +
365A ASP* 3.8 29.4 - - - +
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TYR* 3.6 29.0 - - + +
168A LYS 3.3 7.4 + - - +
169A VAL 3.1 9.3 + - - +
171A ILE* 1.3 81.6 - - - +
173A VAL* 1.3 57.4 + - + +
176A GLY* 3.1 21.3 + - - -
204A ILE* 3.5 45.3 - - + +
206A LEU* 4.6 2.9 - - - +
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A VAL* 3.0 24.5 + - + +
170A SER* 4.0 2.2 - - - +
172A ALA* 1.3 75.7 - - + +
174A ILE* 1.3 61.4 + - - +
176A GLY* 3.3 0.7 + - - -
177A LEU* 3.0 48.3 + - + +
191A VAL* 4.5 9.9 - - + -
196A ILE* 4.1 28.0 - - + -
204A ILE* 5.7 0.2 - - + -
206A LEU* 4.2 14.6 - - + -
249A MET* 3.4 37.5 - - + -
253A LEU* 6.4 0.2 - - + -
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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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170A SER 3.1 19.3 + - - +
171A ILE* 4.0 4.3 - - - +
173A VAL* 1.3 76.4 - - - +
175A LYS* 1.3 53.4 + - - +
177A LEU 3.9 0.5 - - - -
178A THR* 2.6 40.0 + - - +
249A MET* 4.1 16.6 - - + -
337A PHE* 4.0 16.4 - - + -
352A LEU* 4.0 31.1 - - + +
355A LEU* 4.2 14.1 - - + +
356A MET* 3.6 31.6 - - + -
361A ILE* 3.8 30.7 - - + -
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Residues in contact with LYS 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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125A TYR* 3.2 54.6 + - + +
171A ILE* 3.1 38.3 + - + +
174A ILE* 1.3 75.8 - - - +
176A GLY* 1.3 58.0 + - - +
178A THR* 3.8 6.6 - - - -
179A TYR* 3.2 26.2 + - - +
356A MET* 4.0 27.6 - - + -
365A ASP* 4.5 11.6 + - - -
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Residues in contact with GLY 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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125A TYR* 3.9 12.3 - - - -
126A ILE* 3.9 8.8 - - - +
172A ALA 3.1 17.3 + - - -
173A VAL 3.3 1.1 + - - -
175A LYS* 1.3 76.3 - - - +
177A LEU* 1.3 63.2 + - - +
178A THR 3.2 0.2 - - - -
179A TYR* 3.4 5.5 + - - +
180A LEU* 3.2 27.8 + - - +
206A LEU* 3.9 16.2 - - - -
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Residues in contact with LEU 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 VAL* 3.0 33.0 + - + +
176A GLY* 1.3 72.8 - - - +
178A THR* 1.3 64.9 + - - +
180A LEU* 3.4 8.8 + - + +
181A ARG* 3.1 24.6 + - - +
186A ILE 5.0 0.7 - - - +
188A HIS* 4.2 16.2 - - + +
191A VAL* 4.3 9.0 - - + -
206A LEU* 3.3 24.9 - - + -
245A ASP* 4.1 35.0 - - + +
246A ILE* 4.8 5.8 - - + -
249A MET* 5.0 3.1 - - - -
352A LEU* 3.7 32.5 - - + +
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Residues in contact with THR 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* 2.6 24.5 + - - +
175A LYS* 3.8 8.5 - - - -
177A LEU* 1.3 73.2 - - - +
179A TYR* 1.3 67.3 + - - +
181A ARG* 3.5 1.5 + - - +
182A GLU* 3.1 37.2 + - + +
352A LEU* 3.8 24.3 - - + +
356A MET* 3.9 18.4 - - + +
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Residues in contact with TYR 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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120A GLU 3.1 4.5 + - - -
121A CYS* 4.0 13.7 - - + -
122A ASN* 3.0 37.8 + - - +
123A SER* 3.9 28.0 - - - +
126A ILE* 4.0 11.7 - - + -
175A LYS 3.2 18.6 + - - +
176A GLY* 3.6 4.7 - - - +
177A LEU 3.3 0.4 - - - -
178A THR* 1.3 78.0 - - - +
180A LEU* 1.3 65.5 + - + +
182A GLU* 5.3 0.2 - - - -
183A LYS* 3.1 68.1 + - + +
184A HIS* 3.0 32.7 + + - -
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Residues in contact with LEU 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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121A CYS* 4.4 13.2 - - - -
126A ILE* 4.1 14.1 - - + -
176A GLY 3.2 20.0 + - - +
177A LEU* 3.9 9.2 - - + +
178A THR 3.3 0.4 - - - -
179A TYR* 1.3 83.0 - - + +
181A ARG* 1.3 56.7 + - - +
184A HIS* 3.1 13.3 + - + +
185A LYS 2.9 22.3 + - - -
186A ILE* 3.3 30.3 + - + +
188A HIS* 4.3 17.7 - - + +
206A LEU* 5.1 0.2 - - + -
209A PHE* 3.8 54.1 - - + -
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Residues in contact with ARG 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 LEU 3.1 17.1 + - - +
178A THR* 4.0 4.5 - - - +
179A TYR 3.4 0.2 - - - -
180A LEU* 1.3 77.4 - - - +
182A GLU* 1.3 75.8 + - + +
185A LYS* 3.0 56.3 + - - +
186A ILE 3.6 12.3 + - - +
242A VAL* 3.8 36.7 - - + +
352A LEU* 4.8 10.3 - - + -
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Residues in contact with GLU 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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178A THR* 3.1 29.0 + - + +
179A TYR* 4.6 0.9 - - - +
181A ARG* 1.3 95.1 + - + +
183A LYS* 1.3 67.8 + - + +
185A LYS* 4.3 16.0 + - - +
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Residues in contact with LYS 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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122A ASN 5.3 1.0 + - - -
179A TYR* 3.1 47.3 + - + +
182A GLU* 1.3 82.7 - - + +
184A HIS* 1.3 78.6 + - + +
185A LYS* 3.8 2.3 - - - +
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Residues in contact with HIS 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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117A VAL* 4.6 7.9 + - + +
120A GLU* 3.2 34.4 + - + -
121A CYS* 3.8 16.8 - - - -
179A TYR* 3.0 45.8 + + - -
180A LEU* 3.1 13.2 + - + +
183A LYS* 1.3 89.0 + - + +
185A LYS* 1.3 74.3 + - - +
186A ILE* 3.2 22.9 + - + +
211A VAL* 6.2 0.4 - - + -
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Residues in contact with LYS 185 (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 LEU 2.9 3.6 + - - -
181A ARG* 3.0 40.0 + - - +
182A GLU* 4.3 15.7 + - - +
183A LYS 5.1 1.1 - - - +
184A HIS* 1.3 79.1 - - - +
186A ILE* 1.3 64.6 + - - +
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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
------------------------------------------------------------
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