Contacts of the helix formed by residues 371 - 386 (chain A) in PDB entry 2CX9
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 371 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A SER* 5.7 0.9 - - - -
366A ARG 3.4 7.9 - - - -
367A ILE* 3.3 27.9 + - + +
370A GLY* 1.3 78.2 - - - +
372A SER* 1.3 66.5 + - - +
373A GLU* 3.5 19.3 + - - +
374A ILE* 3.1 36.3 + - + +
375A LEU* 3.0 17.3 + - - +
342B GLN* 3.9 8.1 - - - +
345B GLY* 5.0 10.1 - - - -
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Residues in contact with SER 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LYS* 4.7 0.8 + - - +
327A LEU* 3.5 21.8 - - - +
330A SER* 4.1 4.0 + - - -
331A GLU* 2.7 29.8 + - - -
366A ARG* 3.1 22.5 + - - +
371A THR* 1.3 72.8 - - - +
373A GLU* 1.3 73.3 + - - +
375A LEU* 3.3 8.9 + - - +
376A LYS* 3.0 33.6 + - - +
342B GLN* 4.3 1.1 - - - -
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Residues in contact with GLU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLU* 5.5 0.2 - - - +
366A ARG* 5.7 0.5 + - - -
371A THR* 3.5 11.5 - - - +
372A SER* 1.3 84.1 - - - +
374A ILE* 1.3 62.1 + - + +
376A LYS* 3.3 17.4 + - - +
377A LEU* 3.3 20.0 + - + +
286B GLY* 4.7 7.0 - - - +
287B VAL* 6.0 3.1 - - + -
290B LYS* 3.4 31.3 + - - -
342B GLN* 2.9 41.3 + - - +
289C PHE* 3.7 30.7 - - + -
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Residues in contact with ILE 374 (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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134A SER* 3.0 50.0 - - - +
249A ARG* 4.5 9.0 - - - +
370A GLY* 4.2 15.7 - - - -
371A THR* 3.1 38.5 + - + +
373A GLU* 1.3 78.1 - - + +
375A LEU* 1.3 58.3 + - - +
377A LEU* 3.3 14.4 + - + +
378A VAL* 3.1 36.2 + - + +
277B PHE* 5.6 0.4 - - + -
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Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ARG* 3.5 45.1 - - - +
323A ALA* 3.8 18.1 - - + +
326A LYS* 3.5 35.9 - - + +
327A LEU* 3.7 25.4 - - + +
370A GLY* 3.6 11.9 - - - +
371A THR 3.0 15.1 + - - +
372A SER* 3.6 9.4 - - - +
373A GLU 3.3 0.2 - - - -
374A ILE* 1.3 76.1 - - + +
376A LYS* 1.3 59.2 + - - +
378A VAL* 3.2 4.5 + - + +
379A ILE* 2.8 36.1 + - - +
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Residues in contact with LYS 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU* 4.0 29.2 - - + -
331A GLU* 6.1 2.1 - - - -
372A SER* 3.0 22.7 + - - +
373A GLU* 3.3 11.5 + - - +
375A LEU* 1.3 75.8 - - - +
377A LEU* 1.3 58.2 - - - +
379A ILE* 4.3 2.5 - - - -
380A ALA* 2.8 31.2 + - - +
290B LYS* 5.8 2.4 - - - +
288C SER 4.6 0.3 - - - +
289C PHE* 3.6 43.0 - - + -
292C ALA* 3.4 20.1 - - + +
293C GLU* 2.8 37.4 + - + +
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Residues in contact with LEU 377 (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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373A GLU* 3.3 15.7 + - + +
374A ILE* 3.3 14.6 + - + +
375A LEU 3.2 0.2 - - - -
376A LYS* 1.3 74.4 - - - +
378A VAL* 1.3 63.3 + - + +
380A ALA* 3.8 3.5 - - + +
381A ARG* 2.9 60.6 + - - +
277B PHE* 6.2 4.7 - - + -
285C GLU* 3.1 33.7 - - + +
288C SER* 4.1 13.9 - - - +
289C PHE* 3.5 13.9 - - + -
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Residues in contact with VAL 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ARG* 4.3 18.6 - - - +
319A THR* 3.9 20.9 - - + +
320A LEU* 5.4 0.2 - - - -
323A ALA* 4.3 15.0 - - + -
374A ILE* 3.1 25.1 + - + +
375A LEU* 3.4 9.9 - - - +
377A LEU* 1.3 78.1 - - + +
379A ILE* 1.3 62.1 + - - +
381A ARG* 4.8 2.7 - - - +
382A ARG* 3.2 46.2 + - + +
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Residues in contact with ILE 379 (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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320A LEU* 3.6 27.5 - - + +
323A ALA* 3.7 18.6 - - + +
324A GLN* 3.7 35.0 - - + +
327A LEU* 3.8 18.6 - - + -
375A LEU 2.8 22.6 + - - +
376A LYS* 3.6 4.5 - - - +
378A VAL* 1.3 74.6 - - - +
380A ALA* 1.3 65.8 + - - +
382A ARG* 3.3 3.6 + - - +
383A LEU* 3.0 35.5 + - + +
292C ALA* 3.8 25.8 - - + +
296C THR* 3.8 8.7 - - - +
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Residues in contact with ALA 380 (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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376A LYS 2.8 21.2 + - - +
377A LEU* 3.8 4.5 - - - +
379A ILE* 1.3 74.4 - - - +
381A ARG* 1.3 56.9 + - + +
383A LEU* 3.1 13.3 + - - +
384A LEU* 2.9 41.1 + - + +
288C SER* 3.6 39.9 - - - +
291C LEU* 5.2 3.1 - - + -
292C ALA* 4.3 1.3 - - + +
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Residues in contact with ARG 381 (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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377A LEU* 2.9 46.1 + - - +
378A VAL* 4.0 4.9 - - - +
380A ALA* 1.3 76.1 - - + +
382A ARG* 1.3 72.8 + - - +
384A LEU* 3.2 11.1 + - + +
385A GLU* 3.1 34.7 + - + +
277B PHE* 6.0 4.4 - - - -
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Residues in contact with ARG 382 (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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242A LEU* 6.3 1.4 - - - +
319A THR* 3.2 34.5 + - - +
320A LEU* 4.1 34.8 - - + -
378A VAL* 3.2 33.6 + - + +
379A ILE 3.7 4.0 - - - +
381A ARG* 1.3 85.6 - - - +
383A LEU* 1.3 64.3 + - - +
385A GLU* 3.4 28.6 + - - +
386A ALA* 3.6 13.7 + - - +
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Residues in contact with LEU 383 (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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320A LEU* 4.3 20.4 - - + -
324A GLN* 5.1 0.7 - - - +
379A ILE* 3.0 32.0 + - + +
380A ALA* 3.1 10.5 + - - +
382A ARG* 1.3 79.2 - - - +
384A LEU* 1.3 59.1 + - - +
385A GLU 3.6 0.2 + - - -
386A ALA* 3.6 4.0 + - - +
387A VAL* 3.6 18.0 + - - +
264C LEU* 5.5 3.4 - - + -
268C LEU* 3.9 19.3 - - + +
291C LEU* 3.8 22.7 - - + +
292C ALA* 4.2 0.7 - - - -
295C ALA* 3.5 34.8 - - + -
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Residues in contact with LEU 384 (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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380A ALA* 2.9 29.7 + - + +
381A ARG* 3.7 10.1 - - + +
383A LEU* 1.3 76.5 - - - +
385A GLU* 1.3 59.3 - - + +
386A ALA 3.3 0.2 - - - -
387A VAL* 2.8 22.4 - - + +
268C LEU* 3.5 40.6 - - + +
272C LYS* 2.9 25.6 + - + -
282C ALA* 4.1 33.4 - - + +
288C SER* 5.6 0.2 - - - -
291C LEU* 4.5 9.0 - - + -
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Residues in contact with GLU 385 (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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381A ARG* 3.1 19.3 + - + +
382A ARG* 3.4 30.8 + - - +
383A LEU 3.4 0.6 - - - -
384A LEU* 1.3 77.4 - - + +
386A ALA* 1.3 58.9 + - + +
387A VAL 3.5 0.8 + - - -
272C LYS* 4.9 3.8 + - - +
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Residues in contact with ALA 386 (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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382A ARG 3.6 11.6 + - - +
383A LEU* 3.6 5.5 + - - +
384A LEU 3.3 0.4 - - - -
385A GLU* 1.3 77.9 - - + +
387A VAL* 1.3 68.9 + - - +
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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