Contacts of the helix formed by residues 160 - 185 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C ARG 4.5 7.0 - - - +
159C LEU* 1.3 78.2 - - - +
161C ARG* 1.3 59.0 + - - +
162C LYS* 3.1 7.4 - - + +
163C ASP* 3.0 34.2 + - - +
164C ILE* 2.8 27.9 + - - +
207C SER 6.1 0.7 - - - +
209C PRO* 5.3 1.2 - - - +
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Residues in contact with ARG 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C LEU 4.1 0.8 + - - -
160C LYS* 1.3 70.5 - - - +
162C LYS* 1.3 62.5 + - + +
164C ILE* 3.5 20.7 - - + +
165C SER* 2.9 27.4 + - - -
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Residues in contact with LYS 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C LYS* 3.0 4.6 + - + +
161C ARG* 1.3 81.9 - - + +
163C ASP* 1.3 69.7 + - - +
165C SER* 3.2 5.7 + - - -
166C GLU* 3.0 61.1 + - + +
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Residues in contact with ASP 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C LYS* 3.0 39.7 + - - +
162C LYS* 1.3 85.0 - - - +
164C ILE* 1.3 58.5 + - - +
166C GLU* 3.9 10.7 - - - +
167C ALA* 2.9 34.0 + - - +
207C SER 5.8 0.3 - - - +
209C PRO* 3.9 21.9 - - + +
302C GLU* 5.4 3.1 - - - +
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Residues in contact with ILE 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C LEU* 4.0 23.6 - - + +
160C LYS 2.8 17.0 + - - +
161C ARG* 3.5 24.7 - - + +
162C LYS 3.2 0.2 - - - -
163C ASP* 1.3 76.7 - - - +
165C SER* 1.3 58.0 + - - +
167C ALA* 4.1 0.3 - - - +
168C ALA* 2.9 36.5 + - + +
200C TYR* 3.5 24.6 + - + +
209C PRO* 4.1 20.4 - - + -
212C PHE* 5.7 0.2 - - - -
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Residues in contact with SER 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ARG 2.9 19.3 + - - -
162C LYS* 3.2 6.9 + - - -
164C ILE* 1.3 78.0 - - - +
166C GLU* 1.3 65.1 + - - +
168C ALA* 4.0 2.0 - - - +
169C GLU* 3.0 31.5 + - - +
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Residues in contact with GLU 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C LYS* 3.0 50.2 + - + +
163C ASP* 3.9 10.6 - - - +
165C SER* 1.3 79.8 - - - +
167C ALA* 1.3 62.0 + - - +
169C GLU* 3.8 10.0 + - - +
170C THR* 3.3 22.2 + - - -
300C ASN* 4.4 9.8 + - - +
302C GLU* 4.6 15.2 - - - +
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Residues in contact with ALA 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C ASP 2.9 18.2 + - - +
164C ILE 4.1 1.6 - - - +
166C GLU* 1.3 75.9 - - - +
168C ALA* 1.3 65.0 - - - +
170C THR* 3.2 5.2 + - - -
171C VAL* 2.9 28.8 + - - +
209C PRO* 3.8 26.7 - - + +
212C PHE* 4.2 8.3 - - + -
300C ASN* 4.8 1.6 - - - -
304C ILE* 3.8 21.8 - - + -
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Residues in contact with ALA 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C ILE* 2.9 21.7 + - + +
165C SER* 4.0 2.9 - - - +
167C ALA* 1.3 77.2 - - - +
169C GLU* 1.3 63.5 + - - +
171C VAL* 4.4 6.5 - - - -
172C ASN* 2.9 41.2 + - - +
200C TYR* 3.8 20.2 - - + +
212C PHE* 4.6 6.2 - - + -
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Residues in contact with GLU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C SER* 3.0 21.8 + - - +
166C GLU* 3.8 10.3 - - - +
167C ALA 3.2 0.2 - - - -
168C ALA* 1.3 77.1 - - - +
170C THR* 1.3 58.8 + - - +
172C ASN* 3.5 5.1 + - - +
173C LYS* 3.0 49.8 + - + +
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Residues in contact with THR 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C GLU 3.3 12.3 + - - -
167C ALA* 3.2 7.0 + - - -
169C GLU* 1.3 75.3 - - - +
171C VAL* 1.3 68.4 + - - +
173C LYS* 3.0 12.0 + - - +
174C VAL* 3.0 28.6 + - + +
280C ILE* 3.5 42.1 - - + +
298C ILE* 4.2 15.0 - - + -
300C ASN* 3.9 23.0 + - + +
304C ILE* 5.6 1.3 - - - -
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Residues in contact with VAL 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C ALA 2.9 22.6 + - - +
168C ALA* 4.0 5.8 - - - +
170C THR* 1.3 74.3 - - - +
172C ASN* 1.3 63.7 + - - +
174C VAL* 3.4 1.3 + - - +
175C VAL* 2.9 45.2 + - + +
201C TYR* 5.0 4.0 - - - +
212C PHE* 3.8 44.2 - - + -
214C VAL* 5.7 1.1 - - + -
298C ILE* 4.5 11.7 - - + -
304C ILE* 4.0 15.7 - - + -
306C VAL* 4.0 21.1 - - + -
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Residues in contact with ASN 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C ALA* 2.9 34.8 + - - +
169C GLU* 3.7 4.8 - - - +
171C VAL* 1.3 80.7 - - - +
173C LYS* 1.3 63.8 + - - +
175C VAL* 4.0 5.6 - - - +
176C GLU* 2.9 27.5 + - - +
194C GLN* 5.9 0.9 + - - -
201C TYR* 4.6 8.8 + - - -
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Residues in contact with LYS 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C GLU* 3.0 37.5 + - + +
170C THR* 3.0 11.2 + - - +
172C ASN* 1.3 75.8 - - - +
174C VAL* 1.3 66.0 + - + +
176C GLU* 3.5 5.6 - - - +
177C ARG* 3.0 22.8 + - - +
279C ASP* 4.7 12.8 + - - +
280C ILE* 4.3 21.5 - - + +
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Residues in contact with VAL 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C THR 3.0 18.4 + - - +
171C VAL* 3.9 2.9 - - - +
173C LYS* 1.3 71.5 - - - +
175C VAL* 1.3 65.2 + - + +
177C ARG* 3.0 9.8 + - + +
178C LEU* 2.9 34.6 + - + +
274C VAL* 5.5 2.2 - - + -
277C ILE* 4.3 20.9 - - + -
280C ILE* 4.2 22.2 - - + -
282C VAL* 4.5 12.6 - - + -
296C LEU* 4.1 24.5 - - + -
298C ILE* 4.0 21.5 - - + -
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Residues in contact with VAL 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C VAL* 2.9 39.3 + - + +
172C ASN* 4.0 5.6 - - - +
174C VAL* 1.3 73.5 - - + +
176C GLU* 1.3 58.1 + - - +
178C LEU* 3.2 10.9 + - + +
179C LEU* 2.9 28.0 + - + +
194C GLN* 3.6 35.4 - - - +
214C VAL* 4.2 17.7 - - + -
216C PHE* 4.1 15.1 - - + -
296C LEU* 6.1 0.7 - - + -
306C VAL* 4.4 13.2 - - + -
308C ILE* 4.5 5.4 - - + -
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Residues in contact with GLU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C ASN 2.9 20.5 + - - +
173C LYS* 3.5 6.0 - - - +
175C VAL* 1.3 77.5 - - - +
177C ARG* 1.3 64.0 + - - +
179C LEU* 3.3 8.5 + - + +
180C ARG* 2.9 66.7 + - + +
194C GLN* 5.6 1.3 - - - -
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Residues in contact with ARG 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C LYS 3.0 12.0 + - - +
174C VAL* 3.0 12.2 + - + +
176C GLU* 1.3 83.9 + - - +
178C LEU* 1.3 60.1 + - + +
180C ARG* 3.3 5.1 + - - +
181C ARG* 2.9 28.1 + - - +
273C GLU* 3.4 31.3 + - + +
276C GLU* 2.4 33.1 + - - +
277C ILE* 3.3 38.9 - - - +
278C LYS 4.9 0.2 - - - +
279C ASP* 4.7 5.3 + - - -
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Residues in contact with LEU 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C VAL* 2.9 26.5 + - + +
175C VAL* 3.6 6.3 - - - +
177C ARG* 1.3 75.2 - - + +
179C LEU* 1.3 60.8 + - - +
181C ARG* 3.5 5.4 + - - +
182C MET* 2.9 33.4 + - - +
216C PHE* 4.2 12.3 - - + -
270C ILE* 4.3 24.0 - - + +
273C GLU* 4.0 28.7 - - + +
274C VAL* 4.3 16.2 - - + -
277C ILE* 6.1 1.1 - - + -
296C LEU* 3.6 31.6 - - + -
308C ILE* 4.5 13.9 - - + -
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Residues in contact with LEU 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C VAL 2.9 16.8 + - - +
176C GLU* 3.7 8.5 - - + +
178C LEU* 1.3 76.8 - - - +
180C ARG* 1.3 59.2 + - + +
182C MET* 3.1 3.9 + - - +
183C GLN* 2.9 44.1 + - - +
192C VAL* 3.7 38.8 - - + +
193C GLU 4.5 6.3 - - - -
194C GLN* 3.7 31.0 - - + +
216C PHE* 3.9 22.2 - - + -
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Residues in contact with ARG 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C GLU* 2.9 50.6 + - + +
177C ARG* 3.5 6.3 - - - +
179C LEU* 1.3 74.1 - - + +
181C ARG* 1.3 65.8 + - - +
183C GLN* 3.2 8.1 + - - +
184C LYS* 2.9 66.8 + - + +
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Residues in contact with ARG 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C ARG 2.9 12.0 + - - +
178C LEU* 3.7 4.7 - - - +
180C ARG* 1.3 75.5 - - - +
182C MET* 1.3 64.8 + - - +
184C LYS* 3.5 9.1 + - - -
185C ARG* 3.5 60.7 + - - +
187C SER* 4.6 5.0 + - - -
269C ILE* 3.8 38.4 - - + +
272C GLU* 4.0 26.1 + - - +
273C GLU* 3.1 55.1 + - + +
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Residues in contact with MET 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C LEU* 2.9 21.3 + - + +
179C LEU* 3.4 7.6 - - - +
180C ARG 3.1 0.2 - - - -
181C ARG* 1.3 78.6 - - + +
183C GLN* 1.3 61.5 + - - +
184C LYS 3.5 0.3 + - - -
187C SER* 2.5 27.3 + - - -
189C PHE* 3.6 38.4 - - + +
190C LYS* 3.8 1.0 - - - -
192C VAL* 3.5 25.4 - - + -
216C PHE* 4.3 7.4 - - + -
266C PHE* 3.9 20.4 - - + +
269C ILE* 4.1 23.3 - - + -
270C ILE* 3.7 32.1 - - + -
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Residues in contact with GLN 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C LEU* 2.9 39.0 + - - +
180C ARG* 4.1 7.1 - - - +
182C MET* 1.3 76.6 - - - +
184C LYS* 1.3 63.2 + - + +
190C LYS* 3.1 37.5 - - - +
191C GLY* 4.1 14.7 - - - +
192C VAL* 2.6 35.0 + - + +
193C GLU* 4.5 5.9 - - - +
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Residues in contact with LYS 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ARG* 2.9 59.5 + - + +
181C ARG* 4.4 1.6 - - - +
182C MET 3.3 1.4 - - - -
183C GLN* 1.3 80.9 - - + +
185C ARG* 1.3 54.8 + - + +
186C GLU* 2.3 40.0 + - - +
190C LYS* 3.5 5.6 + - - +
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Residues in contact with ARG 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ARG* 3.5 56.5 + - - +
182C MET 5.0 0.2 + - - -
184C LYS* 1.3 72.7 - - + +
186C GLU* 1.3 76.4 + - - +
187C SER* 3.6 1.7 + - - -
272C GLU* 4.9 6.3 + - - -
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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