Contacts of the helix formed by residues 226 - 241 (chain A) in PDB entry 1PS9
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 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLY 5.3 0.4 - - - +
225A GLY* 1.3 76.1 - - - +
227A PHE* 1.3 66.0 + - - +
228A ALA* 3.6 9.1 + - - +
229A GLU* 2.9 41.7 + - - +
230A THR* 3.0 23.9 + - - -
537A LEU 3.7 5.4 - - - -
538A GLN* 3.5 22.2 - - - +
539A GLN 4.4 0.4 - - - -
540A ALA* 4.5 12.3 - - + +
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Residues in contact with PHE 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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217A MET* 5.5 1.8 - - + -
226A THR* 1.3 72.9 - - - +
228A ALA* 1.3 60.5 + - - +
230A THR* 3.1 15.1 + - + -
231A VAL* 2.9 53.7 + - + +
271A VAL 4.9 1.8 - - - -
274A LYS* 3.2 64.6 - - + -
275A LEU* 4.0 11.7 - - + -
278A HIS* 4.2 9.0 - + - -
536A SER 4.0 3.4 - - - +
537A LEU* 2.9 48.6 + - + +
538A GLN* 4.6 5.3 - - + +
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A THR* 3.2 9.7 + - - +
227A PHE* 1.3 81.7 - - - +
229A GLU* 1.3 61.6 + - + +
231A VAL* 3.5 6.9 + - - +
232A GLU* 3.0 24.3 + - - +
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Residues in contact with GLU 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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172A LEU 5.5 0.3 - - - +
187A TYR* 3.3 58.9 + - + +
190A ARG* 4.3 14.1 + - - -
224A GLY 4.4 1.0 - - - +
225A GLY* 3.0 14.7 - - - -
226A THR* 2.9 45.4 + - - +
228A ALA* 1.3 76.5 - - + +
230A THR* 1.3 64.9 + - - +
232A GLU* 3.2 3.6 + - - +
233A LEU* 2.9 21.5 + - - +
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Residues in contact with THR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TYR* 4.7 1.3 - - - -
215A LEU* 3.8 25.6 - - + +
216A SER 4.1 10.0 + - - +
217A MET* 3.9 30.1 + - + -
225A GLY* 5.2 3.1 - - - -
226A THR 3.0 14.2 + - - -
227A PHE* 3.3 24.1 - - + -
229A GLU* 1.3 76.2 - - - +
231A VAL* 1.3 57.3 + - - +
233A LEU* 3.4 5.8 + - - +
234A ALA* 3.0 27.4 + - - +
275A LEU* 4.6 8.5 - - + -
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Residues in contact with VAL 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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227A PHE* 2.9 51.7 + - + +
228A ALA* 3.7 7.2 - - - +
230A THR* 1.3 73.6 - - - +
232A GLU* 1.3 66.4 + - - +
234A ALA* 3.2 1.9 + - - +
235A GLN* 3.1 47.7 + - - +
275A LEU* 3.7 15.7 - - + -
278A HIS* 3.9 24.2 - - + +
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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
----------------------------------------------------------
187A TYR* 4.0 14.1 - - + +
188A ARG* 4.1 24.9 + - - +
191A MET* 3.8 22.0 - - + +
228A ALA 3.0 17.7 + - - +
229A GLU* 3.2 5.2 + - - +
231A VAL* 1.3 77.8 - - - +
233A LEU* 1.3 57.5 + - - +
235A GLN* 3.4 12.6 + - - +
236A ALA* 2.9 28.0 + - + +
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Residues in contact with LEU 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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172A LEU* 3.5 31.6 - - + -
187A TYR* 3.5 19.7 - - - +
191A MET* 3.9 25.9 - - + -
194A ALA* 4.3 8.5 - - + -
195A VAL* 4.3 8.1 - - + -
213A TYR* 4.0 6.5 - - - +
215A LEU* 3.4 25.1 - - + -
229A GLU 2.9 9.6 + - - +
230A THR* 3.7 4.3 - - - +
232A GLU* 1.3 75.7 - - - +
234A ALA* 1.3 55.4 + - - +
236A ALA* 2.9 5.6 + - - +
237A ILE* 2.7 55.1 + - + +
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Residues in contact with ALA 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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215A LEU* 4.1 7.1 - - + +
230A THR 3.0 18.0 + - - +
231A VAL 3.2 5.6 + - - +
233A LEU* 1.3 76.3 - - - +
235A GLN* 1.3 56.9 + - - +
237A ILE* 3.2 4.9 + - - +
238A GLU* 3.0 27.2 + - - +
245A ILE* 3.7 22.2 - - + +
275A LEU* 4.0 22.4 - - + -
279A VAL* 3.7 18.6 - - + +
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Residues in contact with GLN 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 VAL* 3.1 35.4 + - + +
232A GLU* 3.8 10.3 - - - +
234A ALA* 1.3 72.4 - - - +
236A ALA* 1.3 65.3 + - - +
238A GLU* 3.3 8.7 + - - +
239A ALA* 3.1 23.9 + - - +
278A HIS* 3.1 36.2 + - - +
279A VAL* 3.9 7.4 - - + -
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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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191A MET* 3.3 33.0 - - + -
195A VAL* 3.8 16.1 - - + +
199A ARG* 5.1 0.9 + - - -
232A GLU* 2.9 9.6 + - + +
233A LEU 2.9 9.4 + - - +
235A GLN* 1.3 78.0 - - - +
237A ILE* 1.3 56.9 + - - +
239A ALA* 3.3 7.9 + - - +
240A ALA* 2.9 27.6 + - - +
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Residues in contact with ILE 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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194A ALA* 3.9 28.3 - - + +
195A VAL* 4.0 13.5 - - - +
198A VAL* 3.9 14.8 - - + -
213A TYR* 3.7 36.6 - - + -
233A LEU* 2.7 38.2 + - + +
234A ALA* 3.7 7.0 - - - +
236A ALA* 1.3 68.4 - - - +
238A GLU* 1.3 64.2 + - - +
240A ALA* 3.3 8.8 + - - +
241A GLY 3.3 0.9 + - - -
242A ALA* 3.2 36.8 + - + -
245A ILE* 4.5 7.4 - - + -
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Residues in contact with GLU 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 ALA 3.0 13.2 + - - +
235A GLN* 3.5 12.3 - - - +
236A ALA 3.2 0.2 - - - -
237A ILE* 1.3 77.6 - - - +
239A ALA* 1.3 59.1 + - - +
241A GLY* 3.0 20.4 + - - -
242A ALA 3.9 2.9 + - - +
278A HIS 4.6 0.7 - - - +
279A VAL* 3.5 23.1 - - + +
280A SER* 2.8 32.3 + - - -
281A LEU* 3.1 43.8 + - + +
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Residues in contact with ALA 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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199A ARG* 4.5 9.7 + - - +
235A GLN 3.1 12.8 + - - +
236A ALA* 3.7 6.5 - - - +
238A GLU* 1.3 79.2 - - - +
240A ALA* 1.3 61.8 + - - +
241A GLY* 3.3 0.9 + - - -
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Residues in contact with ALA 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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195A VAL* 4.0 28.5 - - + +
198A VAL* 3.9 15.9 - - + +
199A ARG* 3.8 31.0 - - + +
202A ARG* 3.9 9.5 - - - +
236A ALA 2.9 15.7 + - - +
237A ILE* 3.5 12.3 - - - +
238A GLU 3.1 0.6 - - - -
239A ALA* 1.3 77.1 - - - +
241A GLY* 1.3 56.9 + - - +
242A ALA 3.9 0.2 - - - -
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Residues in contact with GLY 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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198A VAL* 4.4 4.9 - - - -
202A ARG* 2.9 43.6 + - - -
211A ILE* 4.2 1.1 - - - +
238A GLU 3.0 9.0 + - - -
239A ALA 3.1 2.1 - - - -
240A ALA* 1.3 80.1 - - - +
242A ALA* 1.3 65.6 + - - +
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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