Contacts of the helix formed by residues 232 - 240 (chain B) in PDB entry 1PJS
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 232 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A GLY 3.4 12.1 - - - -
230A LEU* 3.6 23.6 - - + +
231A LEU 3.3 7.2 - - - -
232A THR* 4.1 2.7 - - + +
233A LEU* 4.3 1.5 - - - +
330A ILE* 4.3 12.8 - - + -
222B GLY 5.0 1.9 + - - +
230B LEU 4.8 3.4 - - - +
231B LEU* 1.3 83.6 - - - +
233B LEU* 1.3 65.5 + - - +
235B GLY* 2.8 22.9 + - - -
236B LEU* 3.0 20.1 + - - +
327B VAL* 3.4 10.9 - - - +
328B PRO 3.5 21.2 + - - +
329B GLY* 4.7 3.6 - - - -
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ALA 4.0 17.0 - - - +
229A GLY* 3.3 9.6 + - - +
231A LEU* 3.0 25.1 + - + +
232A THR 3.3 23.6 - - - +
233A LEU* 3.5 22.9 - - + -
236A LEU* 4.0 23.1 - - + -
258A LEU* 4.4 15.5 - - + -
144B GLU 5.0 3.6 - - - +
145B SER* 4.2 16.7 - - - +
232B THR* 1.3 71.4 - - - +
234B LYS* 1.3 58.3 + - - +
236B LEU* 3.2 3.5 + - - +
237B GLN* 2.9 45.3 + - - +
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Residues in contact with LYS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ASP* 5.0 5.6 + - - +
229A GLY* 2.9 25.1 + - - +
230A LEU* 5.2 2.0 - - + -
339A TYR* 4.3 20.4 + - - +
453A TRP* 4.5 20.2 - - - -
186B ASP* 5.1 10.7 - - - +
190B GLN* 4.6 16.7 - - - +
219B VAL* 6.4 0.2 - - - -
233B LEU* 1.3 77.0 - - - +
235B GLY* 1.3 58.8 + - - +
237B GLN* 3.1 17.2 + - - +
238B GLN* 2.8 51.4 + - + +
325B SER* 5.4 6.0 - - - -
326B VAL 5.0 0.2 + - - -
327B VAL* 4.0 30.2 - - + +
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Residues in contact with GLY 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B VAL* 3.8 22.2 - - - -
231B LEU* 4.2 4.5 - - - -
232B THR* 2.8 22.7 + - - -
234B LYS* 1.3 78.4 - - - +
236B LEU* 1.3 56.3 + - - +
238B GLN* 3.9 3.6 - - - +
239B ILE* 3.0 40.1 + - - +
327B VAL* 3.7 4.6 - - - +
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Residues in contact with LEU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LEU* 3.5 36.6 - - + -
145B SER* 4.2 9.9 - - - +
146B LEU* 3.6 19.1 - - + -
231B LEU* 3.8 15.0 - - + +
232B THR 3.0 12.0 + - - +
233B LEU 3.6 6.3 - - - +
234B LYS 3.1 0.2 - - - -
235B GLY* 1.3 73.4 - - - +
237B GLN* 1.3 73.2 + - - +
239B ILE* 3.1 4.4 + - + +
240B GLN* 2.9 52.4 + - + +
258B LEU* 4.4 21.8 - - + -
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Residues in contact with GLN 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A GLY* 5.5 3.1 - - - -
505A PGE 5.9 2.8 - - - +
144B GLU 4.2 2.2 + - - -
145B SER 2.9 31.6 + - - +
146B LEU 4.3 10.1 - - - +
147B LEU 3.9 2.8 + - - -
148B PRO* 3.5 42.4 - - + +
149B GLN 4.8 1.9 + - - +
186B ASP* 5.5 0.9 - - - +
233B LEU* 2.9 29.6 + - - +
234B LYS* 3.4 20.7 - - - +
236B LEU* 1.3 80.7 - - + +
238B GLN* 1.3 69.8 + - - +
240B GLN* 3.3 12.5 + - - +
241B GLN* 3.4 20.4 - - - +
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Residues in contact with GLN 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B ASP* 2.8 36.0 + - - +
217B GLU* 5.0 1.2 - - - +
219B VAL* 3.8 34.4 - - + +
221B VAL* 4.1 14.4 - - + -
234B LYS* 2.8 35.6 + - + +
235B GLY 3.9 3.8 - - - +
237B GLN* 1.3 77.9 + - - +
239B ILE* 1.3 63.4 + - - +
241B GLN* 3.1 13.8 + - - +
242B ALA 3.3 9.2 + - - -
295B ARG* 3.1 19.7 + - - +
297B VAL* 3.7 12.9 - - + +
325B SER* 5.3 1.0 + - - -
327B VAL* 4.1 12.6 - - + -
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Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B VAL* 4.3 3.4 - - + -
231B LEU* 4.1 19.3 - - + -
235B GLY 3.0 25.6 + - - +
236B LEU* 3.1 6.7 + - + +
238B GLN* 1.3 78.2 - - + +
240B GLN* 1.3 60.6 + - - +
241B GLN 3.2 0.9 + - - -
242B ALA* 3.6 16.4 + - - +
245B VAL* 5.4 2.2 - - + -
255B ILE* 4.8 5.2 - - + +
258B LEU* 3.8 12.3 - - + +
259B VAL* 3.6 37.2 - - + +
260B ARG* 4.0 10.4 + - - +
297B VAL* 4.3 11.2 - - + -
299B LEU* 3.6 40.2 - - + -
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Residues in contact with GLN 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505A PGE 3.7 30.2 + - - +
146B LEU* 3.0 34.4 - - - +
236B LEU* 2.9 31.5 + - + +
237B GLN* 3.3 5.8 + - - +
238B GLN 3.2 0.4 - - - -
239B ILE* 1.3 75.7 - - - +
241B GLN* 1.3 59.3 + - - +
242B ALA 3.6 0.4 - - - -
258B LEU 4.0 17.3 - - - +
260B ARG* 3.5 36.6 + - + +
261B ARG* 4.8 13.0 - - - +
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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