Contacts of the helix formed by residues 226 - 240 (chain A) in PDB entry 5A63
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 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.2 23.8 - - - +
55A ASN 3.7 2.2 - - - -
56A ALA 3.4 10.8 - - - -
57A THR 3.1 23.8 - - - -
58A HIS 4.0 4.9 - - - -
224A VAL 3.1 3.9 + - - +
225A ILE* 1.3 81.6 - - - +
227A THR* 1.3 59.2 + - - +
228A ALA* 2.7 22.5 + - - +
229A THR* 3.1 18.1 + - - +
230A CYS* 3.3 11.1 - - - +
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Residues in contact with THR 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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54A LEU* 3.5 11.3 - - - +
55A ASN 2.8 35.2 + - - +
56A ALA* 3.4 9.6 - - - +
226A SER* 1.3 72.1 - - - +
228A ALA* 1.3 64.3 + - - +
229A THR 3.4 0.2 - - - -
230A CYS* 3.7 0.9 - - - -
231A MET* 2.9 32.2 + - - +
248A CYS* 4.6 0.2 - - - -
635A PHE* 4.1 1.3 - - + -
640A TRP* 3.8 9.4 - - + +
647A THR* 3.3 25.1 + - - +
649A THR* 2.5 36.3 + - - +
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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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56A ALA 4.1 4.5 - - - +
226A SER* 2.7 14.6 + - - +
227A THR* 1.3 76.4 - - - +
229A THR* 1.3 59.2 + - + +
232A ARG* 2.9 34.0 + - - +
640A TRP* 3.8 20.1 - - + -
641A SER* 3.7 34.1 - - - +
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Residues in contact with THR 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A VAL 2.7 26.9 + - - -
225A ILE* 3.6 26.5 - - + -
226A SER* 3.1 11.3 + - - +
228A ALA* 1.3 78.7 - - + +
230A CYS* 1.3 63.3 + - - +
232A ARG* 3.2 35.1 + - - +
233A ARG* 2.9 41.6 + - - +
90D ASP* 4.0 4.3 - - - +
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Residues in contact with CYS 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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54A LEU* 3.5 2.0 - - + -
223A ALA* 3.1 18.8 - - + +
224A VAL 4.9 1.6 - - - +
226A SER 3.3 18.8 + - - +
227A THR 3.5 2.2 + - - +
228A ALA 3.2 0.2 - - - -
229A THR* 1.3 82.8 + - - +
231A MET* 1.3 62.0 + - - +
233A ARG* 3.6 4.0 + - - +
234A SER* 3.1 13.3 + - - -
247A VAL* 2.9 41.6 - - - +
248A CYS* 1.9 56.8 - - - -
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Residues in contact with MET 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A THR* 2.9 31.2 + - - +
228A ALA 3.8 0.7 - - - +
230A CYS* 1.3 76.6 - - - +
232A ARG* 1.3 56.9 + - - +
234A SER* 3.6 5.8 - - - +
235A SER* 2.9 31.0 + - - -
248A CYS* 3.4 42.2 - - + +
250A PRO* 4.2 16.8 - - + -
635A PHE* 4.3 12.8 - - + -
640A TRP* 3.5 46.9 - - + -
649A THR* 4.2 7.4 - - + -
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Residues in contact with ARG 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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228A ALA* 2.9 19.6 + - - +
229A THR* 3.2 40.2 + - - +
231A MET* 1.3 74.4 - - - +
233A ARG* 1.3 61.1 + - - +
235A SER* 2.4 28.1 + - - +
236A ILE* 2.9 30.2 + - + +
640A TRP* 3.7 15.0 - - + -
86D GLY* 3.7 13.3 + - - -
87D ALA* 3.7 44.3 - - - +
90D ASP* 3.5 20.2 + - - -
91D TYR* 5.1 3.8 - - + -
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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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223A ALA* 5.3 2.0 - - - +
224A VAL* 3.6 21.9 + - - +
225A ILE* 5.5 1.6 - - - +
229A THR* 2.9 29.0 + - - +
230A CYS* 3.6 8.1 - - - +
232A ARG* 1.3 75.2 - - - +
234A SER* 1.3 59.2 + - - +
236A ILE* 3.2 11.5 + - - +
237A GLN* 2.9 35.0 + - + +
245A GLU 6.1 0.2 - - - +
247A VAL* 3.9 21.1 - - + -
82D ARG* 4.8 2.0 - - - +
90D ASP* 2.8 41.4 + - - +
96D ILE* 3.2 49.4 - - + +
97D PRO 4.1 4.2 + - - -
98D LEU* 5.2 2.9 + - - -
100D THR 3.7 4.8 + - - -
101D PRO 2.9 28.9 + - - -
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Residues in contact with SER 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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230A CYS 3.1 19.4 + - - -
231A MET* 3.6 8.9 - - - +
233A ARG* 1.3 78.7 - - - +
235A SER* 1.3 56.7 + - - +
237A GLN* 3.2 4.2 + - - +
238A SER* 2.9 29.0 + - - -
245A GLU 4.2 11.2 - - - -
246A ILE* 3.1 36.9 - - - +
247A VAL* 3.8 13.2 - - - +
248A CYS 4.2 6.4 + - - -
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Residues in contact with SER 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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231A MET 2.9 15.1 + - - -
232A ARG* 2.4 30.7 + - - +
234A SER* 1.3 76.1 - - - +
236A ILE* 1.3 62.8 + - - +
238A SER* 2.4 28.4 + - - -
239A THR* 2.9 21.1 + - - +
640A TRP* 4.0 16.8 - - - -
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Residues in contact with ILE 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 ARG* 2.9 27.0 + - + +
233A ARG* 3.3 6.5 - - - +
235A SER* 1.3 82.2 + - - +
237A GLN* 1.3 69.4 + - - +
239A THR* 2.5 24.1 + - - -
240A PHE* 2.7 36.2 + - + +
195B TYR* 5.9 1.3 - - + -
90D ASP* 3.7 27.6 - - + +
91D TYR* 3.4 55.2 - - + +
93D SER 5.1 1.6 - - - +
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Residues in contact with GLN 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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233A ARG* 2.9 19.9 + - + +
234A SER 3.2 5.3 + - - +
236A ILE* 1.3 89.8 - - - +
238A SER* 1.3 60.7 + - - +
241A SER* 2.9 50.9 + - - +
244A PRO* 3.2 8.6 - - + +
245A GLU* 3.7 44.6 + - + +
187B LYS* 4.7 4.7 - - - -
195B TYR* 6.2 0.4 - - - -
90D ASP 4.6 0.8 + - - -
93D SER 4.6 6.9 + - - -
94D PHE* 4.4 10.2 - - - +
96D ILE* 3.3 38.7 + - + +
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Residues in contact with SER 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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234A SER 2.9 13.3 + - - -
235A SER* 2.4 30.4 + - - -
237A GLN* 1.3 77.8 - - - +
239A THR* 1.3 67.1 + - - +
241A SER 4.4 3.3 - - - +
244A PRO* 3.7 14.7 - - - +
246A ILE* 4.2 15.3 - - - -
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Residues in contact with THR 239 (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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235A SER* 2.9 15.9 + - - +
236A ILE* 2.5 23.9 + - - -
238A SER* 1.3 87.5 + - - +
240A PHE* 1.3 91.6 + - + +
241A SER 4.9 0.3 - - - +
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Residues in contact with PHE 240 (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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236A ILE* 2.7 31.7 + - + +
239A THR* 1.3 102.4 + - + +
241A SER* 1.3 63.0 + - - +
242A ILE* 3.7 9.4 + - - +
195B TYR* 3.7 21.8 + + + +
91D TYR* 3.7 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
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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