Contacts of the helix formed by residues 229 - 239 (chain D) in PDB entry 1FM9
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 THR 229 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222D TYR* 4.5 8.7 - - + -
223D ILE* 3.6 31.4 - - + -
226D PHE* 4.1 15.5 - - - +
227D PRO 3.6 1.0 + - - -
228D LEU* 1.3 94.9 - - - +
230D LYS* 1.3 59.2 + - - +
231D ALA* 3.6 3.5 + - - +
232D LYS* 3.2 41.0 + - - +
233D ALA* 2.9 10.8 + - - +
329D MET* 6.3 0.4 - - - -
332D SER* 5.3 0.9 - - - -
381D ASP* 3.2 18.1 + - - -
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Residues in contact with LYS 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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222D TYR* 4.5 1.6 + - - +
229D THR* 1.3 69.6 - - - +
231D ALA* 1.3 63.5 + - - +
233D ALA* 3.1 3.8 + - - +
234D ARG* 2.8 57.0 + - + +
332D SER* 3.6 34.2 - - - +
374D PHE* 5.8 2.6 - - - -
375D ASN* 4.1 26.6 + - - +
378D GLU* 4.3 5.5 - - - +
379D LEU* 2.6 43.1 + - - +
380D ASP* 4.5 2.9 - - - -
381D ASP* 2.8 23.0 + - - +
384D LEU* 3.9 11.1 - - + +
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Residues in contact with ALA 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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229D THR* 3.9 3.4 - - - +
230D LYS* 1.3 77.4 - - - +
232D LYS* 1.3 64.2 + - + +
234D ARG* 4.0 4.5 - - - +
235D ALA* 3.1 22.6 + - - +
381D ASP* 2.9 16.7 + - - +
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Residues in contact with LYS 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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223D ILE* 5.6 7.1 + - - +
226D PHE 5.2 0.4 + - - -
227D PRO 3.2 26.7 + - - +
228D LEU* 3.8 9.4 - - + -
229D THR* 3.2 30.6 + - - +
231D ALA* 1.3 75.1 - - + +
233D ALA* 1.3 67.0 + - - +
235D ALA* 3.0 9.6 + - - +
236D ILE* 2.9 29.8 + - + +
241D THR* 5.0 0.2 - - - +
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Residues in contact with ALA 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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228D LEU* 3.2 6.8 - - + +
229D THR 2.9 15.6 + - - +
230D LYS* 3.1 5.6 + - - +
232D LYS* 1.3 76.5 - - - +
234D ARG* 1.3 57.5 + - - +
236D ILE* 3.1 5.6 + - - +
237D LEU* 2.8 34.3 + - - +
332D SER 3.5 13.2 - - - +
333D LEU* 3.3 34.1 - - + -
340D LEU* 3.6 10.7 - - + +
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Residues in contact with ARG 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 LYS* 2.8 41.9 + - + +
231D ALA* 4.0 4.7 - - - +
233D ALA* 1.3 73.7 - - - +
235D ALA* 1.3 52.4 + - - +
237D LEU* 3.6 11.7 - - - +
238D THR* 2.5 48.3 + - + +
331D ALA 3.3 4.4 + - - -
332D SER* 2.6 40.7 + - - +
334D MET 2.5 34.4 + - - +
335D ASN* 3.6 16.6 - - - +
375D ASN* 3.6 17.1 + - - +
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Residues in contact with ALA 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 ALA 3.1 14.5 + - - +
232D LYS* 3.0 14.0 + - - +
234D ARG* 1.3 75.5 - - - +
236D ILE* 1.3 62.2 + - - +
238D THR* 3.2 10.1 + - - -
239D GLY 3.2 0.2 + - - -
240D LYS* 3.0 35.1 + - + +
241D THR* 3.5 19.3 - - + +
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Residues in contact with ILE 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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228D LEU* 5.0 6.7 - - + -
232D LYS* 2.9 24.5 + - + +
233D ALA* 3.5 5.2 - - - +
235D ALA* 1.3 76.6 - - - +
237D LEU* 1.3 64.1 + - - +
239D GLY* 3.2 13.7 + - - -
241D THR* 3.8 17.5 - - + -
243D ASP* 5.7 2.5 - - - +
244D LYS 5.9 0.7 - - - +
245D SER* 5.7 0.4 - - - -
246D PRO* 3.7 35.6 - - + +
340D LEU* 4.1 16.4 - - + -
343D GLU 4.8 4.3 - - - +
344D GLY* 4.2 26.2 - - - +
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Residues in contact with LEU 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 ALA 2.8 26.7 + - - +
234D ARG* 3.6 24.7 - - - +
236D ILE* 1.3 78.5 - - - +
238D THR* 1.3 60.2 + - + +
246D PRO* 6.4 0.7 - - + -
332D SER 4.2 0.7 - - - +
333D LEU 3.7 21.1 - - - +
334D MET 4.7 0.2 - - - -
335D ASN* 3.9 25.5 - - + +
340D LEU* 3.7 23.8 - - + -
347D PHE* 3.3 40.6 - - + -
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Residues in contact with THR 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 ARG* 2.5 33.4 + - + +
235D ALA* 3.2 12.8 + - - -
237D LEU* 1.3 76.3 - - + +
239D GLY* 1.3 58.0 + - - +
240D LYS* 3.9 26.6 + - - +
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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 ALA 3.2 0.4 + - - -
236D ILE 3.2 13.7 + - - -
237D LEU 3.7 0.2 + - - -
238D THR* 1.3 76.5 - - - +
240D LYS* 1.3 83.0 + - - +
241D THR* 3.8 3.1 + - - -
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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