Contacts of the helix formed by residues 224 - 238 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A SER* 5.0 3.4 + - - -
170A ASP* 6.1 1.1 - - - -
223A ALA* 1.3 76.8 - - - +
225A GLU* 1.3 59.0 + - - +
226A ASP* 3.7 5.0 + - - +
227A ASP* 3.2 34.8 + - - +
228A ALA* 2.8 26.3 + - - +
252A ARG* 3.5 25.8 - - - +
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Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PRO* 3.7 38.1 - - + +
223A ALA 3.9 0.2 + - - -
224A SER* 1.3 75.2 - - - +
226A ASP* 1.3 72.6 + - - +
228A ALA* 4.5 0.2 - - - -
229A ALA 3.6 4.5 + - - -
252A ARG* 3.2 37.9 + - + +
255A SER* 3.3 25.1 - - - +
256A GLY* 3.4 6.6 - - - -
257A ASN* 3.3 19.8 + - - +
258A ALA* 3.4 27.3 + - - +
237C MET* 5.7 2.9 - - - +
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Residues in contact with ASP 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A SER* 3.3 4.8 + - - +
225A GLU* 1.3 85.9 - - - +
227A ASP* 1.3 66.9 + - - +
228A ALA 3.2 0.2 - - - -
229A ALA* 3.4 7.7 + - - +
230A THR* 3.3 21.7 + - - -
233A ARG* 5.5 0.5 + - - -
257A ASN* 2.7 37.3 + - - +
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Residues in contact with ASP 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A SER* 4.7 2.8 - - - -
197A PHE* 3.7 27.4 - - + -
199A PRO* 3.8 7.4 - - - +
200A GLY* 3.0 40.6 + - - -
201A THR* 4.2 5.4 + - - +
204A VAL* 6.0 0.2 - - - +
223A ALA* 3.9 1.6 - - + -
224A SER* 3.2 33.5 + - - +
226A ASP* 1.3 76.6 - - - +
228A ALA* 1.3 65.1 + - - +
230A THR* 3.2 15.9 + - - -
231A VAL* 3.0 19.0 + - - +
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A LEU* 4.1 8.5 - - + -
223A ALA* 3.8 6.9 - - + +
224A SER 2.8 16.8 + - - +
225A GLU 3.7 7.6 - - - +
226A ASP 3.2 0.2 - - - -
227A ASP* 1.3 77.3 - - - +
229A ALA* 1.3 57.6 + - - +
231A VAL* 3.3 11.6 + - - +
232A TYR* 2.9 52.6 + - + -
253A GLU* 4.0 13.5 - - - -
258A ALA* 3.8 7.0 - - + -
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Residues in contact with ALA 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A GLU 3.6 3.7 + - - +
226A ASP 3.4 10.0 + - - +
227A ASP 3.3 0.4 - - - -
228A ALA* 1.3 79.0 - - - +
230A THR* 1.3 61.7 + - - +
232A TYR* 3.2 12.5 + - - +
233A ARG* 3.1 39.4 + - - +
257A ASN* 3.9 15.7 - - + +
258A ALA* 3.9 6.9 - - - +
261A TYR* 3.6 29.0 - - + +
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Residues in contact with THR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A THR* 3.6 25.8 + - + +
202A LYS* 4.1 27.8 + - - +
204A VAL* 4.1 21.5 - - + +
226A ASP 3.3 11.1 + - - -
227A ASP* 3.2 13.4 + - - -
229A ALA* 1.3 77.7 - - - +
231A VAL* 1.3 58.4 + - - +
233A ARG* 3.7 21.0 + - - +
234A ALA* 3.2 26.7 + - + +
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Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LEU* 4.0 22.2 - - + -
197A PHE* 5.1 5.8 - - + -
204A VAL* 4.3 19.1 - - + -
208A LEU* 3.7 11.0 - - + +
221A LEU* 3.9 22.0 - - + -
223A ALA* 5.0 1.1 - - + -
227A ASP 3.0 18.6 - - - +
228A ALA* 3.3 14.4 - - - +
230A THR* 1.3 73.5 - - - +
232A TYR* 1.3 54.6 + - + +
234A ALA* 4.3 5.6 - - - -
235A ALA* 2.7 37.6 + - - +
247A TRP* 4.2 22.0 - - + -
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Residues in contact with TYR 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A LEU* 3.5 19.0 - - + +
228A ALA* 2.9 34.7 + - + +
229A ALA* 3.2 10.7 + - - +
231A VAL* 1.3 76.4 - - - +
233A ARG* 1.3 57.9 + - - +
235A ALA* 3.8 3.6 - - - +
236A ALA* 3.1 25.5 + - - +
241A THR* 4.9 1.2 + - - -
247A TRP* 4.0 20.9 - + - -
249A VAL* 3.3 15.1 - - - +
253A GLU* 2.6 33.8 + - - +
258A ALA* 3.8 7.6 - - + -
261A TYR 3.5 20.3 - - - +
262A ALA* 3.9 20.2 - - + -
263A PRO* 3.8 14.6 - - + +
266A ILE* 3.1 27.9 - - + +
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Residues in contact with ARG 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LYS* 5.7 4.2 - - - +
226A ASP 5.5 0.6 + - - -
229A ALA* 3.1 25.2 + - - +
230A THR* 3.7 25.4 + - - +
232A TYR* 1.3 73.9 - - - +
234A ALA* 1.3 67.6 + - - +
235A ALA 3.1 1.3 - - - -
236A ALA* 3.9 6.0 - - - +
237A MET* 3.1 27.6 + - - +
257A ASN* 5.7 1.6 - - - +
261A TYR* 3.5 56.8 + - + -
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Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A VAL* 4.5 5.2 - - + +
205A THR* 4.4 23.3 - - - +
208A LEU* 3.6 18.9 - - + +
230A THR* 3.2 21.6 + - + +
231A VAL* 4.3 1.1 - - - -
233A ARG* 1.3 76.6 - - - +
235A ALA* 1.3 59.2 + - - +
237A MET* 3.9 13.6 - - + +
238A LEU* 3.3 30.0 + - - +
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Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LEU* 3.5 13.4 - - + +
231A VAL 2.7 19.8 + - - +
232A TYR* 3.8 5.8 - - - +
234A ALA* 1.3 75.6 - - - +
236A ALA* 1.3 62.1 + - - +
237A MET 3.1 1.6 - - - -
238A LEU 3.6 0.7 + - - -
239A ASN 3.1 6.8 + - - -
240A MET* 2.8 38.2 + - + +
241A THR* 4.6 1.6 - - - +
247A TRP* 3.8 30.3 - - + -
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Residues in contact with ALA 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A TYR 3.1 18.8 + - - +
233A ARG* 3.4 7.2 + - + +
235A ALA* 1.3 76.0 - - - +
237A MET* 1.3 60.7 + - - +
239A ASN* 3.6 10.3 + - - +
240A MET 4.6 0.2 - - - +
241A THR* 3.6 25.5 + - + +
261A TYR 5.7 1.8 - - - +
263A PRO* 6.0 1.1 - - + -
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Residues in contact with MET 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A THR* 3.9 18.4 - - + +
233A ARG 3.1 13.1 + - - +
234A ALA* 3.9 23.1 - - + +
235A ALA 3.1 0.4 - - - -
236A ALA* 1.3 76.7 - - - +
238A LEU* 1.3 64.9 + - + +
239A ASN* 2.9 10.8 + - - +
406A NAG 5.3 5.4 - - - +
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Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A THR* 3.5 39.5 - - + +
208A LEU* 3.7 23.6 - - + +
209A MET* 3.7 30.5 - - - +
212A ARG* 2.7 39.7 + - - +
234A ALA 3.3 12.7 + - - +
235A ALA 3.6 0.4 + - - -
237A MET* 1.3 82.1 - - + +
239A ASN* 1.3 67.8 + - - +
240A MET* 3.4 16.4 - - + -
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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