Contacts of the helix formed by residues 366 - 384 (chain A) in PDB entry 2CEA
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 VAL 366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A PRO* 5.5 4.3 - - + -
203A PRO 3.8 10.5 - - - +
204A GLY* 3.3 26.5 - - - +
205A THR* 4.0 20.9 - - + -
330A PRO* 4.5 13.9 - - + -
331A PRO* 4.1 5.8 - - - -
364A GLY 4.1 7.9 - - - +
365A PHE* 1.3 77.8 - - - +
367A GLY* 1.3 67.6 + - - +
368A ALA* 3.8 5.6 - - + +
369A ASP* 2.8 35.2 + - - +
370A LEU* 3.1 13.1 + - - +
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Residues in contact with GLY 367 (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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204A GLY 3.2 3.2 + - - -
205A THR* 4.7 2.2 - - - +
331A PRO* 4.7 2.4 - - - +
339A ILE* 3.9 23.0 - - - +
366A VAL* 1.3 74.1 - - - +
368A ALA* 1.3 63.4 + - - +
370A LEU* 3.1 4.5 + - - +
371A GLU* 3.0 23.6 + - - +
1604A ADP 3.4 33.5 + - - -
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Residues in contact with ALA 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLY* 2.9 32.4 + - - -
366A VAL* 3.0 4.9 + - + -
367A GLY* 1.3 75.4 - - - +
369A ASP* 1.3 62.8 + - - +
371A GLU* 3.7 3.8 + - - +
372A ASN* 3.3 28.5 + - - +
1604A ADP 3.3 24.2 - - - +
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Residues in contact with ASP 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLY 4.5 1.4 - - - +
365A PHE* 3.5 29.4 - - + -
366A VAL* 2.8 40.6 + - - +
368A ALA* 1.3 71.7 - - - +
370A LEU* 1.3 61.0 + - - +
372A ASN* 3.3 11.3 + - - +
373A LEU* 3.0 26.7 + - - +
401A VAL* 3.8 13.3 - - + +
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Residues in contact with LEU 370 (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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336A ARG* 3.7 44.4 - - + +
339A ILE* 4.0 25.1 - - + -
340A LEU* 4.0 23.6 - - + -
343A HIS* 5.2 0.9 - - - -
362A THR* 4.0 19.7 - - + +
365A PHE* 3.7 24.9 - - + -
366A VAL 3.1 12.9 + - - +
367A GLY 3.1 6.7 + - - +
369A ASP* 1.3 74.0 - - - +
371A GLU* 1.3 65.7 + - - +
372A ASN 3.0 1.1 - - - -
373A LEU* 3.0 7.3 + - + +
374A VAL* 2.9 29.1 + - - +
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Residues in contact with GLU 371 (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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343A HIS* 3.5 39.2 + - + +
367A GLY 3.0 14.1 + - - +
368A ALA 3.9 4.8 - - - +
370A LEU* 1.3 76.0 - - - +
372A ASN* 1.3 61.9 + - - +
374A VAL* 3.3 2.9 + - - +
375A ASN* 3.0 40.4 + - - +
1604A ADP 2.8 41.8 + - - +
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Residues in contact with ASN 372 (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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368A ALA* 3.3 18.1 + - - +
369A ASP* 3.3 15.4 + - - +
370A LEU 3.0 0.2 - - - -
371A GLU* 1.3 78.1 - - - +
373A LEU* 1.3 60.4 + - - +
375A ASN* 3.0 11.7 + - - +
376A GLU* 2.8 35.6 + - + +
401A VAL* 4.0 15.0 - - + +
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Residues in contact with LEU 373 (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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340A LEU* 4.9 2.2 - - + -
358A ILE* 4.0 12.1 - - + -
362A THR* 3.9 18.4 - - + -
365A PHE* 4.4 7.0 - - + -
369A ASP 3.0 13.4 + - - +
370A LEU* 3.4 16.4 - - + +
372A ASN* 1.3 73.8 - - - +
374A VAL* 1.3 67.5 + - + +
376A GLU* 3.2 2.1 + - - +
377A ALA 2.9 16.8 + - - -
394A PHE* 3.8 24.5 - - + +
397A ALA* 3.3 23.8 - - + -
398A ILE* 3.6 26.7 - - + +
401A VAL* 3.5 17.5 - - + +
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Residues in contact with VAL 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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340A LEU* 4.0 18.2 - - + -
343A HIS* 3.5 35.9 - - + +
344A THR* 4.4 10.5 - - - +
347A LYS* 4.1 17.7 - - + -
370A LEU 2.9 18.8 + - - +
371A GLU* 3.6 8.3 - - - +
373A LEU* 1.3 75.2 - - - +
375A ASN* 1.3 65.1 + - - +
377A ALA* 3.1 4.9 + - - +
378A ALA* 3.0 19.8 + - + +
389A ILE* 5.2 2.8 - - + +
394A PHE* 3.9 28.7 - - + -
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Residues in contact with ASN 375 (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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347A LYS* 3.5 29.3 - - - +
371A GLU* 3.0 32.0 + - - +
372A ASN* 3.0 15.9 + - - +
374A VAL* 1.3 79.5 - - - +
376A GLU* 1.3 57.3 + - + +
378A ALA* 3.0 7.4 + - - +
379A LEU* 2.9 40.1 + - + +
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Residues in contact with GLU 376 (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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372A ASN* 2.8 23.4 + - + +
373A LEU* 3.6 7.2 - - - +
375A ASN* 1.3 73.7 - - + +
377A ALA* 1.3 65.0 + - - +
379A LEU* 4.0 19.4 - - - +
380A LEU* 3.1 24.3 + - - +
383A ARG* 4.8 5.5 + - - -
397A ALA* 4.0 14.7 - - + +
400A ARG* 3.7 34.1 + - + -
401A VAL* 4.3 13.5 - - + +
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Residues in contact with ALA 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 LEU 2.9 12.6 + - - +
374A VAL 3.1 11.4 - - - +
376A GLU* 1.3 77.1 - - - +
378A ALA* 1.3 61.5 + - - +
380A LEU* 3.2 13.0 + - - +
381A ALA* 3.2 10.7 + - - +
389A ILE* 3.8 27.2 - - + +
393A ASP* 4.0 11.7 - - - +
394A PHE* 4.0 24.7 - - + -
397A ALA* 3.8 8.0 - - + +
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Residues in contact with ALA 378 (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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347A LYS* 4.5 17.5 - - + +
374A VAL 3.0 10.5 + - - +
375A ASN* 3.0 11.1 + - - +
377A ALA* 1.3 75.5 - - - +
379A LEU* 1.3 65.4 + - + +
380A LEU 3.2 0.2 + - - -
381A ALA* 3.3 3.5 + - - +
382A ALA* 3.0 24.8 + - - +
389A ILE* 4.1 25.1 - - + +
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Residues in contact with LEU 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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375A ASN* 2.9 26.2 + - + +
376A GLU* 4.0 24.0 - - - +
378A ALA* 1.3 77.4 - - + +
380A LEU* 1.3 52.6 + - - +
382A ALA* 3.6 7.1 - - + +
383A ARG* 2.7 55.6 + - - +
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Residues in contact with LEU 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 GLU 3.1 15.3 + - - +
377A ALA 3.3 10.1 - - - +
379A LEU* 1.3 74.4 - - - +
381A ALA* 1.3 64.8 + - - +
383A ARG* 3.3 27.4 + - + +
384A GLU* 3.2 41.8 + - + +
386A ARG* 4.9 0.9 - - - +
393A ASP* 3.4 30.3 - - - +
396A GLU* 3.6 41.3 - - + +
397A ALA* 4.7 3.1 - - - +
400A ARG* 4.6 13.5 - - - +
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Residues in contact with ALA 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 ALA 3.2 7.1 + - - +
378A ALA 3.8 6.3 - - - +
380A LEU* 1.3 78.9 - - - +
382A ALA* 1.3 63.8 + - - +
384A GLU* 2.9 13.7 + - - +
386A ARG* 3.0 48.0 + - - +
388A LYS 4.0 10.5 - - - +
389A ILE* 4.4 9.9 - - + -
393A ASP* 3.7 18.1 + - - +
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Residues in contact with ALA 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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378A ALA 3.0 17.3 + - - +
379A LEU* 3.6 10.1 - - + +
381A ALA* 1.3 76.6 - - - +
383A ARG* 1.3 65.5 + - - +
385A GLY* 2.8 15.9 + - - +
386A ARG 4.2 8.4 + - - +
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Residues in contact with ARG 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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376A GLU* 4.8 4.9 + - - -
379A LEU* 2.7 48.0 + - - +
380A LEU* 3.3 30.8 - - - +
381A ALA 3.2 0.2 - - - -
382A ALA* 1.3 74.4 - - - +
384A GLU* 1.3 64.0 + - + +
385A GLY 3.4 0.3 + - - -
400A ARG* 3.6 38.4 - - - +
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Residues in contact with GLU 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 LEU* 3.2 26.3 - - + +
381A ALA 2.9 9.4 + - - +
383A ARG* 1.3 82.1 - - + +
385A GLY* 1.3 60.9 + - - +
386A ARG* 3.2 37.0 + - + +
396A GLU* 6.1 0.7 - - - -
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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
------------------------------------------------------------
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