Contacts of the helix formed by residues 226 - 239 (chain D) in PDB entry 3A4Y
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 GLU 226 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141D HIS 4.4 1.6 - - - +
142D LEU* 3.6 24.8 - - + +
143D PRO* 3.7 17.9 - - + -
168D LYS* 4.4 4.9 + - - -
170D VAL* 3.7 20.1 - - + +
171D LEU* 3.3 28.5 - - - +
223D PHE* 4.2 0.8 + - - +
225D VAL* 1.3 81.2 - - + +
227D ARG* 1.3 74.0 + - - +
228D ALA 3.4 1.8 - - - -
229D GLN* 3.1 16.8 - - - +
230D GLU* 3.2 24.7 + - - +
261D TYR* 2.9 21.7 - - - +
379D GLY* 5.9 1.2 - - - -
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Residues in contact with ARG 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D LYS* 3.9 7.3 - - - +
222D THR* 4.3 3.4 - - - -
223D PHE* 3.6 38.7 + - + +
226D GLU* 1.3 81.5 + - - +
228D ALA* 1.3 67.2 + - - +
230D GLU* 3.2 29.2 + - - +
231D ILE* 3.3 17.6 + - + +
339D VAL* 4.0 24.6 + - + -
340D GLY* 4.1 6.5 - - - -
377D PHE* 2.4 34.2 + - - +
378D SER* 3.1 2.2 - - - +
379D GLY* 3.1 10.2 - - - +
440D SO4 2.6 47.4 + - - -
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Residues in contact with ALA 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D THR* 3.5 20.6 + - - +
223D PHE 3.0 17.1 + - - +
224D ALA* 4.3 1.1 - - - -
226D GLU 3.4 0.4 - - - -
227D ARG* 1.3 76.7 - - - +
229D GLN* 1.3 74.3 + - - +
231D ILE* 3.3 12.4 + - - +
232D LEU* 3.4 16.7 + - - +
249D LEU* 4.5 10.8 - - + -
251D SER* 6.1 0.4 - - - -
254D ALA* 4.1 19.5 - - + -
310D LEU* 3.9 5.6 - - + +
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Residues in contact with GLN 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D ALA 2.9 23.0 + - - -
225D VAL 3.4 5.8 + - - -
226D GLU 3.1 21.4 - - - +
228D ALA* 1.3 85.1 - - - +
230D GLU* 1.3 59.6 + - - +
232D LEU* 3.2 16.1 + - - +
233D TYR 3.0 17.0 + - - -
254D ALA* 3.5 10.4 - - - +
257D VAL* 2.9 30.5 - - - +
258D LEU* 3.6 21.8 + - + +
261D TYR* 3.3 34.1 - - + +
283D PHE* 3.4 11.0 - - + -
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Residues in contact with GLU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D LYS* 2.7 52.7 + - - +
169D ASP 4.9 0.3 + - - -
170D VAL* 3.5 27.6 - - + +
171D LEU* 6.4 0.2 - - - -
197D TYR* 3.8 12.5 + - - +
226D GLU* 3.2 21.7 + - - +
227D ARG* 3.2 24.8 + - - +
229D GLN* 1.3 76.0 - - - +
231D ILE* 1.3 58.2 + - + +
233D TYR* 3.1 9.6 + - - +
234D VAL* 3.0 31.1 + - + +
283D PHE* 4.8 1.3 - - - -
377D PHE* 4.8 8.1 - - - +
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Residues in contact with ILE 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D PHE* 4.0 11.4 - - + -
220D ILE* 3.9 26.0 - - + -
222D THR* 4.4 18.2 - - + -
227D ARG* 3.5 15.0 - - + +
228D ALA* 3.3 7.5 + - - +
229D GLN 3.2 0.2 - - - -
230D GLU* 1.3 74.6 - - + +
232D LEU* 1.3 61.9 + - - +
233D TYR 3.0 1.3 - - - -
234D VAL* 2.8 7.2 + - + +
235D LEU* 2.8 42.5 + - + +
310D LEU* 4.5 9.0 - - + -
339D VAL* 3.8 18.6 - - + -
377D PHE* 3.4 39.5 - - + -
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Residues in contact with LEU 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D ALA 3.5 9.9 - - - +
229D GLN* 3.2 19.0 + - - +
231D ILE* 1.3 76.8 - - - +
233D TYR* 1.3 53.2 + - - +
235D LEU* 3.3 9.3 + - + +
236D TYR* 2.7 36.1 + - - +
247D ILE* 4.3 9.0 - - + -
249D LEU* 3.7 20.4 - - + -
258D LEU* 3.9 12.6 - - + -
282D PRO 4.6 1.3 - - - -
283D PHE 3.8 23.8 - - - +
285D PRO* 3.7 6.8 - - + +
288D LEU* 3.3 37.0 - - + -
310D LEU* 3.6 22.9 - - + -
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Residues in contact with TYR 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D ASP* 4.4 12.3 - - + -
170D VAL* 3.7 16.8 - - + -
229D GLN 3.0 4.6 + - - +
230D GLU* 3.1 13.7 - - - +
231D ILE 3.0 0.2 - - - -
232D LEU* 1.3 76.2 - - - +
234D VAL* 1.3 64.2 + - + +
237D THR* 2.8 52.9 + - + +
271D GLU* 2.4 38.5 + - - +
272D VAL* 3.7 20.4 - - + +
275D HIS* 3.4 17.2 + - - -
282D PRO* 3.0 46.2 + - + -
283D PHE* 3.7 27.8 - + + -
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Residues in contact with VAL 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D TYR* 3.5 23.8 - - - +
201D VAL* 4.2 16.8 - - + -
204D PHE* 4.4 22.4 - - + -
205D LEU* 5.1 3.3 - - + +
230D GLU* 3.1 17.9 - - + +
231D ILE* 2.8 13.3 + - - +
233D TYR* 1.3 82.3 - - + +
235D LEU* 1.3 62.4 + - - +
237D THR* 3.5 4.9 - - - -
238D HIS* 3.1 40.8 + - + +
242D LEU* 4.9 0.3 - - - +
377D PHE* 4.3 11.4 - - + -
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Residues in contact with LEU 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D PHE* 4.3 11.2 - - + -
205D LEU* 6.2 0.4 - - + -
208D LEU* 4.1 21.1 - - + -
220D ILE* 5.8 0.2 - - + -
231D ILE* 2.8 26.4 + - + +
232D LEU* 3.5 16.8 - - + +
234D VAL* 1.3 79.5 - - - +
236D TYR* 1.3 59.6 + - - +
238D HIS 2.9 1.0 + - - -
239D GLY* 2.7 36.3 + - - -
242D LEU* 3.8 23.1 - - + -
247D ILE* 3.7 38.4 - - + -
285D PRO* 4.2 10.5 - - + +
308D VAL* 4.7 14.6 - - + -
310D LEU* 5.2 0.9 - - + -
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Residues in contact with TYR 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D LEU 2.7 20.8 + - - +
233D TYR 3.9 0.7 - - - +
235D LEU* 1.3 73.3 - - - +
237D THR* 1.3 68.1 + - + +
238D HIS 3.7 0.2 + - - -
239D GLY* 4.2 4.2 + - - -
275D HIS* 5.3 5.8 - + - -
280D LYS* 3.5 36.4 - - + +
281D ASN 3.3 19.5 - - - -
282D PRO* 3.4 36.6 - - + +
284D ARG 3.4 26.2 - - - -
285D PRO* 3.6 18.7 - - + +
286D ALA 5.1 0.9 - - - -
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Residues in contact with THR 237 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233D TYR* 2.8 61.2 + - + +
234D VAL* 3.2 3.6 + - - -
236D TYR* 1.3 86.2 - - + +
238D HIS* 1.3 87.9 + - - +
239D GLY 3.7 0.4 - - - -
240D HIS* 3.9 10.8 - - - -
271D GLU* 5.5 0.2 - - - +
275D HIS* 4.3 10.5 - - + -
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Residues in contact with HIS 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D VAL* 4.0 16.2 - - + +
205D LEU* 3.8 32.9 - - + +
234D VAL* 3.1 37.5 + - + +
235D LEU 2.9 3.5 + - - -
237D THR* 1.3 97.5 + - - +
239D GLY* 1.3 54.5 + - - +
240D HIS* 2.7 35.2 + - - +
241D ARG* 3.2 14.6 + - + +
242D LEU* 3.1 15.5 - - + +
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Residues in contact with GLY 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D LEU 2.7 20.2 + - - -
236D TYR* 4.2 4.0 + - - -
237D THR 3.7 1.6 - - - -
238D HIS* 1.3 70.3 - - - +
240D HIS* 1.3 59.7 + - - +
241D ARG 3.4 1.1 - - - -
242D LEU* 3.6 27.9 - - - +
285D PRO* 6.4 0.4 - - - -
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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