Contacts of the helix formed by residues 226 - 243 (chain A) in PDB entry 4WLQ
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 ASP 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A LYS* 5.9 3.6 - - - -
29A GLY* 2.9 27.3 + - - +
30A ALA* 4.2 4.0 - - - +
31A GLN* 3.1 19.4 - - - +
225A SER* 1.3 69.5 - - - +
227A ARG* 1.3 68.5 + - - +
228A LYS* 3.9 11.7 + - - +
229A MET* 2.8 53.5 + - + +
230A ILE* 3.1 10.3 + - - +
273A GLU* 4.8 1.7 - - - +
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Residues in contact with ARG 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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31A GLN* 2.7 34.6 + - - +
33A GLU* 5.3 6.5 - - - +
44A GLU 4.8 1.6 + - - -
45A LYS 2.6 29.4 + - - -
46A LEU* 3.7 13.5 + - - +
47A LYS 3.4 21.4 + - - -
48A PRO* 4.3 2.0 - - - +
224A VAL* 4.1 10.5 - - - +
225A SER 3.1 12.4 + - - -
226A ASP* 1.3 70.3 - - - +
228A LYS* 1.3 57.6 + - - +
230A ILE* 3.0 27.3 + - - +
231A TYR* 2.9 69.6 + - + +
234A LYS* 4.8 4.9 - - - +
273A GLU* 3.6 23.3 - - + +
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Residues in contact with LYS 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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226A ASP* 3.1 12.9 + - - +
227A ARG* 1.3 77.7 - - - +
229A MET* 1.3 63.6 + - - +
231A TYR* 4.0 7.5 - - - +
232A GLU* 2.6 60.0 + - - +
270A ILE* 4.1 23.1 - - + +
273A GLU* 4.1 15.0 - - + +
274A VAL* 4.0 29.6 - - + +
277A LEU* 6.0 6.1 - - + -
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Residues in contact with MET 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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29A GLY* 5.3 9.2 - - - -
226A ASP* 2.8 42.8 + - + +
228A LYS* 1.3 77.1 - - - +
230A ILE* 1.3 60.7 + - + +
232A GLU* 3.6 11.3 - - - +
233A GLN* 2.9 46.4 + - + +
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Residues in contact with ILE 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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47A LYS 5.1 3.8 - - - +
48A PRO* 4.6 7.4 - - + -
104A ASP* 3.9 21.8 - - - +
225A SER* 4.1 10.5 - - - -
226A ASP 3.6 14.1 - - - +
227A ARG* 3.0 42.2 + - - +
229A MET* 1.3 77.1 - - + +
231A TYR* 1.3 55.6 + - + +
233A GLN* 3.1 24.0 + - - +
234A LYS* 2.8 54.0 + - + +
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Residues in contact with TYR 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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45A LYS* 4.3 9.2 + - - +
227A ARG* 2.9 70.7 + - + +
230A ILE* 1.3 73.4 - - + +
232A GLU* 1.3 63.3 + - - +
234A LYS* 3.0 17.8 + - + +
235A ILE* 2.9 27.0 + - - +
266A ASN* 3.6 25.9 - - - +
269A LEU* 3.5 46.9 - - + +
270A ILE* 3.4 29.6 - - + -
273A GLU* 4.1 11.3 + - + -
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Residues in contact with GLU 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 LYS* 2.6 58.7 + - - +
229A MET* 3.6 10.5 + - - +
231A TYR* 1.3 76.3 - - - +
233A GLN* 1.3 56.1 + - + +
235A ILE* 3.3 6.2 + - + +
236A ALA* 2.9 30.1 + - - +
270A ILE* 3.4 20.2 - - + -
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Residues in contact with GLN 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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103A GLN* 5.9 2.6 - - - +
104A ASP* 5.1 8.5 + - - +
229A MET* 2.9 37.9 + - + +
230A ILE* 3.1 21.9 + - - +
232A GLU* 1.3 69.4 - - - +
234A LYS* 1.3 70.4 + - - +
236A ALA* 3.4 7.6 + - - +
237A GLU* 3.2 25.5 + - + +
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Residues in contact with LYS 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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44A GLU 5.6 4.2 + - - -
227A ARG* 4.8 4.0 - - - +
230A ILE* 2.8 33.5 + - + +
231A TYR* 3.0 29.2 + - + +
233A GLN* 1.3 75.8 - - - +
235A ILE* 1.3 65.1 + - - +
237A GLU* 2.9 12.3 + - - +
238A LEU* 3.1 18.9 + - + +
262A GLU* 5.9 0.9 - - - +
265A ARG* 4.6 14.8 - - - +
266A ASN* 3.4 31.2 - - - +
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Residues in contact with ILE 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 TYR 2.9 14.8 + - - +
232A GLU* 3.6 8.1 - - + +
234A LYS* 1.3 73.5 - - - +
236A ALA* 1.3 68.0 + - - +
237A GLU 2.9 1.7 + - - -
238A LEU* 2.9 19.9 + - - +
239A GLN* 3.0 39.8 + - - +
263A VAL* 3.8 17.7 - - + -
266A ASN* 3.5 29.8 - - + +
267A GLN* 3.6 33.2 - - + +
270A ILE* 3.9 15.7 - - + -
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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 GLU 2.9 21.1 + - - +
233A GLN* 3.7 9.4 - - - +
234A LYS 3.3 0.2 + - - -
235A ILE* 1.3 73.5 - - - +
237A GLU* 1.3 68.5 + - - +
239A GLN* 3.8 13.6 + - - +
240A ARG* 3.3 18.9 + - - +
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Residues in contact with GLU 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 GLN* 3.2 11.9 + - + +
234A LYS* 2.9 10.3 + - - +
236A ALA* 1.3 85.6 - - - +
238A LEU* 1.3 69.3 + - + +
239A GLN 3.3 1.1 - - - -
240A ARG* 3.0 33.3 + - - +
241A GLN* 3.2 16.7 + - - +
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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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234A LYS* 3.1 15.2 + - + +
235A ILE* 2.9 4.2 + - - +
237A GLU* 1.3 78.2 - - + +
239A GLN* 1.3 54.4 + - - +
241A GLN* 2.7 39.4 + - - +
242A LEU* 2.9 15.5 + - - +
259A ILE* 3.6 19.5 - - + +
262A GLU* 3.6 33.9 - - + +
263A VAL* 3.4 26.9 - - + +
266A ASN* 3.8 21.3 - - - +
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Residues in contact with GLN 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 ILE* 3.0 37.0 + - + +
236A ALA* 4.0 11.1 - - - +
238A LEU* 1.3 72.9 - - - +
240A ARG* 1.3 66.3 + - - +
241A GLN 3.3 0.2 + - - -
242A LEU* 4.0 13.9 - - + +
243A ALA* 3.4 23.2 + - - +
263A VAL* 4.5 16.0 - - + +
267A GLN* 4.7 4.8 - - - +
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Residues in contact with ARG 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 ALA 3.3 12.0 + - - +
237A GLU* 3.0 34.8 + - - +
238A LEU 3.0 0.2 - - - -
239A GLN* 1.3 78.4 - - - +
241A GLN* 1.3 55.2 + - + +
243A ALA* 3.6 3.0 + - - +
244A GLU* 3.0 54.6 + - - +
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Residues in contact with GLN 241 (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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237A GLU* 3.8 14.0 + - - +
238A LEU* 2.7 27.7 + - - +
240A ARG* 1.3 70.2 - - + +
242A LEU* 1.3 55.8 + - - +
243A ALA 2.9 3.8 - - - -
244A GLU* 2.6 45.9 + - + +
245A GLU* 3.6 8.1 + - - +
256A LEU* 5.7 0.6 - - - +
259A ILE* 3.3 29.7 - - + +
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Residues in contact with LEU 242 (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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238A LEU 2.9 16.2 + - - +
239A GLN* 4.0 14.1 - - + +
241A GLN* 1.3 74.1 - - - +
243A ALA* 1.3 57.2 + - - +
245A GLU 4.1 10.4 - - - +
256A LEU* 3.7 38.5 - - + +
259A ILE* 3.6 33.4 - - + -
260A GLN* 3.8 29.2 - - + +
263A VAL* 4.5 11.2 - - + -
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Residues in contact with ALA 243 (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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239A GLN 3.4 15.9 + - - +
240A ARG* 3.8 2.7 - - - +
241A GLN 2.9 0.6 - - - -
242A LEU* 1.3 77.8 - - + +
244A GLU* 1.3 62.9 + - - +
245A GLU 3.5 2.8 - - - -
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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