Contacts of the helix formed by residues 221 - 236 (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 GLY 221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C TYR* 3.4 21.9 - - - -
105C LEU* 3.9 11.5 - - - +
219C GLU 3.6 2.4 - - - -
220C ARG* 1.3 80.8 - - - +
222C TRP* 1.3 63.9 + - - +
223C GLU* 3.4 3.7 + - - -
224C GLN* 3.5 22.3 + - - -
225C PHE* 3.2 16.5 + - - +
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Residues in contact with TRP 222 (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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102C PHE* 4.8 2.0 - + - -
105C LEU* 3.7 31.1 - - + +
106C MET* 3.7 28.7 - - + -
109C VAL* 4.3 4.5 - - + +
125C VAL* 4.0 5.6 - - + -
126C PHE* 4.0 19.7 - + - -
205C ALA 3.5 14.5 - - - +
206C VAL* 3.6 21.1 - - + -
207C LEU* 3.5 46.7 - - + -
208C THR* 2.8 41.5 + - + +
217C HIS* 4.2 10.5 + - + +
220C ARG* 3.8 1.8 - - + +
221C GLY* 1.3 77.2 - - - +
223C GLU* 1.3 57.5 + - - +
225C PHE* 2.8 25.1 + + - +
226C THR* 2.7 34.8 + - - +
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Residues in contact with GLU 223 (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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205C ALA* 3.7 4.0 + - + +
206C VAL* 3.5 22.6 - - + +
218C LYS* 3.7 10.7 + - - +
219C GLU* 2.8 44.1 + - + +
220C ARG 4.1 0.2 + - - -
221C GLY 4.2 1.2 + - - -
222C TRP* 1.3 80.9 + - - +
224C GLN* 1.3 56.1 + - + +
226C THR* 3.7 7.2 - - - -
227C ASP* 2.7 45.3 + - - +
248C TYR* 3.7 22.1 + - - +
252C LYS* 3.3 5.9 + - - +
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Residues in contact with GLN 224 (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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96C GLU* 4.7 0.5 - - - +
101C TYR* 3.8 49.2 + - + +
221C GLY* 3.9 13.8 + - - +
222C TRP 3.2 0.6 - - - -
223C GLU* 1.3 79.0 - - + +
225C PHE* 1.3 58.4 + - - +
227C ASP* 3.4 10.2 - - - +
228C ALA* 3.0 27.5 + - - +
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Residues in contact with PHE 225 (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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85C PHE* 3.9 26.2 - + - -
93C LEU* 4.7 9.4 - - + -
96C GLU* 4.0 19.5 - - + -
97C PHE* 4.4 7.2 - + - -
101C TYR* 3.5 19.6 + - + +
102C PHE* 3.7 27.1 - + + -
105C LEU* 4.8 0.2 - - + -
126C PHE* 4.0 19.7 - + - -
128C TRP* 4.1 16.2 - + - -
207C LEU* 4.4 0.7 - - + -
221C GLY 3.2 11.6 + - - +
222C TRP* 2.8 30.0 + + + +
224C GLN* 1.3 79.1 - - - +
226C THR* 1.3 66.5 + - + +
228C ALA* 3.2 13.1 + - + +
229C VAL* 3.2 24.2 + - + +
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Residues in contact with THR 226 (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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203C LEU* 4.2 14.8 - - + +
204C ASN 3.5 17.3 - - - +
205C ALA 2.8 27.0 + - - +
207C LEU* 4.1 18.8 - - + -
222C TRP 2.7 16.1 + - - +
223C GLU 3.4 0.2 + - - -
225C PHE* 1.3 79.1 - - + +
227C ASP* 1.3 64.6 + - - +
229C VAL* 3.2 7.8 + - + +
230C VAL* 3.0 27.5 + - - +
252C LYS* 2.8 32.1 + - - -
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Residues in contact with ASP 227 (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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223C GLU* 2.7 32.3 + - - +
224C GLN* 3.4 11.5 - - - +
226C THR* 1.3 72.5 + - - +
228C ALA* 1.3 56.3 + - - +
230C VAL* 3.3 6.2 + - - +
231C SER* 2.9 29.3 + - - -
252C LYS* 2.7 37.2 + - - +
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Residues in contact with ALA 228 (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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93C LEU* 4.5 5.1 - - + +
96C GLU* 3.7 34.8 - - + +
224C GLN 3.0 13.3 + - - +
225C PHE* 3.4 11.0 - - + +
226C THR 3.1 0.4 - - - -
227C ASP* 1.3 78.1 - - - +
229C VAL* 1.3 52.0 + - - +
231C SER* 3.2 7.2 + - - -
232C TRP* 2.8 35.0 + - - +
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Residues in contact with VAL 229 (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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89C TRP* 4.4 7.9 - - + -
93C LEU* 4.0 25.1 - - + -
128C TRP* 3.8 33.2 - - + -
134C ILE* 6.2 0.4 - - + -
201C LEU* 4.4 0.4 - - + -
203C LEU* 3.6 22.7 - - + -
225C PHE* 3.2 22.6 + - + +
226C THR* 3.2 11.6 + - + +
228C ALA* 1.3 73.3 - - - +
230C VAL* 1.3 67.4 + - - +
232C TRP* 3.4 1.9 + - - +
233C LEU* 3.1 42.3 + - + +
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Residues in contact with VAL 230 (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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140C VAL* 5.4 2.2 - - + -
142C LEU* 4.1 31.2 - - + -
203C LEU* 4.4 8.5 - - + -
226C THR 3.0 16.1 + - - +
227C ASP* 3.6 9.0 - - - +
229C VAL* 1.3 75.4 - - - +
231C SER* 1.3 58.3 + - - +
233C LEU* 3.2 10.4 + - + +
234C ASN* 2.8 27.8 + - + +
242C PHE* 4.3 20.2 - - + -
252C LYS* 4.5 21.5 - - + +
256C ILE* 4.4 15.7 - - + -
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Residues in contact with SER 231 (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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227C ASP 2.9 15.4 + - - -
228C ALA* 3.2 12.3 + - - -
230C VAL* 1.3 74.2 - - - +
232C TRP* 1.3 68.8 + - - +
234C ASN* 3.0 7.3 + - - -
235C GLN* 2.9 45.5 + - - +
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Residues in contact with TRP 232 (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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92C HIS* 3.4 60.8 + + + +
93C LEU* 4.0 16.2 - - + -
134C ILE* 3.5 38.4 - - + -
135C LYS* 5.7 4.5 - - + -
228C ALA 2.8 16.3 + - - +
229C VAL 3.7 3.8 - - - +
231C SER* 1.3 77.8 - - - +
233C LEU* 1.3 81.5 + - + +
235C GLN* 5.0 0.7 - - - -
236C ASN* 2.8 79.0 + - + +
237C SER* 4.3 5.6 - - - -
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Residues in contact with LEU 233 (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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89C TRP* 5.0 1.1 - - + -
134C ILE* 4.3 14.6 - - + +
137C VAL* 4.2 22.2 - - + -
140C VAL* 4.3 15.0 - - + -
201C LEU* 3.6 28.7 - - + -
203C LEU* 5.5 0.7 - - + -
229C VAL* 3.1 32.8 + - + +
230C VAL* 3.5 7.6 - - - +
232C TRP* 1.3 99.7 - - + +
234C ASN* 1.3 65.3 + - - +
235C GLN 3.4 0.3 + - - -
237C SER* 2.7 30.0 + - - +
240C LEU* 3.7 14.2 - - + +
242C PHE* 4.8 4.3 - - + -
261C HIS* 3.7 3.8 + - - -
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Residues in contact with ASN 234 (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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230C VAL* 2.8 18.4 + - + +
231C SER* 3.0 13.7 + - - +
233C LEU* 1.3 74.5 - - - +
235C GLN* 1.3 70.3 + - - +
237C SER 3.8 0.2 - - - +
242C PHE* 5.0 2.8 - - - -
255C ALA* 3.2 24.4 + - - +
256C ILE* 3.5 12.9 - - + +
257C ASP* 3.0 28.9 + - - +
260C ARG* 3.0 17.8 + - - -
261C HIS* 2.9 38.4 + - - -
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Residues in contact with GLN 235 (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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231C SER* 2.9 41.9 + - - +
232C TRP* 5.6 0.2 - - - -
234C ASN* 1.3 89.2 - - + +
236C ASN* 1.3 72.2 + - - +
260C ARG* 2.9 23.4 + - - +
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Residues in contact with ASN 236 (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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232C TRP* 2.8 78.2 + - + +
235C GLN* 1.3 92.1 - - - +
237C SER* 1.3 61.8 + - - +
238C ASN* 5.2 1.3 - - - -
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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
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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