Contacts of the helix formed by residues 179 - 200 (chain L) in PDB entry 6Y5D
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 ILE 179 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175L SER 4.5 1.3 - - - +
176L ARG* 2.9 34.8 + - + +
177L ASP 3.3 0.2 - - - -
178L ASP* 1.3 79.2 - - + +
180L SER* 1.3 57.1 + - - +
181L THR 2.9 3.6 - - - -
182L ALA* 2.5 38.7 + - + -
183L ALA* 2.8 31.2 + - + +
215L TYR* 5.3 6.3 - - + -
217L HIS* 4.4 7.9 - - - +
223L PRO* 3.0 37.2 - - + +
224L ASN* 3.6 18.4 - - - +
226L PHE* 3.9 11.7 - - + -
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Residues in contact with SER 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176L ARG 4.5 0.8 + - - -
177L ASP 4.5 7.8 + - - -
178L ASP 3.4 2.3 + - - -
179L ILE* 1.3 76.2 - - - +
181L THR* 1.3 63.7 + - - +
183L ALA* 3.7 8.8 + - - +
184L GLY* 3.1 21.0 + - - -
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Residues in contact with THR 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178L ASP 4.0 7.4 + - - -
179L ILE 2.6 4.9 + - - -
180L SER* 1.3 79.6 + - - +
182L ALA* 1.3 63.5 + - - +
184L GLY* 3.1 3.1 + - - -
185L MET* 3.0 37.8 + - + +
315L LYS* 5.8 5.4 - - - +
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Residues in contact with ALA 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178L ASP 4.6 1.7 + - - +
179L ILE* 2.5 30.4 + - + +
181L THR* 1.3 75.4 - - - +
183L ALA* 1.3 62.2 + - - +
185L MET* 3.2 11.6 + - + +
186L VAL* 3.0 25.3 + - - +
224L ASN* 4.6 2.0 - - - +
226L PHE* 3.7 13.2 - - + -
315L LYS* 6.4 0.7 - - + -
316L ILE* 3.4 28.6 - - + +
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Residues in contact with ALA 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179L ILE* 2.8 27.0 + - + +
180L SER* 3.8 8.3 - - - +
182L ALA* 1.3 72.4 - - - +
184L GLY* 1.3 57.2 + - - +
186L VAL* 3.3 4.7 + - - +
187L LYS* 2.9 30.5 + - - +
214L TYR* 4.6 3.3 - - + +
215L TYR* 3.7 34.3 - - + -
226L PHE* 4.0 9.9 - - - -
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Residues in contact with GLY 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180L SER 3.1 15.6 + - - -
181L THR* 3.1 5.1 + - - -
182L ALA 3.1 0.6 - - - -
183L ALA* 1.3 76.8 - - - +
185L MET* 1.3 55.8 + - - +
187L LYS* 3.2 10.7 + - - +
188L GLY* 2.9 26.7 + - - -
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Residues in contact with MET 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181L THR* 3.0 25.2 + - + +
182L ALA* 3.2 18.8 + - - +
184L GLY* 1.3 74.1 - - - +
186L VAL* 1.3 63.5 + - - +
188L GLY* 3.3 2.5 + - - -
189L VAL* 3.2 27.1 + - - +
294L THR* 5.3 13.3 + - + +
312L ILE* 4.4 19.3 - - + -
313L SER* 5.1 10.3 - - - -
315L LYS* 4.3 23.3 - - + +
316L ILE* 3.6 27.4 - - + -
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Residues in contact with VAL 186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182L ALA 3.0 14.9 + - - +
183L ALA* 3.5 7.9 - - - +
185L MET* 1.3 75.6 - - - +
187L LYS* 1.3 53.5 + - - +
189L VAL* 3.1 4.9 + - - +
190L VAL* 2.8 46.2 + - + +
214L TYR 3.3 25.1 - - - +
226L PHE* 3.7 24.0 - - + -
228L VAL* 4.4 6.5 - - + -
312L ILE* 4.3 6.3 - - - -
316L ILE* 3.4 27.4 - - + -
318L VAL* 3.9 14.4 - - + -
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Residues in contact with LYS 187 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183L ALA 2.9 17.4 + - - +
184L GLY* 3.4 9.4 - - - +
186L VAL* 1.3 72.8 - - - +
188L GLY* 1.3 67.5 + - - +
190L VAL 3.1 0.3 + - - -
191L ASP* 2.8 53.5 + - - +
214L TYR* 3.6 50.6 + - + -
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Residues in contact with GLY 188 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184L GLY 2.9 15.0 + - - -
185L MET* 3.3 3.8 + - - -
186L VAL 3.3 0.2 - - - -
187L LYS* 1.3 77.8 - - - +
189L VAL* 1.3 63.5 + - - +
191L ASP* 4.2 3.6 - - - +
192L HIS* 3.3 21.1 + - - +
291L ILE* 6.1 1.8 - - - -
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Residues in contact with VAL 189 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185L MET 3.2 12.5 + - - +
186L VAL 3.1 7.5 + - - +
188L GLY* 1.3 75.8 - - - +
190L VAL* 1.3 65.5 + - + +
192L HIS* 3.3 3.3 + - - +
193L LEU* 3.0 27.7 + - + +
291L ILE* 3.8 23.6 - - + -
294L THR* 4.3 13.2 - - + -
296L VAL* 3.6 25.8 - - + -
310L LEU* 3.9 27.6 - - + -
312L ILE* 3.7 19.5 - - + -
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Residues in contact with VAL 190 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186L VAL* 2.8 39.0 + - + +
187L LYS 3.8 2.5 - - - +
189L VAL* 1.3 75.0 - - + +
191L ASP* 1.3 66.8 + - - +
193L LEU* 3.2 5.3 + - + +
194L LEU* 2.9 44.2 + - + +
208L LEU* 3.9 6.3 - - + -
214L TYR* 3.8 20.6 - - + -
228L VAL* 4.4 15.5 - - + -
230L PHE* 3.7 24.7 - - + -
318L VAL* 5.1 4.7 - - + -
320L ILE* 5.8 1.3 - - + -
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Residues in contact with ASP 191 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187L LYS* 2.8 46.2 + - - +
188L GLY* 4.2 3.8 - - - +
190L VAL* 1.3 72.8 - - - +
192L HIS* 1.3 63.0 + - - +
194L LEU* 3.3 8.1 + - - +
195L LEU* 3.1 33.6 + - + +
214L TYR* 2.6 35.1 + - - -
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Residues in contact with HIS 192 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188L GLY 3.3 12.4 + - - +
189L VAL 3.4 9.0 - - - +
190L VAL 3.2 0.4 - - - -
191L ASP* 1.3 82.1 - - - +
193L LEU* 1.3 62.8 + - + +
195L LEU* 3.3 18.8 + - - +
196L ARG 3.4 8.5 + - - -
287L GLU* 2.7 52.6 + - + +
290L ASP* 3.7 21.7 + - + +
291L ILE* 3.2 31.3 - - + +
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Residues in contact with LEU 193 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189L VAL* 3.0 26.6 + - + +
190L VAL* 3.7 6.5 - - + +
192L HIS* 1.3 80.0 - - + +
194L LEU* 1.3 58.7 + - - +
196L ARG* 3.2 4.5 + - - +
197L LEU* 2.9 36.5 + - + +
230L PHE* 4.5 12.1 - - + -
284L ILE* 4.0 20.6 - - + -
287L GLU* 3.7 28.0 - - + -
288L ILE* 3.7 23.3 - - + +
291L ILE* 4.8 0.9 - - + -
310L LEU* 3.7 29.8 - - + -
320L ILE* 4.3 11.0 - - + -
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Residues in contact with LEU 194 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190L VAL* 2.9 39.1 + - + +
191L ASP* 3.9 9.4 - - - +
192L HIS 3.3 0.2 - - - -
193L LEU* 1.3 76.5 - - - +
195L LEU* 1.3 57.2 + - + +
197L LEU* 3.8 3.6 - - + +
198L LYS* 2.8 48.4 + - - +
206L VAL* 3.9 23.6 - - + -
207L GLY* 4.4 9.2 - - - -
208L LEU* 3.7 26.5 - - + +
214L TYR* 5.3 0.2 - - + -
230L PHE* 3.7 35.0 - - + -
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Residues in contact with LEU 195 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191L ASP* 3.1 24.1 + - + +
192L HIS* 3.6 12.3 - - - +
193L LEU 3.2 0.2 - - - -
194L LEU* 1.3 77.1 - - - +
196L ARG* 1.3 57.4 + - - +
198L LYS* 3.4 16.8 + - + +
199L CYS* 3.0 34.3 + - - -
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Residues in contact with ARG 196 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192L HIS 3.4 2.0 + - - -
193L LEU 3.2 4.0 + - - +
195L LEU* 1.3 77.3 - - - +
197L LEU* 1.3 66.1 + - - +
199L CYS* 3.1 33.7 + - - +
200L ASP* 3.1 19.6 + - - +
283L ILE* 3.8 22.1 - - + +
286L GLU* 5.5 5.9 + - - -
287L GLU* 3.2 47.9 + - + +
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Residues in contact with LEU 197 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193L LEU 2.9 22.4 + - - +
194L LEU* 3.8 6.7 - - + +
196L ARG* 1.3 73.3 - - - +
198L LYS* 1.3 58.8 + - - +
200L ASP* 2.9 31.8 + - - +
203L PHE* 3.3 28.3 - - + +
206L VAL* 3.6 16.4 - - + -
230L PHE* 3.8 24.7 - - + -
280L PHE* 3.7 43.1 - - + +
283L ILE* 3.9 24.2 - - + -
284L ILE* 4.5 9.2 - - + -
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Residues in contact with LYS 198 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194L LEU* 2.8 34.6 + - - +
195L LEU* 3.5 17.3 - - + +
197L LEU* 1.3 77.0 - - - +
199L CYS* 1.3 57.9 + - - +
200L ASP 3.3 0.2 - - - -
203L PHE 3.8 6.3 - - - -
204L ARG* 3.4 29.5 - - - +
206L VAL* 3.0 33.4 - - + +
207L GLY* 4.6 6.7 - - - -
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Residues in contact with CYS 199 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195L LEU* 3.0 28.1 + - - -
196L ARG* 3.1 32.5 + - - +
198L LYS* 1.3 76.7 - - - +
200L ASP* 1.3 61.4 + - - +
201L SER* 3.7 1.9 + - - -
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Residues in contact with ASP 200 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196L ARG* 3.1 17.4 + - - +
197L LEU 2.9 11.2 + - - +
199L CYS* 1.3 77.6 - - - +
201L SER* 1.3 65.4 + - - +
202L ALA* 2.8 36.6 + - - +
203L PHE 3.2 2.0 + - - +
204L ARG* 2.9 25.4 + - - +
279L LYS* 3.4 14.4 + - - -
283L ILE* 3.3 36.3 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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