Contacts of the helix formed by residues 225 - 236 (chain D) in PDB entry 4WNP
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 225 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223D ALA* 3.1 5.3 - - - +
224D SER* 1.3 82.2 + - - +
226D PRO* 1.3 70.6 - - - +
227D GLN* 3.3 9.7 + - - +
228D ASP* 3.1 27.4 + - - +
229D LEU* 2.9 28.2 + - - +
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Residues in contact with PRO 226 (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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185D PRO* 4.0 33.7 - - + -
193D ILE* 3.6 12.1 - - + +
225D SER* 1.3 88.0 - - - +
227D GLN* 1.3 60.1 + - + +
229D LEU* 3.7 7.9 - - + -
230D ARG* 3.0 25.6 + - - +
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Residues in contact with GLN 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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225D SER* 3.0 9.0 + - - +
226D PRO* 1.3 84.4 + - + +
228D ASP* 1.3 63.4 + - - +
230D ARG* 2.7 44.6 + - - +
231D LEU* 3.1 38.8 + - + +
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Residues in contact with ASP 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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223D ALA* 3.7 11.7 - - + +
224D SER* 2.9 25.7 + - - +
225D SER* 3.1 19.1 + - - +
227D GLN* 1.3 78.6 - - - +
229D LEU* 1.3 59.1 + - - +
231D LEU* 3.4 20.3 + - - +
232D PHE* 3.0 27.5 + - - +
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Residues in contact with LEU 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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185D PRO* 3.2 36.3 - - + +
186D MET* 4.3 9.6 - - + -
193D ILE* 4.0 10.3 - - + -
221D PHE* 3.7 30.3 - - + +
222D GLN 4.5 2.7 - - - +
223D ALA* 3.4 14.3 - - + +
225D SER 2.9 13.8 + - - +
226D PRO* 3.6 9.6 - - + +
228D ASP* 1.3 75.6 - - - +
230D ARG* 1.3 64.3 + - - +
232D PHE* 3.2 11.1 + - + +
233D TYR* 3.1 52.3 + - + +
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Residues in contact with ARG 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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193D ILE* 3.0 42.5 + - + +
194D MET* 3.7 29.6 + - + +
195D SER* 4.8 5.1 + - - -
226D PRO 3.0 14.0 + - - +
227D GLN* 2.7 40.6 + - - +
228D ASP 3.3 0.2 - - - -
229D LEU* 1.3 76.3 - - - +
231D LEU* 1.3 58.2 + - - +
233D TYR* 3.1 5.1 + - - +
234D GLU* 3.0 55.0 + - - +
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Residues in contact with LEU 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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227D GLN* 3.1 27.5 + - + +
228D ASP* 3.7 24.9 - - - +
229D LEU 3.3 0.2 - - - -
230D ARG* 1.3 72.7 - - - +
232D PHE* 1.3 66.5 + - - +
234D GLU* 3.3 23.2 + - - +
235D LYS* 3.0 60.0 + - - +
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Residues in contact with PHE 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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221D PHE* 3.7 28.7 - + + -
222D GLN 6.0 2.9 - - - -
223D ALA* 5.5 2.7 - - + -
228D ASP 3.0 14.1 + - - +
229D LEU* 3.4 17.5 - - + +
231D LEU* 1.3 77.9 - - - +
233D TYR* 1.3 78.4 + + - +
235D LYS* 5.1 1.8 - - - -
236D ASN* 3.0 59.8 + - - +
238D THR 5.5 0.7 - - - -
239D LEU* 3.4 29.8 - - + -
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Residues in contact with TYR 233 (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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185D PRO 5.0 0.9 + - - -
186D MET* 5.2 4.2 + - - -
188D MET 4.3 9.3 + - - -
190D PRO* 3.8 22.7 - - + -
193D ILE* 3.6 28.5 - - + -
194D MET* 4.4 12.8 - - - -
205D TRP* 3.5 20.8 + + - -
221D PHE* 3.7 20.2 + + + +
229D LEU* 3.1 39.3 + - + +
230D ARG* 3.1 7.1 + - - +
232D PHE* 1.3 100.6 - + - +
234D GLU* 1.3 61.3 + - - +
236D ASN 3.2 7.4 - - - +
239D LEU* 3.6 25.6 - - + -
261D ARG* 2.8 30.0 + - - +
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Residues in contact with GLU 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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194D MET* 3.9 17.8 - - + +
230D ARG* 3.0 55.6 + - - +
231D LEU* 3.6 27.4 - - - +
232D PHE 3.3 0.2 - - - -
233D TYR* 1.3 78.7 - - - +
235D LYS* 1.3 65.3 + - + +
236D ASN 3.5 0.3 + - - -
237D LYS* 3.8 10.4 - - - -
261D ARG* 3.5 15.8 + - - +
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Residues in contact with LYS 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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231D LEU* 3.0 56.1 + - - +
232D PHE* 5.2 0.9 - - - -
234D GLU* 1.3 80.5 - - + +
236D ASN* 1.3 69.8 + - - +
237D LYS* 4.1 5.4 + - - +
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Residues in contact with ASN 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 PHE* 3.0 51.1 + - - +
233D TYR 3.2 2.6 - - - +
234D GLU 3.3 0.4 - - - -
235D LYS* 1.3 87.8 - - - +
237D LYS* 1.3 63.1 + - - +
238D THR 3.4 9.1 - - - +
239D LEU* 4.0 18.5 - - + +
261D ARG* 2.9 25.6 + - - -
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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