Contacts of the helix formed by residues 372 - 390 (chain A) in PDB entry 2BEW
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 PRO 372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368A TYR* 3.5 35.7 - - + -
370A GLU* 3.5 17.7 - - + +
371A MET* 1.3 90.6 - - + +
373A ALA* 1.3 61.9 - - - +
374A GLN* 4.4 5.6 - - + +
375A LEU* 2.9 33.7 + - + +
376A ARG* 3.0 10.7 + - - +
259B PRO* 4.1 24.7 - - + -
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Residues in contact with ALA 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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371A MET 3.6 1.4 + - - -
372A PRO* 1.3 73.7 - - - +
374A GLN* 1.3 62.2 + - + +
376A ARG* 3.3 25.2 + - - +
377A LYS* 3.0 25.8 + - - +
263B ASP* 6.2 0.2 - - - +
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Residues in contact with GLN 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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372A PRO* 3.2 4.2 - - + +
373A ALA* 1.3 80.4 + - + +
375A LEU* 1.3 62.6 + - - +
377A LYS* 3.5 32.1 + - - +
378A GLN* 3.4 28.4 + - - +
259B PRO* 6.5 1.3 - - + -
260B TRP 5.1 4.5 - - - +
262B VAL* 3.8 40.1 - - + +
263B ASP* 4.6 7.9 + - - -
1345B GOL 3.4 35.6 - - - +
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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
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364A PHE* 3.5 41.0 - - + +
367A VAL* 3.9 28.0 - - + -
368A TYR* 5.1 2.2 - - + +
371A MET* 4.1 13.2 - - + -
372A PRO* 2.9 27.8 + - + +
374A GLN* 1.3 75.7 - - - +
376A ARG* 1.3 67.4 + - - +
377A LYS 3.1 0.2 - - - -
378A GLN* 3.0 26.6 + - - +
379A GLN* 3.0 20.6 + - - +
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Residues in contact with ARG 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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371A MET* 2.6 50.2 + - - +
372A PRO 3.0 6.5 + - - +
373A ALA* 3.5 28.1 - - - +
375A LEU* 1.3 77.9 - - - +
377A LYS* 1.3 56.3 + - - +
379A GLN* 3.2 15.5 + - - +
380A GLU* 2.8 52.6 + - + +
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Residues in contact with LYS 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 ALA 3.0 12.7 + - - +
374A GLN* 3.5 36.3 + - - +
376A ARG* 1.3 76.9 - - - +
378A GLN* 1.3 60.6 + - + +
380A GLU* 3.5 16.2 + - - +
381A SER* 3.0 26.6 + - - -
384A ARG* 4.9 6.3 + - - +
298B GLU* 3.4 28.3 + - - -
1345B GOL 6.2 1.2 - - - -
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Residues in contact with GLN 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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364A PHE* 3.8 19.3 - - + -
374A GLN* 3.4 18.7 + - - +
375A LEU* 3.0 26.2 + - - +
377A LYS* 1.3 76.9 - - + +
379A GLN* 1.3 64.4 + - - +
381A SER* 3.2 8.5 + - - -
382A LEU* 3.0 20.1 + - - +
1345B GOL 5.5 9.5 - - - -
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Residues in contact with GLN 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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361A ASN* 3.4 48.0 + - - +
364A PHE* 3.4 30.5 - - + +
371A MET* 3.7 30.2 - - - +
375A LEU 3.0 11.0 + - - +
376A ARG* 3.4 18.3 - - - +
378A GLN* 1.3 75.2 - - - +
380A GLU* 1.3 65.7 + - + +
382A LEU* 3.3 4.3 + - - +
383A ALA* 3.0 21.9 + - - +
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Residues in contact with GLU 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 ARG* 2.8 40.8 + - + +
377A LYS* 3.7 15.4 - - - +
378A GLN 3.3 0.2 - - - -
379A GLN* 1.3 78.8 - - + +
381A SER* 1.3 58.2 + - - +
383A ALA* 3.3 7.3 + - - +
384A ARG* 2.9 47.2 + - - +
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Residues in contact with SER 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 LYS* 3.0 14.8 + - - -
378A GLN* 3.3 13.5 - - - -
380A GLU* 1.3 78.4 - - - +
382A LEU* 1.3 57.0 + - - +
384A ARG* 3.4 26.3 + - - +
385A HIS* 2.9 27.9 + - - +
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Residues in contact with LEU 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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360A PRO* 4.5 20.0 - - + +
361A ASN* 5.9 1.3 - - - +
363A LEU* 4.2 15.3 - - + -
364A PHE* 3.7 27.6 - - + -
378A GLN 3.0 12.1 + - - +
379A GLN 3.3 8.0 + - - +
381A SER* 1.3 73.0 + - - +
383A ALA* 1.3 66.4 + - - +
385A HIS* 3.1 14.5 + - + +
386A LEU* 2.9 50.1 + - + +
393A TYR* 5.9 2.5 - - + -
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Residues in contact with ALA 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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361A ASN* 5.5 5.4 - - - +
379A GLN 3.0 13.5 + - - +
380A GLU* 3.3 11.2 + - - +
382A LEU* 1.3 76.9 - - - +
384A ARG* 1.3 63.8 + - + +
386A LEU* 3.3 8.1 + - - +
387A GLN* 3.1 26.7 + - - +
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Residues in contact with ARG 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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377A LYS* 4.9 6.5 + - - +
380A GLU* 2.9 36.4 + - - +
381A SER* 3.5 29.4 + - - +
383A ALA* 1.3 76.8 - - + +
385A HIS* 1.3 65.4 + - - +
387A GLN* 3.2 22.3 - - - +
388A THR* 3.4 10.6 + - - -
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Residues in contact with HIS 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 SER* 2.9 15.5 + - - +
382A LEU* 3.1 19.0 + - + +
384A ARG* 1.3 76.9 - - - +
386A LEU* 1.3 62.1 + - + +
388A THR* 3.2 2.3 + - - -
389A TYR* 2.8 63.8 + + - +
393A TYR* 2.8 42.2 + + - -
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Residues in contact with LEU 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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360A PRO* 4.9 11.7 - - + -
382A LEU* 2.9 46.7 + - + +
383A ALA* 3.9 7.0 - - - +
385A HIS* 1.3 76.2 - - + +
387A GLN* 1.3 63.1 + - - +
390A GLY* 2.8 31.3 + - - +
393A TYR* 3.8 44.4 - - + -
395A LEU* 4.1 26.1 - - + +
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Residues in contact with GLN 387 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383A ALA 3.1 16.8 + - - +
384A ARG* 3.2 15.0 - - - +
386A LEU* 1.3 79.6 - - - +
388A THR* 1.3 61.8 + - - +
390A GLY 4.9 0.3 + - - -
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Residues in contact with THR 388 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384A ARG 3.4 8.1 + - - -
385A HIS* 3.2 4.0 + - - -
387A GLN* 1.3 84.2 + - - +
389A TYR* 1.3 90.2 + - + +
390A GLY 3.6 1.2 + - - -
391A GLU* 5.6 3.3 - - - +
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Residues in contact with TYR 389 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A HIS* 2.8 59.1 + + - +
388A THR* 1.3 97.5 - - + +
390A GLY* 1.3 65.6 + - - +
391A GLU* 3.1 3.8 - - - -
392A HIS* 2.9 38.9 + + + -
393A TYR* 3.3 13.6 - - + -
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Residues in contact with GLY 390 (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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386A LEU* 2.8 24.2 + - - -
387A GLN 4.9 0.2 + - - -
388A THR 3.6 2.4 + - - -
389A TYR* 1.3 76.9 - - - +
391A GLU* 1.3 61.4 + - - +
392A HIS 2.9 3.1 + - - -
393A TYR* 3.0 26.4 + - - +
395A LEU* 3.7 26.2 - - - +
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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