Contacts of the helix formed by residues 160 - 184 (chain A) in PDB entry 4LEY
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 LYS 160 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ARG 4.5 6.3 - - - +
159A LEU* 1.3 79.3 - - - +
161A ARG* 1.3 60.8 + - - +
162A LYS* 3.2 5.8 - - + +
163A ASP* 3.1 30.9 + - - +
164A ILE* 2.9 31.4 + - - +
209A PRO* 5.4 0.4 - - - +
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Residues in contact with ARG 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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159A LEU 4.3 0.2 + - - -
160A LYS* 1.3 72.4 - - - +
162A LYS* 1.3 57.8 + - + +
164A ILE* 3.7 14.6 - - + +
165A SER* 2.9 33.8 + - - -
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Residues in contact with LYS 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LYS* 3.2 4.4 - - + +
161A ARG* 1.3 79.2 - - + +
163A ASP* 1.3 64.8 + - - +
165A SER* 3.8 3.6 - - - -
166A GLU* 2.9 47.6 + - - +
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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
----------------------------------------------------------
160A LYS* 3.1 34.9 + - - +
162A LYS* 1.3 82.2 - - - +
164A ILE* 1.3 57.3 + - - +
166A GLU* 3.9 10.6 - - - +
167A ALA* 2.9 33.3 + - - +
207A SER 5.5 2.3 - - - +
209A PRO* 3.6 24.8 - - + +
302A GLU* 5.1 2.6 - - - +
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Residues in contact with ILE 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU* 3.7 28.7 - - + +
160A LYS 2.9 25.6 + - - +
161A ARG* 3.7 12.8 - - + +
163A ASP* 1.3 73.4 - - - +
165A SER* 1.3 60.8 + - - +
167A ALA* 4.0 1.0 - - - +
168A ALA* 2.9 34.9 + - + +
200A TYR* 3.6 26.5 + - + +
209A PRO* 4.0 21.3 - - + -
212A PHE* 5.4 0.3 - - - -
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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
----------------------------------------------------------
161A ARG* 2.9 22.6 + - - -
162A LYS* 3.8 4.5 - - - -
164A ILE* 1.3 77.2 - - - +
166A GLU* 1.3 64.9 + - - +
168A ALA* 3.1 5.5 + - - +
169A GLU* 3.0 39.9 + - - +
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Residues in contact with GLU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LYS* 2.9 39.9 + - - +
163A ASP* 3.9 8.2 - - - +
165A SER* 1.3 74.5 - - - +
167A ALA* 1.3 60.8 + - - +
169A GLU* 3.6 20.5 + - - +
170A THR* 3.5 8.5 + - - -
300A ASN* 2.9 23.6 - - - +
302A GLU* 4.1 18.9 - - - +
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Residues in contact with ALA 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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163A ASP 2.9 19.2 + - - +
164A ILE 4.0 1.6 - - - +
166A GLU* 1.3 76.7 - - - +
168A ALA* 1.3 61.8 + - - +
170A THR* 3.3 4.9 + - - -
171A VAL* 2.9 32.0 + - - +
209A PRO* 3.7 20.2 - - + +
212A PHE* 4.0 10.3 - - + -
300A ASN* 4.2 0.4 - - - -
302A GLU* 4.5 3.5 + - + +
304A ILE* 3.7 27.8 - - + -
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Residues in contact with ALA 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ILE* 2.9 20.8 + - + +
165A SER* 3.9 3.8 - - - +
167A ALA* 1.3 74.1 - - - +
169A GLU* 1.3 65.3 + - - +
171A VAL* 4.3 7.2 - - - -
172A ASN* 2.7 45.5 + - - +
200A TYR* 4.0 18.4 - - + +
212A PHE* 4.5 5.3 - - + -
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Residues in contact with GLU 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 SER* 3.0 32.0 + - - +
166A GLU* 3.6 22.2 - - - +
167A ALA 3.2 0.2 - - - -
168A ALA* 1.3 78.0 - - - +
170A THR* 1.3 59.4 + - - +
172A ASN* 3.7 3.8 - - - +
173A LYS* 3.0 44.6 + - - +
300A ASN* 5.8 0.2 + - - -
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Residues in contact with THR 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 GLU 3.5 2.8 + - - -
167A ALA 3.3 6.8 + - - -
169A GLU* 1.3 78.6 + - - +
171A VAL* 1.3 66.5 + - - +
173A LYS* 3.1 7.9 + - - +
174A VAL* 3.0 27.4 + - - +
280A ILE* 3.5 42.3 - - + +
298A ILE* 3.7 17.0 - - + -
300A ASN* 2.4 45.4 + - - +
304A ILE* 5.3 0.4 - - - -
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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 ALA 2.9 20.8 + - - +
168A ALA* 4.1 5.6 - - - +
170A THR* 1.3 75.4 - - - +
172A ASN* 1.3 64.5 + - - +
174A VAL* 3.4 1.1 + - - +
175A VAL* 2.9 47.6 + - + +
201A TYR* 4.7 4.7 - - - +
212A PHE* 3.6 52.7 - - + -
214A VAL* 5.4 1.1 - - + -
298A ILE* 4.2 11.2 - - + -
304A ILE* 3.9 15.0 - - + -
306A VAL* 4.1 12.1 - - + -
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Residues in contact with ASN 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 ALA* 2.7 41.8 + - - +
169A GLU* 3.7 4.0 - - - +
171A VAL* 1.3 79.4 - - - +
173A LYS* 1.3 65.1 + - - +
175A VAL* 4.2 4.0 - - - +
176A GLU* 2.9 30.4 + - - +
194A GLN* 5.6 4.2 + - - -
196A ASN* 5.7 2.3 + - - -
201A TYR* 4.8 7.1 + - - -
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Residues in contact with LYS 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 GLU* 3.0 30.1 + - - +
170A THR* 3.4 8.8 + - - +
172A ASN* 1.3 77.0 - - + +
174A VAL* 1.3 63.1 + - - +
176A GLU* 3.7 5.4 - - - +
177A ARG* 3.0 24.1 + - - +
279A ASP* 4.7 13.1 + - - +
280A ILE* 3.9 25.8 - - + +
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Residues in contact with VAL 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 THR 3.0 16.4 + - - +
171A VAL 3.8 3.1 - - - +
173A LYS* 1.3 75.3 - - - +
175A VAL* 1.3 65.2 + - + +
177A ARG* 3.0 10.2 + - - +
178A LEU* 2.9 27.0 + - + +
274A VAL* 5.3 1.1 - - + -
277A ILE* 4.0 23.8 - - + -
280A ILE* 4.0 23.8 - - + -
282A VAL* 4.6 7.4 - - + -
296A LEU* 3.8 29.4 - - + -
298A ILE* 4.1 20.4 - - + -
306A VAL* 6.3 0.4 - - + -
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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* 2.9 31.0 + - + +
172A ASN* 4.2 4.7 - - - +
174A VAL* 1.3 76.4 - - + +
176A GLU* 1.3 58.1 + - - +
178A LEU* 3.3 8.3 + - - +
179A LEU* 2.9 28.5 + - + +
194A GLN* 3.7 35.0 - - - +
214A VAL* 4.0 30.1 - - + -
216A PHE* 4.1 9.5 - - + -
306A VAL* 4.3 6.5 - - + -
308A ILE* 4.3 12.1 - - + -
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Residues in contact with GLU 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 ASN* 2.9 21.5 + - - +
173A LYS* 3.7 5.8 - - - +
175A VAL* 1.3 77.7 - - - +
177A ARG* 1.3 58.2 + - - +
179A LEU* 3.3 11.6 + - + +
180A ARG* 2.9 59.3 + - + +
194A GLN* 5.8 0.9 - - - -
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Residues in contact with ARG 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 LYS 3.0 14.1 + - - +
174A VAL* 3.2 11.4 - - - +
176A GLU* 1.3 78.5 - - - +
178A LEU* 1.3 56.7 + - - +
180A ARG* 3.3 9.3 + - - +
181A ARG* 2.9 27.4 + - - +
273A GLU* 2.7 29.7 + - + +
276A GLU* 3.5 41.7 + - - +
277A ILE* 3.7 28.7 - - + +
278A LYS 4.7 1.2 - - - +
279A ASP* 4.7 5.9 + - - -
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Residues in contact with LEU 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 VAL* 2.9 23.3 + - + +
175A VAL* 3.7 6.1 - - - +
177A ARG* 1.3 73.2 - - - +
179A LEU* 1.3 60.5 + - - +
181A ARG* 3.4 5.2 + - + +
182A MET* 2.9 38.8 + - + +
216A PHE* 4.2 12.6 - - + -
270A ILE* 4.1 21.8 - - + +
273A GLU* 4.0 26.0 - - + -
274A VAL* 4.1 17.7 - - + -
277A ILE* 5.3 2.7 - - + -
296A LEU* 3.7 30.1 - - + -
308A ILE* 4.3 19.3 - - + -
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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* 2.9 18.8 + - + +
176A GLU* 3.6 10.1 - - + +
177A ARG 3.3 0.2 - - - -
178A LEU* 1.3 75.5 - - - +
180A ARG* 1.3 58.0 + - - +
182A MET* 3.5 2.0 + - - +
183A GLN* 2.9 55.4 + - - +
192A VAL* 4.3 9.4 - - + +
193A GLU* 5.9 0.2 - - - -
194A GLN* 3.9 40.4 - - + +
216A PHE* 3.9 30.7 - - + -
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Residues in contact with ARG 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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176A GLU* 2.9 41.0 + - + +
177A ARG* 3.4 11.6 - - - +
179A LEU* 1.3 74.4 - - + +
181A ARG* 1.3 62.4 + - - +
183A GLN* 4.7 1.6 - - - -
184A LYS* 2.6 62.9 + - + +
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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 ARG 2.9 16.3 + - - +
178A LEU* 3.6 5.2 - - - +
180A ARG* 1.3 76.6 - - - +
182A MET* 1.3 64.3 + - + +
184A LYS* 5.5 0.2 - - - -
185A ARG* 3.3 76.7 + - - +
186A GLU 4.9 3.4 + - - -
187A SER* 3.3 14.0 + - - -
269A ILE* 3.4 46.3 + - + +
270A ILE* 6.2 0.2 - - - -
272A GLU* 3.9 20.4 + - - +
273A GLU* 3.4 41.1 + - + +
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Residues in contact with MET 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 LEU* 2.9 23.8 + - + +
179A LEU* 3.8 4.3 - - - +
181A ARG* 1.3 79.1 - - + +
183A GLN* 1.3 58.6 + - - +
187A SER* 2.7 26.7 + - - -
189A PHE* 3.3 45.5 - - + +
192A VAL* 4.0 15.3 - - + -
216A PHE* 4.3 9.0 - - + -
266A PHE* 3.7 28.7 - - + -
269A ILE* 3.9 25.6 - - + -
270A ILE* 3.6 32.1 - - + -
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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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179A LEU* 2.9 37.2 + - - +
180A ARG* 4.0 1.3 - - - +
182A MET* 1.3 79.0 - - - +
184A LYS* 1.3 70.8 + - - +
185A ARG 3.2 5.9 - - - +
189A PHE 4.5 0.4 - - - -
190A LYS* 3.3 26.1 - - + +
191A GLY* 3.6 24.5 + - - +
192A VAL* 2.8 28.0 + - + +
193A GLU* 4.9 5.3 - - - +
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Residues in contact with LYS 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ARG* 2.6 45.5 + - + +
183A GLN* 1.3 77.7 - - - +
185A ARG* 1.3 64.1 + - + +
186A GLU* 5.0 0.5 - - - +
190A LYS* 3.5 20.2 + - - +
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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
------------------------------------------------------------
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