Contacts of the helix formed by residues 224 - 237 (chain C) in PDB entry 3Q41
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 SER 224 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C PRO* 5.9 0.9 - - - -
168C SER* 5.2 0.8 + - - -
223C ALA* 1.3 77.0 - - - +
225C GLU* 1.3 64.9 + - - +
226C ASP* 3.1 13.6 + - - +
227C ASP* 3.2 23.6 + - - -
228C ALA* 2.8 27.9 + - - +
252C ARG* 3.6 33.4 - - - +
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Residues in contact with GLU 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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98C PRO* 3.1 44.1 - - + +
224C SER* 1.3 74.6 - - - +
226C ASP* 1.3 65.8 + - + +
229C ALA* 3.0 28.8 + - - +
252C ARG* 3.4 41.2 + - - +
255C SER* 3.2 36.7 - - - +
256C GLY* 5.4 1.7 - - - -
257C ASN* 4.4 5.4 - - + +
258C ALA* 3.5 13.5 + - + +
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Residues in contact with ASP 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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202C LYS* 5.3 7.8 + - - +
224C SER* 3.2 8.3 + - - +
225C GLU* 1.3 87.0 - - + +
227C ASP* 1.3 67.0 + - - +
229C ALA* 3.3 7.9 + - - +
230C THR* 3.2 24.6 + - - -
233C ARG* 5.3 0.2 + - - -
257C ASN* 4.1 19.8 - - - +
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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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168C SER* 4.8 4.0 - - - -
170C ASP* 5.7 0.5 - - - +
197C PHE* 3.5 29.3 - - + -
199C PRO* 2.9 31.5 - - - +
200C GLY 3.9 8.7 - - - +
201C THR 4.7 3.1 - - - +
223C ALA* 3.8 6.7 - - + -
224C SER* 3.2 21.2 + - - +
226C ASP* 1.3 77.3 - - - +
228C ALA* 1.3 66.1 + - - +
230C THR* 3.3 9.2 + - - -
231C VAL* 3.1 28.6 + - - +
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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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221C LEU* 3.9 14.8 - - + -
223C ALA* 3.8 2.2 - - + +
224C SER 2.8 18.5 + - - +
225C GLU 3.7 4.0 - - - +
227C ASP* 1.3 74.4 - - - +
229C ALA* 1.3 64.9 + - - +
231C VAL* 3.1 12.6 + - - +
232C TYR* 2.9 45.7 + - + -
253C GLU* 4.0 12.3 - - + -
258C ALA* 3.8 8.7 - - + -
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Residues in contact with ALA 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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225C GLU 3.0 17.8 + - - +
226C ASP* 3.3 7.6 + - - +
228C ALA* 1.3 74.7 - - - +
230C THR* 1.3 61.8 + - - +
232C TYR* 3.3 12.5 + - - +
233C ARG* 3.1 48.1 + - - +
257C ASN* 3.8 26.5 - - + +
258C ALA* 4.2 1.1 - - - +
261C TYR* 4.0 7.3 - - + +
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Residues in contact with THR 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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201C THR 4.1 9.0 + - - +
202C LYS* 3.9 35.6 + - - +
204C VAL* 3.7 24.7 - - + +
226C ASP 3.2 14.4 + - - -
227C ASP* 3.5 13.7 + - - -
228C ALA 3.1 0.8 - - - -
229C ALA* 1.3 77.0 - - - +
231C VAL* 1.3 56.6 + - - +
233C ARG* 3.5 22.4 + - + +
234C ALA* 3.2 25.3 + - + +
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Residues in contact with VAL 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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166C LEU* 4.9 7.2 - - + -
197C PHE* 4.8 12.1 - - + -
204C VAL* 3.7 31.4 - - + -
208C LEU* 3.6 10.3 - - + +
221C LEU* 3.7 39.0 - - + -
227C ASP 3.1 14.3 + - - +
228C ALA 3.1 15.0 + - - +
230C THR* 1.3 74.6 - - - +
232C TYR* 1.3 63.4 + - + +
234C ALA* 3.8 7.2 - - - -
235C ALA* 3.0 27.5 + - - +
247C TRP* 4.4 7.0 - - + -
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Residues in contact with TYR 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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221C LEU* 4.0 16.2 - - + -
228C ALA* 2.9 31.5 + - + +
229C ALA* 3.3 7.2 + - - +
231C VAL* 1.3 81.1 - - + +
233C ARG* 1.3 58.4 + - - +
235C ALA* 3.2 6.0 + - - +
236C ALA* 2.9 27.7 + - - +
241C THR* 4.5 3.1 + - - -
247C TRP* 4.1 20.0 - + - -
249C VAL* 3.5 4.5 - - - +
253C GLU* 2.7 42.5 + - - +
258C ALA* 3.5 22.4 - - + -
261C TYR 3.1 21.1 - - - +
262C ALA* 3.7 8.3 - - + -
263C PRO* 3.8 13.8 - - + +
266C ILE* 3.2 31.4 - - + +
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Residues in contact with ARG 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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256A GLY* 6.3 3.8 - - - -
257A ASN* 5.6 2.9 + - - -
260A ARG* 4.8 7.4 - - - +
202C LYS* 5.8 3.4 - - - +
226C ASP 5.3 0.4 + - - -
229C ALA* 3.1 25.9 + - - +
230C THR* 3.5 29.9 + - - +
232C TYR* 1.3 74.9 - - - +
234C ALA* 1.3 67.9 + - - +
236C ALA* 3.8 7.1 - - - +
237C MET* 3.1 24.1 + - - +
257C ASN* 5.1 3.6 + - - -
261C TYR* 3.2 60.0 + - + -
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Residues in contact with ALA 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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204C VAL* 4.8 10.8 - - + +
205C THR* 4.9 13.0 - - - +
208C LEU* 3.4 22.4 - - + -
230C THR* 3.2 22.2 + - + +
231C VAL* 3.9 2.2 - - - +
233C ARG* 1.3 78.6 - - - +
235C ALA* 1.3 60.8 + - - +
237C MET* 3.4 23.7 - - - +
238C LEU* 3.6 15.6 + - - +
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Residues in contact with ALA 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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208C LEU* 3.7 8.0 - - + +
231C VAL 3.0 19.0 + - - +
232C TYR* 3.4 6.1 - - + +
233C ARG 3.2 0.2 - - - -
234C ALA* 1.3 74.1 - - - +
236C ALA* 1.3 56.2 + - - +
238C LEU* 2.8 22.9 + - - -
240C MET* 3.2 35.5 + - + +
241C THR* 4.4 7.0 - - - +
247C TRP* 3.7 29.2 - - + -
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Residues in contact with ALA 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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259A LEU* 6.1 3.1 - - + -
260A ARG* 5.3 12.6 - - - +
275A LYS* 5.4 0.7 + - - +
232C TYR 2.9 17.2 + - - +
233C ARG* 3.8 9.4 - - - +
234C ALA 3.4 0.2 - - - -
235C ALA* 1.3 75.5 - - - +
237C MET* 1.3 60.3 + - - +
238C LEU 3.1 1.1 + - - -
239C ASN* 3.6 8.3 + - - -
241C THR* 4.0 24.6 + - + +
261C TYR 5.9 1.3 - - - +
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Residues in contact with MET 237 (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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96A PRO* 4.5 5.4 - - + +
97A THR* 3.1 47.1 - - + +
98A PRO* 4.1 11.7 - - + -
225A GLU* 5.7 2.7 - - - +
255A SER* 6.6 0.4 - - - -
275A LYS* 2.8 38.1 + - - +
205C THR* 3.8 16.8 - - + +
233C ARG 3.1 13.6 + - - +
234C ALA* 3.4 17.9 - - - +
235C ALA 3.1 0.2 - - - -
236C ALA* 1.3 76.2 - - - +
238C LEU* 1.3 86.5 + - + +
239C ASN 3.6 0.9 - - - -
406C NAG 5.1 5.2 - - - -
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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
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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