Contacts of the helix formed by residues 372 - 384 (chain A) in PDB entry 2EZT
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 GLN 372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A LYS* 2.9 20.9 + - - +
370A PRO 3.9 8.7 - - - +
371A LEU* 1.3 75.9 - - - +
373A ALA* 1.3 66.3 + - - +
374A TYR* 3.1 27.1 + - + -
375A GLN* 2.9 42.1 + - - +
376A VAL* 3.3 16.3 + - - +
544A ILE* 3.6 9.4 - - - -
545A THR* 3.5 18.6 - - + +
547A ASP* 2.9 24.7 + - + +
575A GLU* 3.0 22.4 + - - -
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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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372A GLN* 1.3 74.0 - - - +
374A TYR* 1.3 66.6 + - + +
376A VAL* 3.3 5.2 + - - +
377A LEU* 3.0 26.3 + - - +
400A ASN* 3.5 32.3 - - + +
472A PHE* 3.9 19.9 - - + -
544A ILE* 3.6 25.3 - - + +
545A THR* 5.4 0.2 + - - -
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Residues in contact with TYR 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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359A TYR* 5.4 1.7 + - - -
363A LEU* 3.8 51.3 - - + +
364A GLU* 3.8 8.6 - - - +
372A GLN* 3.1 41.9 - - + -
373A ALA* 1.3 80.8 - - + +
375A GLN* 1.3 61.2 + - - +
377A LEU* 3.4 4.3 + - - +
378A ARG* 3.1 23.9 + - - +
400A ASN* 3.8 20.9 - - - -
404A HIS* 3.4 32.4 + + + +
547A ASP* 4.5 10.3 + - + +
548A ARG 3.9 6.6 + - - -
549A PRO* 3.6 27.1 - - + +
550A LEU 4.7 1.6 + - - -
574A TYR* 5.8 0.5 - - - -
575A GLU* 4.5 2.7 + - - -
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Residues in contact with GLN 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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363A LEU 2.7 28.6 + - - +
364A GLU 3.7 10.3 - - - +
366A LYS* 3.9 20.4 - - + +
371A LEU* 4.2 1.8 - - + -
372A GLN* 2.9 55.4 + - - +
373A ALA 3.4 0.4 - - - -
374A TYR* 1.3 75.8 - - - +
376A VAL* 1.3 61.3 + - - +
378A ARG* 3.2 17.2 + - - +
379A ALA* 2.8 24.8 + - - +
519A ILE* 3.2 22.1 - - + +
522A LEU* 3.5 24.6 - - + +
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Residues in contact with VAL 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A LEU* 3.8 21.8 - - + -
372A GLN 3.3 16.8 - - - +
373A ALA* 3.4 7.2 - - - +
375A GLN* 1.3 77.5 - - - +
377A LEU* 1.3 61.9 + - - +
379A ALA* 3.1 6.4 + - - +
380A VAL* 3.0 21.7 + - + +
470A VAL* 3.7 30.1 - - + -
472A PHE* 3.7 13.2 - - + -
522A LEU* 3.9 7.5 - - + +
526A PHE* 3.9 12.3 - - + -
542A ALA* 3.8 20.6 - - + -
544A ILE* 4.0 7.4 - - + -
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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 ALA 3.0 15.4 + - - +
374A TYR 3.8 4.3 - - - +
375A GLN 3.3 0.2 - - - -
376A VAL* 1.3 71.5 - - - +
378A ARG* 1.3 65.8 + - - +
380A VAL* 3.1 10.3 + - + +
381A ASN* 3.0 28.0 + - - +
397A ILE* 4.3 4.3 - - + -
400A ASN* 3.4 46.4 - - + +
401A ALA* 3.8 4.3 - - - +
404A HIS* 3.6 23.1 - - + -
405A LEU* 4.1 13.7 - - + -
444A LEU* 4.1 23.8 - - + -
472A PHE* 4.0 23.8 - - + -
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Residues in contact with ARG 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 GLU* 2.9 44.9 + - + +
365A ASP* 4.9 5.6 - - - +
366A LYS 2.8 28.9 + - - -
367A GLN* 4.3 15.3 + - - +
374A TYR 3.1 13.7 + - - +
375A GLN* 3.4 14.6 + - - +
377A LEU* 1.3 74.8 - - - +
379A ALA* 1.3 61.5 + - - +
381A ASN* 3.3 15.6 + - + +
382A LYS* 3.0 53.2 + - + +
519A ILE* 3.7 15.4 + - - +
522A LEU* 4.2 20.2 - - - +
523A PRO* 4.5 15.0 - - - +
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Residues in contact with ALA 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 GLN 2.8 16.3 + - - +
376A VAL 3.1 9.2 + - - +
378A ARG* 1.3 77.4 - - - +
380A VAL* 1.3 65.6 + - - +
382A LYS* 3.4 14.5 + - - +
383A ILE* 3.4 18.9 + - - +
522A LEU* 4.1 16.4 - - + +
523A PRO* 5.9 1.1 - - + -
526A PHE* 3.7 36.0 - - + +
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Residues in contact with VAL 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 VAL* 3.0 22.1 + - + +
377A LEU* 3.3 15.9 - - + +
379A ALA* 1.3 73.4 - - - +
381A ASN* 1.3 65.9 + - - +
383A ILE* 3.1 10.9 + - - +
384A ALA* 3.0 24.1 + - - +
390A TYR* 3.8 30.5 - - + +
405A LEU* 4.1 10.3 - - + -
442A PHE* 3.8 16.3 - - + -
444A LEU* 4.1 21.3 - - + -
470A VAL* 4.4 6.3 - - + -
526A PHE* 3.9 15.7 - - + -
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Residues in contact with ASN 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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364A GLU* 4.7 5.7 + - - -
377A LEU 3.0 18.2 + - - -
378A ARG* 3.4 16.0 - - + +
380A VAL* 1.3 74.7 - - - +
382A LYS* 1.3 65.0 + - + +
384A ALA* 3.4 20.1 + - - +
390A TYR* 5.0 2.8 + - - -
404A HIS 2.9 24.2 + - - -
405A LEU* 3.6 15.1 - - - +
406A LYS* 3.5 44.2 + - + +
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Residues in contact with LYS 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 ARG* 3.0 44.2 + - - +
379A ALA* 3.8 7.9 - - - +
380A VAL 3.1 0.8 - - - -
381A ASN* 1.3 78.5 - - + +
383A ILE* 1.3 63.3 + - + +
384A ALA 5.0 1.0 - - - +
527A GLU* 4.9 6.3 - - - +
530A LYS* 5.6 0.7 - - - +
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Residues in contact with ILE 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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379A ALA 3.4 8.7 + - - +
380A VAL* 3.5 11.0 - - - +
382A LYS* 1.3 78.5 - - + +
384A ALA* 1.3 59.8 + - - +
440A GLN* 2.9 11.3 + - - -
442A PHE* 4.0 20.2 - - + -
468A ILE* 4.1 19.5 - - + -
526A PHE* 3.5 56.3 - - + +
527A GLU* 3.7 23.3 - - - +
529A ALA* 5.0 0.4 - - + -
530A LYS* 2.8 47.9 + - + +
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Residues in contact with ALA 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A VAL 3.0 17.1 + - - +
381A ASN* 3.4 15.5 + - - +
382A LYS 5.0 0.9 - - - +
383A ILE* 1.3 79.4 - - - +
385A GLU* 1.3 65.8 + - - +
386A PRO* 4.0 1.4 - - - +
388A ALA* 4.5 0.2 - - + -
390A TYR* 3.2 27.1 - - - +
440A GLN* 3.2 9.4 - - - +
442A PHE* 4.0 4.9 - - + -
530A LYS* 4.9 0.6 + - - -
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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