Contacts of the helix formed by residues 232 - 241 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A GLY 5.1 1.7 + - - +
230A LEU 4.8 3.6 - - - +
231A LEU* 1.3 80.9 - - - +
233A LEU* 1.3 65.9 + - - +
234A LYS 3.7 0.7 + - - -
235A GLY* 2.8 22.0 + - - -
236A LEU 2.9 19.1 + - - -
327A VAL* 3.5 11.4 - - - +
328A PRO 3.8 18.2 - - - +
329A GLY* 5.0 2.2 - - - -
229B GLY 3.3 11.8 + - - -
230B LEU* 3.6 25.6 - - + +
231B LEU 3.2 7.2 - - - -
232B THR* 4.1 2.2 - - + +
233B LEU* 3.3 7.2 - - - +
330B ILE* 4.0 14.1 - - + -
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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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232A THR* 1.3 71.9 - - - +
234A LYS* 1.3 57.6 + - - +
236A LEU* 3.3 6.8 + - - +
237A GLN* 3.0 24.9 + - - +
141B GLU* 5.1 1.6 - - - +
145B SER* 4.3 12.6 - - - +
228B ALA 3.9 17.3 - - - +
229B GLY* 3.2 10.1 + - - +
231B LEU* 3.0 22.4 + - + +
233B LEU* 3.5 36.1 - - + -
236B LEU* 3.5 36.1 - - + -
258B LEU* 4.5 9.6 - - + -
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Residues in contact with LYS 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A VAL* 6.2 0.2 - - - -
232A THR* 4.3 2.2 - - - +
233A LEU* 1.3 74.5 - - - +
235A GLY* 1.3 61.6 + - - +
237A GLN* 3.2 20.3 + - - +
238A GLN* 2.9 42.1 + - + +
325A SER* 5.0 6.5 + - - -
326A VAL 5.1 0.6 + - - -
327A VAL* 4.1 27.6 - - + +
227B ASP* 5.0 5.9 + - - +
229B GLY* 3.0 25.0 + - - +
230B LEU* 4.7 2.0 - - + -
339B TYR* 4.3 18.3 + - - +
453B TRP* 4.3 24.2 - - - -
454B PHE* 6.2 0.8 - - - -
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Residues in contact with GLY 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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221A VAL* 3.9 15.7 - - - -
231A LEU* 3.5 16.4 - - - -
232A THR* 2.8 19.9 + - - -
234A LYS* 1.3 77.3 - - - +
236A LEU* 1.3 62.2 + - - +
238A GLN* 3.5 3.1 + - - +
239A ILE* 3.1 30.8 + - - +
327A VAL* 3.9 5.8 - - - +
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Residues in contact with LEU 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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231A LEU* 3.6 15.4 - - + +
232A THR 2.9 12.3 + - - +
233A LEU* 3.5 8.5 - - - +
234A LYS 3.2 0.2 - - - -
235A GLY* 1.3 75.4 - - - +
237A GLN* 1.3 67.3 + - - +
239A ILE* 3.3 3.3 + - + +
240A GLN* 2.9 49.0 + - + +
258A LEU* 4.0 34.5 - - + +
141B GLU* 3.5 28.3 - - + +
144B GLU* 4.2 3.1 - - + -
145B SER* 3.7 26.7 - - - +
233B LEU* 4.0 13.5 - - + -
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Residues in contact with GLN 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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233A LEU 3.0 13.3 + - - +
234A LYS* 3.2 21.5 + - - +
236A LEU* 1.3 76.1 - - - +
238A GLN* 1.3 80.5 + - - +
240A GLN* 3.1 2.4 + - - +
241A GLN* 3.0 50.4 + - - +
295A ARG* 5.7 0.2 - - - +
141B GLU* 3.6 36.6 - - - +
142B LYS* 5.9 0.7 + - - -
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Residues in contact with GLN 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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217A GLU* 4.8 0.5 - - - +
219A VAL* 3.6 37.8 - - + +
221A VAL* 3.9 15.3 - - + -
234A LYS* 2.9 30.0 + - + +
235A GLY 3.8 4.7 - - - +
236A LEU 3.3 0.2 - - - -
237A GLN* 1.3 104.2 - - - +
239A ILE* 1.3 60.1 + - - +
241A GLN* 3.7 3.8 + - - +
242A ALA* 3.3 26.5 + - - +
295A ARG* 4.3 25.1 + - - +
297A VAL* 3.5 9.5 - - + +
325A SER* 5.7 0.2 - - - -
327A VAL* 4.2 11.4 - - + -
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Residues in contact with ILE 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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221A VAL* 4.4 7.9 - - + -
231A LEU* 4.0 18.8 - - + -
235A GLY 3.1 13.6 + - - +
236A LEU* 3.4 11.2 - - + +
238A GLN* 1.3 76.1 - - - +
240A GLN* 1.3 63.5 + - - +
241A GLN 3.4 0.4 - - - -
242A ALA* 4.2 8.4 + - - +
245A VAL* 4.9 2.7 - - + -
255A ILE* 4.0 12.1 - - + +
258A LEU* 3.4 41.7 - - + +
259A VAL* 3.6 18.0 - - + +
260A ARG* 3.0 23.9 + - - +
297A VAL* 4.2 19.5 - - + -
299A LEU* 4.4 16.6 - - + -
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Residues in contact with GLN 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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236A LEU* 2.9 35.4 + - + +
237A GLN 3.1 5.4 + - - +
239A ILE* 1.3 79.3 - - - +
241A GLN* 1.3 58.0 + - - +
242A ALA 3.7 0.7 - - - -
258A LEU* 2.8 22.7 + - - +
260A ARG* 2.9 22.2 - - - +
137B ARG* 3.7 14.6 - - + +
140B ARG* 3.4 45.0 + - - +
141B GLU* 3.5 40.1 + - + +
144B GLU* 3.9 11.5 - - - +
507B PO4 4.6 2.1 + - - -
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Residues in contact with GLN 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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176A ARG* 2.5 39.0 + - - +
180A GLU* 4.3 8.3 + - - +
237A GLN* 3.0 40.0 + - - +
238A GLN* 3.7 5.5 + - - +
240A GLN* 1.3 80.5 - - - +
242A ALA* 1.3 60.8 + - - +
260A ARG* 4.2 4.5 - - - +
295A ARG* 3.4 37.8 - - - +
137B ARG* 4.3 11.0 - - + +
138B LEU* 5.1 9.7 - - - +
141B GLU* 3.6 16.8 - - - +
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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