Contacts of the helix formed by residues 229 - 245 (chain D) in PDB entry 5E9W
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 ALA 229 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227D ASP* 2.8 13.7 + - - +
228D ILE* 1.3 80.0 - - + +
230D ASP* 1.3 64.5 + - - +
231D VAL* 3.3 2.7 - - + +
232D SER* 3.2 20.0 + - - +
233D VAL* 3.0 24.4 + - - +
501D SAH 4.0 8.7 - - - +
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Residues in contact with ASP 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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228D ILE 3.5 5.1 + - - -
229D ALA* 1.3 72.9 - - - +
231D VAL* 1.3 60.7 + - + +
233D VAL* 3.4 1.4 + - - +
234D LYS* 3.0 58.9 + - - +
259D THR* 2.7 39.5 + - + +
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Residues in contact with VAL 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D LYS* 6.3 1.3 - - - -
229D ALA* 3.3 2.8 - - + +
230D ASP* 1.3 79.1 - - + +
232D SER* 1.3 60.4 + - - +
234D LYS* 3.4 6.6 + - - +
235D GLN* 3.0 38.3 + - - +
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Residues in contact with SER 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D GLY* 3.2 33.0 - - - +
208D LYS* 3.7 27.1 - - - +
227D ASP* 4.7 2.7 - - - -
229D ALA* 3.2 24.7 + - - +
231D VAL* 1.3 77.0 - - - +
233D VAL* 1.3 54.7 + - - +
235D GLN* 3.2 3.7 + - - +
236D CYS 2.7 31.2 + - - -
501D SAH 4.9 2.5 + - - -
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Residues in contact with VAL 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D CYS* 4.9 2.9 - - - -
207D GLY 4.4 1.8 - - - -
225D CYS 4.8 2.2 - - - +
226D THR 4.8 0.7 - - - -
227D ASP* 3.7 34.3 - - + +
229D ALA 3.0 15.1 + - - +
230D ASP* 3.5 7.0 - - - +
232D SER* 1.3 76.3 - - - +
234D LYS* 1.3 60.6 + - + +
236D CYS* 3.1 8.6 + - - +
237D GLN* 2.8 28.8 + - + +
257D PHE* 4.0 27.0 - - + -
258D ILE 4.1 11.4 - - - +
259D THR* 3.4 23.6 - - - +
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Residues in contact with LYS 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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230D ASP* 3.0 46.7 + - - +
231D VAL* 3.9 6.5 - - - +
233D VAL* 1.3 80.3 - - + +
235D GLN* 1.3 58.6 + - - +
237D GLN* 3.3 21.3 + - - +
238D GLN* 2.9 27.2 + - - +
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Residues in contact with GLN 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D LYS* 3.3 46.6 + - + +
231D VAL* 3.0 28.6 + - - +
232D SER* 3.4 5.8 - - - +
234D LYS* 1.3 74.9 - - - +
236D CYS* 1.3 65.1 + - - +
238D GLN* 3.2 7.0 + - + +
239D ARG* 3.0 27.9 + - + +
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Residues in contact with CYS 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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206D CYS* 4.0 6.1 - - - -
207D GLY 3.6 11.2 - - - +
208D LYS 3.4 12.7 + - - -
209D GLY* 3.6 21.5 - - - -
212D LEU* 3.5 11.0 - - - +
225D CYS* 3.8 33.7 - - - -
232D SER 2.7 17.0 + - - +
233D VAL* 3.3 11.4 - - - +
235D GLN* 1.3 72.3 - - - +
237D GLN* 1.3 61.9 + - - +
239D ARG* 3.3 1.6 + - - -
240D TYR* 3.0 19.8 + - - +
257D PHE* 3.9 7.4 - - + -
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Residues in contact with GLN 237 (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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233D VAL* 2.8 13.5 + - - +
234D LYS* 3.5 24.1 + - - +
236D CYS* 1.3 78.2 - - - +
238D GLN* 1.3 58.2 + - - +
240D TYR* 3.2 4.3 + - - +
241D GLU* 2.9 37.8 + - + +
257D PHE* 3.4 48.1 - - + +
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Residues in contact with GLN 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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234D LYS 2.9 16.6 + - - +
235D GLN* 3.2 8.5 + - + +
237D GLN* 1.3 77.1 - - - +
239D ARG* 1.3 57.9 + - - +
241D GLU* 3.1 14.5 + - - +
242D ASP* 2.6 66.8 + - - +
245D ASN* 5.7 1.0 - - - +
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Residues in contact with ARG 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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208D LYS* 3.4 25.8 + - - +
209D GLY 2.9 27.2 + - - -
210D GLY* 3.5 17.4 + - - +
212D LEU* 3.7 10.9 - - + +
213D LEU* 6.0 5.5 - - - +
235D GLN* 3.0 18.6 + - + +
236D CYS 3.5 9.0 - - - +
238D GLN* 1.3 76.0 - - - +
240D TYR* 1.3 58.2 + - - +
242D ASP* 3.3 11.2 + - + +
243D MET* 2.9 34.9 + - - +
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Residues in contact with TYR 240 (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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212D LEU* 3.7 12.8 - - + +
236D CYS 3.0 9.4 + - - +
237D GLN 3.2 7.2 + - - +
239D ARG* 1.3 77.9 - - - +
241D GLU* 1.3 80.4 + - - +
243D MET* 3.2 8.0 + - - +
244D LYS* 2.9 57.4 + - - +
252D ILE* 3.7 16.4 - - + -
253D PHE* 2.6 57.2 + + - -
254D SER* 3.6 1.2 - - - -
255D ALA* 3.6 23.9 + - + -
257D PHE* 3.6 30.3 - + + -
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Residues in contact with GLU 241 (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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237D GLN* 2.9 27.1 + - + +
238D GLN* 3.4 21.8 - - - +
240D TYR* 1.3 96.7 - - - +
242D ASP* 1.3 56.6 + - - +
244D LYS* 3.1 14.5 + - - +
245D ASN* 2.8 57.3 + - - +
257D PHE* 5.7 0.3 - - - -
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Residues in contact with ASP 242 (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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238D GLN* 2.6 51.0 + - - +
239D ARG* 3.6 10.8 - - - +
240D TYR 3.2 0.2 - - - -
241D GLU* 1.3 75.1 - - - +
243D MET* 1.3 63.4 + - - +
245D ASN* 3.3 15.1 + - - +
246D ARG* 3.4 18.5 + - - +
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Residues in contact with MET 243 (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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212D LEU* 3.8 36.3 - - + +
213D LEU* 3.8 23.6 - - + -
216D LYS* 3.6 42.2 - - + -
239D ARG* 2.9 22.7 + - + +
240D TYR* 3.2 9.2 + - - +
242D ASP* 1.3 78.1 - - + +
244D LYS* 1.3 61.6 + - - +
246D ARG* 3.3 22.6 + - - +
249D SER* 3.9 10.0 + - - -
252D ILE* 3.8 16.6 - - + -
253D PHE* 4.7 3.1 - - + -
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Residues in contact with LYS 244 (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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240D TYR* 2.9 48.6 + - - +
241D GLU* 3.1 20.7 + - - +
243D MET* 1.3 78.1 - - - +
245D ASN* 1.3 67.1 + - - +
246D ARG 3.2 9.2 + - - +
249D SER* 4.5 6.7 + - - -
252D ILE* 3.7 29.3 + - + +
253D PHE 4.8 0.4 + - - -
254D SER* 5.3 3.0 - - - +
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Residues in contact with ASN 245 (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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238D GLN* 5.7 0.4 - - - +
241D GLU* 2.8 42.8 + - - +
242D ASP* 3.3 11.9 + - - +
243D MET 3.2 0.4 - - - -
244D LYS* 1.3 88.7 - - - +
246D ARG* 1.3 60.0 + - - +
247D ARG 4.0 0.7 + - - -
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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