Contacts of the helix formed by residues 284 - 294 (chain A) in PDB entry 2P3Z
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 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A LEU* 4.9 9.9 - - + -
127A SER* 5.9 0.2 - - - +
129A SER* 3.9 14.4 - - - -
134A MET* 3.8 28.6 - - + +
283A GLY* 1.3 81.7 + - - +
285A LEU* 1.3 66.6 + - - +
286A GLN* 3.7 12.1 + - - -
287A SER* 3.2 23.9 + - - -
288A PHE* 3.2 15.2 - - - -
306A CYS 3.1 16.7 + - - -
311A THR* 4.4 4.9 - - - -
258B GLN* 3.7 17.4 - - - +
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Residues in contact with LEU 285 (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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284A THR* 1.3 72.2 - - - +
286A GLN* 1.4 74.7 + - - +
288A PHE* 3.1 8.8 + - - +
289A ARG* 3.0 25.1 + - + +
311A THR* 4.0 10.9 - - + +
314A GLU* 3.5 55.2 - - + +
315A ILE* 3.7 23.1 - - + +
318A LEU* 4.1 13.7 - - + -
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Residues in contact with GLN 286 (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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284A THR* 3.2 10.5 - - - +
285A LEU* 1.4 95.5 + - - +
287A SER* 1.3 61.8 + - - +
289A ARG* 3.3 11.2 + - + +
290A THR* 3.2 24.3 + - - -
258B GLN* 3.9 28.1 - - + +
259B GLN* 4.0 32.5 - - + +
261B GLU* 5.1 1.1 - - - +
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Residues in contact with SER 287 (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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129A SER* 4.1 8.0 + - - -
260A TYR* 3.7 22.1 + - - -
282A HIS* 4.6 6.7 - - - -
283A GLY 3.0 34.2 + - - -
284A THR* 3.2 9.3 + - - -
286A GLN* 1.3 79.1 - - - +
288A PHE* 1.3 57.9 + - - +
290A THR* 3.1 7.3 + - - -
291A LEU* 2.8 27.5 + - - +
258B GLN* 3.8 15.0 - - - +
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Residues in contact with PHE 288 (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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279A GLY* 3.3 38.4 - - - -
282A HIS* 3.5 31.9 - - + -
283A GLY* 3.9 1.8 - - - -
284A THR 3.2 19.7 - - - -
285A LEU 3.1 7.7 + - - +
287A SER* 1.3 75.7 - - - +
289A ARG* 1.4 56.3 + - - +
291A LEU* 4.0 7.9 - - + -
292A ALA* 2.7 35.9 + - - +
299A MET* 3.4 23.9 - - + +
301A PRO* 3.7 29.2 - - + -
306A CYS* 4.0 7.0 - - + -
315A ILE* 3.6 37.2 - - + -
318A LEU* 3.8 9.0 - - + -
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Residues in contact with ARG 289 (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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285A LEU* 3.0 12.3 + - + +
286A GLN* 3.5 13.0 - - + +
287A SER 3.3 0.2 - - - -
288A PHE* 1.4 75.7 - - - +
290A THR* 1.3 61.7 + - - +
292A ALA* 3.4 3.4 + - - +
293A GLU* 2.8 60.8 + - + +
318A LEU* 3.5 20.9 - - + +
259B GLN* 6.3 0.2 - - - +
261B GLU* 3.5 51.2 + - - +
262B GLY 5.2 1.2 - - - +
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Residues in contact with THR 290 (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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260A TYR* 3.7 40.6 - - + -
264A ARG* 5.0 2.1 + - - +
286A GLN 3.2 9.8 + - - -
287A SER* 3.1 10.2 + - - -
289A ARG* 1.3 75.7 - - - +
291A LEU* 1.3 64.2 + - - +
293A GLU* 3.2 14.9 + - - +
294A THR* 3.4 13.2 + - - +
258B GLN 4.4 6.1 + - - -
260B TYR* 4.6 10.0 - - + -
261B GLU* 2.7 33.1 + - - +
290B THR* 5.5 3.6 - - + -
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A TYR* 3.7 16.5 - - + -
263A TYR* 4.6 12.1 - - + -
278A SER* 4.1 9.4 - - - +
279A GLY* 3.6 21.5 - - - +
282A HIS* 3.6 39.5 - - + +
287A SER 2.8 15.7 + - - +
288A PHE* 3.6 13.2 - - + +
289A ARG 3.3 0.2 - - - -
290A THR* 1.3 78.1 - - - +
292A ALA* 1.3 60.3 + - - +
294A THR* 2.7 30.9 + - + +
296A ILE* 3.8 22.5 - - + +
299A MET* 4.1 15.5 - - + -
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Residues in contact with ALA 292 (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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288A PHE 2.7 21.6 + - - +
289A ARG 3.8 4.9 - - - +
291A LEU* 1.3 72.7 - - - +
293A GLU* 1.3 59.3 + - + +
295A GLY* 3.0 19.2 + - - -
296A ILE* 4.3 6.6 + - - +
299A MET* 3.7 23.3 - - + -
318A LEU* 4.5 8.3 - - + -
322A ARG* 3.1 42.8 + - - +
324A GLN* 5.1 2.0 - - - +
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Residues in contact with GLU 293 (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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264A ARG* 3.0 22.1 + - - +
289A ARG* 2.8 54.3 + - + +
290A THR* 3.2 6.0 + - - +
292A ALA* 1.3 74.5 - - + +
294A THR* 1.3 57.2 + - - +
295A GLY 3.1 5.7 + - - -
322A ARG* 4.2 18.4 - - - +
261B GLU* 4.2 10.9 - - - +
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Residues in contact with THR 294 (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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260A TYR* 3.3 43.7 - - + +
263A TYR* 4.1 4.2 - - + +
264A ARG* 3.4 45.5 - - - +
267A LYS* 4.4 4.0 - - - +
290A THR* 3.4 12.1 + - + +
291A LEU* 2.7 26.3 + - + +
293A GLU* 1.3 76.2 - - - +
295A GLY* 1.3 58.9 + - - +
296A ILE* 3.4 21.0 + - - +
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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