Contacts of the helix formed by residues 165 - 187 (chain A) in PDB entry 4LZ6
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 ASN 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ARG* 4.4 16.7 + - - +
160A ILE* 2.8 26.6 + - + +
161A ARG* 4.4 1.0 + - - -
163A GLU* 4.2 2.2 + - - +
164A GLY* 1.3 68.0 - - - +
166A ALA* 1.3 61.0 + - - +
167A THR* 3.0 12.7 + - - +
168A PHE* 3.3 48.9 + - + +
169A ALA* 3.3 15.6 + - - +
216A TYR* 4.4 7.9 + - - -
222A SER* 4.7 5.9 - - - -
223A THR* 3.0 25.0 + - - +
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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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22A LEU* 3.7 31.4 - - + +
25A PRO* 3.1 41.5 - - + +
26A ALA 5.1 0.9 - - - +
161A ARG* 4.9 10.5 - - + +
164A GLY 2.7 8.2 + - - +
165A ASN* 1.3 73.9 - - - +
167A THR* 1.3 61.9 + - - +
169A ALA* 2.9 22.8 - - + +
170A MET* 3.2 5.2 + - - +
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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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9A ARG* 4.2 26.5 + - - +
22A LEU* 6.2 0.2 - - - +
25A PRO* 4.7 4.8 - - + +
164A GLY 5.2 0.2 + - - -
165A ASN* 3.0 7.8 + - - -
166A ALA* 1.3 81.4 + - - +
168A PHE* 1.3 66.3 + - - +
169A ALA 3.0 0.9 - - - -
170A MET* 3.0 36.2 - - + +
171A VAL* 3.0 8.4 - - + +
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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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160A ILE* 3.5 36.3 - - + -
163A GLU* 5.5 1.3 - - - -
165A ASN* 3.3 36.4 + - + +
167A THR* 1.3 78.6 - - - +
169A ALA* 1.3 66.0 + - - +
171A VAL* 3.0 19.4 + - + +
172A THR* 3.0 23.4 + - + -
212A LEU* 4.3 6.7 - - + -
213A VAL* 3.6 24.2 - - + -
216A TYR* 3.1 70.7 - + + -
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Residues in contact with ALA 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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25A PRO* 5.4 1.1 - - + -
26A ALA 6.0 0.4 - - - +
157A ASN* 3.3 17.3 - - - +
160A ILE* 3.7 3.3 - - + +
161A ARG* 4.1 19.5 - - + +
165A ASN 3.3 18.0 + - - +
166A ALA* 2.9 18.2 - - - +
168A PHE* 1.3 70.1 - - - +
170A MET* 1.3 53.9 + - - +
171A VAL 2.3 4.8 + - - -
172A THR* 2.2 49.4 + - - -
173A MET* 3.1 4.9 + - - -
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Residues in contact with MET 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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24A ILE* 4.4 10.8 - - + -
25A PRO* 3.1 61.1 + - + +
28A ILE* 3.7 21.3 - - + -
29A GLY* 4.3 1.6 - - - -
161A ARG* 5.4 0.4 - - - +
166A ALA 3.2 4.9 + - - +
167A THR* 3.0 28.7 - - + +
169A ALA* 1.3 73.7 - - - +
171A VAL* 1.3 57.3 + - + +
173A MET* 3.7 8.6 - - - +
174A ILE* 2.4 58.8 + - + +
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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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167A THR* 3.0 21.5 - - + +
168A PHE* 3.2 20.0 - - + +
169A ALA 2.3 10.3 + - - -
170A MET* 1.3 76.0 - - + +
172A THR* 1.3 62.8 + - - -
173A MET 3.6 0.2 - - - +
174A ILE* 3.8 17.5 - - + -
175A VAL* 3.2 34.8 - - + +
209A VAL* 4.5 0.5 - - - +
212A LEU* 4.7 14.4 - - + +
216A TYR* 5.5 7.2 - - - +
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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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153A ALA* 5.4 3.1 - - - +
156A ALA* 5.3 1.6 - - + -
157A ASN* 2.3 45.9 + - + +
160A ILE* 4.2 2.7 - - + -
168A PHE* 3.0 39.1 + - + +
169A ALA 2.2 28.4 + - - -
171A VAL* 1.3 69.3 - - - +
173A MET* 1.3 54.5 + - - +
176A PRO* 2.7 28.6 - - - +
209A VAL* 3.6 13.5 - - + +
212A LEU* 5.0 2.2 - - + -
213A VAL* 4.4 18.4 - - + -
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Residues in contact with MET 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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29A GLY* 3.8 32.8 - - - +
30A MET* 5.0 5.4 - - - -
33A MET* 4.6 26.2 - - + +
153A ALA 5.6 1.6 - - - +
154A PHE* 5.4 12.8 - - + -
157A ASN* 3.3 31.9 - - + +
161A ARG* 4.0 15.0 - - - +
169A ALA 3.1 9.1 + - - +
170A MET* 3.1 3.8 - - - +
172A THR* 1.3 79.0 - - - +
174A ILE* 1.3 53.0 - - - +
175A VAL 1.9 27.0 + - - -
176A PRO* 2.4 24.2 - - + +
177A ALA* 4.5 3.6 - - - -
206A GLN* 6.1 2.7 - - - +
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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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28A ILE* 4.9 2.7 - - + -
29A GLY* 4.5 1.7 - - - -
32A VAL* 4.3 25.1 - - + +
170A MET* 2.4 57.1 + - + +
171A VAL* 3.8 15.7 - - + -
173A MET* 1.3 68.6 - - - +
175A VAL* 1.3 77.6 + - + +
177A ALA* 3.0 11.7 - - - +
178A VAL* 2.8 43.6 + - + +
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Residues in contact with VAL 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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171A VAL* 3.2 25.8 - - + +
173A MET 1.9 18.0 + - - -
174A ILE* 1.3 88.2 - - + +
176A PRO* 1.3 74.0 - - + +
178A VAL* 3.5 10.0 - - + +
179A LEU* 3.1 19.1 + - + +
208A SER 5.0 9.0 - - - +
209A VAL* 4.0 13.2 - - + +
212A LEU* 5.3 6.1 - - + -
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Residues in contact with PRO 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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33A MET* 4.5 19.7 - - + -
172A THR 2.7 23.6 - - - +
173A MET* 2.4 33.0 - - + +
175A VAL* 1.3 73.6 - - + +
177A ALA* 1.3 70.4 + - + +
179A LEU* 2.6 14.8 + - + +
180A ASN* 2.5 26.0 + - + +
205A ALA* 4.4 13.9 - - + +
206A GLN* 3.7 24.2 - - - +
209A VAL* 3.8 8.3 - - + -
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Residues in contact with ALA 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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32A VAL* 3.9 21.8 - - + -
33A MET* 4.5 19.6 - - + +
36A TYR* 4.5 13.2 - - + +
173A MET 4.2 1.6 - - - +
174A ILE* 3.0 21.3 - - - +
176A PRO* 1.3 78.6 - - - +
178A VAL* 1.3 66.3 + - + +
180A ASN* 2.8 17.1 + - - +
181A ILE* 3.0 18.4 + - - +
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Residues in contact with VAL 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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32A VAL* 6.1 2.7 - - + -
174A ILE* 2.8 25.3 + - + +
175A VAL* 3.5 25.1 - - + +
176A PRO 2.9 0.8 + - - -
177A ALA* 1.3 76.4 - - + +
179A LEU* 1.3 55.4 + - - +
181A ILE* 3.4 4.5 + - - +
182A LEU* 2.7 45.4 - - + +
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Residues in contact with LEU 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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175A VAL* 3.1 12.8 + - + +
176A PRO* 2.6 15.1 + - + +
178A VAL* 1.3 75.3 - - - +
180A ASN* 1.3 49.0 + - - -
181A ILE 3.0 0.3 + - - -
182A LEU* 3.2 7.9 + - + +
183A LEU* 2.7 62.3 + - + +
204A ILE* 3.2 14.8 - - + +
205A ALA* 2.9 44.2 - - + +
208A SER* 4.5 11.7 - - - +
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Residues in contact with ASN 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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33A MET* 5.8 2.9 - - + +
36A TYR* 3.1 31.5 - - + -
176A PRO* 2.5 25.5 + - + +
177A ALA 2.8 5.3 + - - +
179A LEU* 1.3 69.1 - - - +
181A ILE* 1.3 60.0 + - - +
183A LEU* 4.3 3.4 - - - +
184A ASP* 2.5 37.9 + - - +
201A ALA* 3.6 10.3 - - - +
202A THR* 2.4 50.0 + - - +
205A ALA* 3.7 14.1 - - + +
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Residues in contact with ILE 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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36A TYR* 3.5 27.1 - - + +
39A VAL* 3.3 40.2 - - + +
40A ASP* 4.6 1.8 - - + -
43A PHE* 4.8 8.1 - - + -
177A ALA 3.0 11.6 + - - +
178A VAL* 3.8 7.6 - - - +
180A ASN* 1.3 85.7 - - - +
182A LEU* 1.3 70.8 + - + +
183A LEU 2.7 5.0 + - - -
184A ASP* 2.6 26.7 + - + +
185A VAL* 3.1 23.9 + - + +
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Residues in contact with LEU 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 VAL* 2.7 38.6 - - + +
179A LEU* 4.0 5.8 - - + +
181A ILE* 1.3 92.0 - - + +
183A LEU* 1.3 56.2 + - - +
185A VAL* 4.1 8.7 - - - +
186A LEU* 3.3 28.4 + - - +
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Residues in contact with LEU 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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179A LEU* 2.7 39.8 + - + +
180A ASN* 4.2 6.5 - - - +
182A LEU* 1.3 74.9 - - - +
184A ASP* 1.3 69.9 + - - +
186A LEU* 3.0 27.8 - - + +
187A PHE* 3.0 36.8 - - + -
201A ALA* 3.5 32.5 - - - +
204A ILE* 3.7 29.6 - - + -
205A ALA 4.7 0.4 - - - +
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Residues in contact with ASP 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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36A TYR* 3.6 10.7 - - - -
40A ASP* 3.8 12.7 - - + +
43A PHE* 4.4 9.9 - - + -
180A ASN* 2.5 32.1 + - - +
181A ILE* 2.6 9.6 + - - +
183A LEU* 1.3 75.9 - - - +
185A VAL* 1.3 55.9 - - - +
186A LEU 2.1 21.0 + - - -
187A PHE* 2.4 17.9 + - - +
188A ILE* 3.2 20.6 + - + +
198A ALA* 3.2 36.3 - - - +
201A ALA* 3.4 7.8 - - - +
202A THR* 4.4 1.2 + - - -
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Residues in contact with VAL 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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43A PHE* 3.5 31.1 - - + -
181A ILE* 3.1 18.7 + - + +
182A LEU* 4.1 8.1 - - - +
184A ASP* 1.3 73.8 - - - +
186A LEU* 1.3 55.0 + - + +
188A ILE* 3.4 11.7 - - - +
189A PHE* 4.7 7.6 - - + +
190A GLY* 2.7 38.3 + - - +
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Residues in contact with LEU 186 (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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182A LEU 3.3 15.1 + - - +
183A LEU* 3.0 29.4 - - + +
184A ASP 2.1 11.1 + - - -
185A VAL* 1.3 72.5 - - - +
187A PHE* 1.3 72.9 + - + +
190A GLY* 3.3 4.1 - - - -
191A LEU* 2.8 42.5 + - + +
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Residues in contact with PHE 187 (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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183A LEU* 3.0 53.4 - - + -
184A ASP* 2.4 16.4 + - - +
186A LEU* 1.3 76.9 - - + +
188A ILE* 1.3 71.4 + - - +
189A PHE 3.3 0.2 + - - -
191A LEU* 2.7 50.0 + - + +
192A ASN 3.5 0.2 + - - -
193A MET* 3.6 24.7 - - + +
197A GLY 3.8 21.1 - - - +
200A ILE* 3.5 30.7 - - + -
201A ALA* 3.9 6.3 - - + -
204A ILE* 4.7 9.0 - - + -
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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