Contacts of the helix formed by residues 167 - 181 (chain C) in PDB entry 5AYR
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 167 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C TYR* 3.4 32.1 - - + +
158C PHE 4.4 3.1 - - - +
160C VAL* 3.8 26.5 - - + -
165C PRO 3.4 0.8 - - - +
166C PRO* 1.3 86.5 - - + +
168C PRO* 1.4 65.5 - - + +
169C SER 3.1 0.7 - - - +
170C LEU* 2.8 38.5 + - + +
171C GLU* 2.9 11.6 + - - +
26D GLU* 3.3 20.2 - - - +
57D TYR* 3.8 12.8 - - + +
62D HIS* 4.3 0.2 - - - -
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Residues in contact with PRO 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C PRO* 1.4 88.5 - - + +
169C SER* 1.3 62.1 + - - +
171C GLU* 3.6 4.1 + - + +
172C ASN* 3.2 28.4 + - - +
271C PRO* 3.4 29.3 - - + +
26D GLU* 3.8 13.5 - - + +
55D THR* 4.1 15.9 - - + -
57D TYR* 3.4 40.4 - - + -
62D HIS* 4.0 10.3 - - + -
67D TYR* 4.1 9.4 - - + +
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Residues in contact with SER 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C TYR* 4.5 0.7 - - - -
158C PHE* 3.8 24.6 - - - -
167C PRO 3.1 0.6 - - - -
168C PRO* 1.3 80.1 - - - +
170C LEU* 1.3 59.4 + - - +
172C ASN* 3.2 4.5 + - - +
173C ILE* 2.9 31.3 + - - +
268C HIS* 3.3 24.9 - - - -
269C PRO* 3.8 13.1 - - - +
270C SER* 3.6 4.9 - - - +
26D GLU* 2.7 29.9 + - - -
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Residues in contact with LEU 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C TYR* 5.8 0.2 - - - +
158C PHE* 3.4 24.7 - - + +
166C PRO* 4.1 6.3 - - + -
167C PRO* 2.8 22.1 + - + +
169C SER* 1.3 78.6 - - - +
171C GLU* 1.3 58.4 + - - +
172C ASN 3.2 0.2 - - - -
173C ILE* 3.2 27.0 + - + -
174C TYR* 2.8 57.6 + - + +
190C GLY* 3.6 35.4 - - - +
192C LEU* 4.3 16.4 - - + -
195C TRP* 5.0 0.2 - - + -
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Residues in contact with GLU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C PRO* 3.4 22.9 - - - +
167C PRO 2.9 10.0 + - - +
168C PRO* 3.7 9.4 - - + +
170C LEU* 1.3 76.0 - - - +
172C ASN* 1.3 62.3 + - - +
174C TYR* 3.3 8.0 + - - +
175C LYS* 2.9 44.1 + - - +
186C HIS* 3.0 34.2 + - - -
62D HIS* 3.6 38.4 + - + +
67D TYR* 4.7 4.9 - - - +
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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 PRO 3.2 12.4 + - - +
169C SER 3.5 3.6 - - - +
170C LEU 3.2 0.8 - - - -
171C GLU* 1.3 77.4 - - - +
173C ILE* 1.3 67.0 + - - +
175C LYS* 3.1 18.1 + - - +
176C GLU 3.0 19.6 + - - -
269C PRO* 2.7 31.0 + - + +
271C PRO* 3.5 19.4 - - - +
274C VAL* 3.6 23.4 - - + +
278C PHE* 3.6 8.5 - - - -
279C PHE* 3.7 18.1 - - + -
67D TYR* 6.2 0.3 - - - -
87D HIS* 5.7 1.4 - - - -
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Residues in contact with ILE 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C PHE* 3.9 24.7 - - + -
169C SER 2.9 19.6 + - - +
170C LEU* 3.5 27.1 - - + +
172C ASN* 1.3 75.4 - - - +
174C TYR* 1.3 57.1 + - - +
176C GLU* 3.4 2.8 + - - +
177C LEU* 3.0 38.4 + - + +
195C TRP* 4.1 12.8 - - + -
245C TRP* 3.5 24.9 - - + -
269C PRO* 4.0 6.1 - - + -
278C PHE* 3.9 22.0 - - + -
284C PHE* 3.7 21.0 - - + -
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Residues in contact with TYR 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C PRO* 4.3 3.8 - - + -
170C LEU* 2.8 45.1 + - + +
171C GLU* 3.4 9.2 - - - +
172C ASN 3.2 0.2 - - - -
173C ILE* 1.3 76.0 - - - +
175C LYS* 1.3 63.6 + - - +
177C LEU* 3.4 3.8 + - + -
178C SER* 3.1 22.9 + - - -
184C PHE* 3.7 27.9 - + + -
186C HIS* 3.5 36.8 - + + -
187C PRO* 3.5 20.4 - - + +
189C HIS* 2.7 30.1 + - - -
190C GLY* 3.5 10.9 - - - -
191C ASP 4.6 0.5 + - - -
192C LEU* 4.0 6.6 - - + +
195C TRP* 4.7 3.1 - + - -
304C LEU* 4.0 21.6 - - + +
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Residues in contact with LYS 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C GLU* 2.9 31.5 + - - +
172C ASN* 3.1 20.2 + - - +
174C TYR* 1.3 73.6 - - - +
176C GLU* 1.3 67.8 + - - +
178C SER* 2.7 23.5 + - - +
179C THR* 3.4 12.0 + - - +
279C PHE* 3.6 29.4 - - + -
65D ASN* 4.8 11.9 + - - -
67D TYR* 5.7 2.4 + - - -
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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
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172C ASN 3.0 3.4 + - - +
173C ILE 3.8 2.5 - - - +
175C LYS* 1.3 79.6 - - - +
177C LEU* 1.3 63.3 + - - +
179C THR* 3.1 15.5 + - - -
180C ASP* 2.9 26.1 + - + +
278C PHE* 3.5 33.4 - - + +
279C PHE* 3.5 10.3 - - + -
280C GLY* 2.8 29.0 + - - -
281C CYS* 3.2 5.4 + - - -
282C ARG* 2.7 37.0 + - - +
284C PHE* 3.7 22.2 - - + -
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Residues in contact with LEU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C ILE* 3.0 28.1 + - + +
174C TYR* 3.7 2.9 - - + +
175C LYS 3.1 0.2 - - - -
176C GLU* 1.3 77.8 - - - +
178C SER* 1.3 55.9 + - - +
180C ASP* 2.8 4.2 + - - -
181C ILE* 2.6 43.8 + - + +
184C PHE* 3.7 32.5 - - + -
195C TRP* 3.7 32.5 - - + -
284C PHE* 3.4 39.7 - - + -
301C TRP* 3.8 22.9 - - + -
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Residues in contact with SER 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C TYR 3.1 12.5 + - - -
175C LYS* 2.7 23.0 + - - +
177C LEU* 1.3 77.1 - - - +
179C THR* 1.3 64.2 + - - +
181C ILE 4.0 7.8 - - - +
182C GLU* 5.7 0.2 - - - -
183C ASP 5.3 1.2 + - - -
184C PHE* 3.4 32.1 + - - +
185C VAL* 5.5 0.4 - - - -
186C HIS 5.6 1.8 - - - -
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Residues in contact with THR 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C LYS 3.7 11.2 - - - +
176C GLU* 3.1 24.3 + - - -
178C SER* 1.3 84.1 - - - +
180C ASP* 1.3 60.5 + - - +
181C ILE 3.5 1.6 + - - -
280C GLY* 6.0 0.2 - - - -
282C ARG* 4.5 7.6 + - - +
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Residues in contact with ASP 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 25.4 + - - +
177C LEU* 2.8 6.5 + - - +
179C THR* 1.3 79.3 - - - +
181C ILE* 1.3 66.0 + - + +
182C GLU 4.1 0.7 + - - -
282C ARG* 2.8 55.6 + - - +
284C PHE* 3.1 21.0 + - + +
285C SER* 2.9 39.7 + - - -
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Residues in contact with ILE 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C LEU* 2.6 32.3 + - + +
178C SER 4.0 6.5 - - - +
179C THR 3.5 1.1 - - - -
180C ASP* 1.3 82.0 - - - +
182C GLU* 1.3 74.6 + - - +
183C ASP 3.2 0.7 + - - -
184C PHE* 3.1 25.3 + - + +
284C PHE* 4.0 6.5 - - + -
285C SER* 4.1 20.9 - - - +
288C ASN* 4.4 6.7 - - - +
301C TRP* 3.9 35.7 - - + +
302C LYS* 4.6 17.0 - - + +
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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
------------------------------------------------------------
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