Contacts of the helix formed by residues 372 - 384 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366B LYS* 2.8 26.4 + - - +
370B PRO 3.9 9.5 - - - +
371B LEU* 1.3 76.2 - - - +
373B ALA* 1.3 65.5 + - - +
374B TYR* 3.1 27.7 + - + -
375B GLN* 2.8 32.7 + - - +
376B VAL* 3.3 17.2 + - - +
544B ILE* 3.6 6.3 - - - -
545B THR* 3.5 19.1 - - + +
547B ASP* 2.7 25.1 + - + +
575B GLU* 3.2 22.0 + - - -
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Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B GLN* 1.3 73.9 - - - +
374B TYR* 1.3 65.9 + - + +
376B VAL* 3.4 2.9 + - - +
377B LEU* 3.1 28.4 + - - +
400B ASN* 3.5 31.6 - - + +
472B PHE* 4.0 16.1 - - + -
544B ILE* 3.7 30.7 - - + +
545B THR 5.8 0.2 + - - -
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Residues in contact with TYR 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B TYR* 5.2 2.3 + - - -
363B LEU* 3.6 56.6 - - + +
364B GLU* 3.6 15.3 - - - +
372B GLN* 3.1 45.3 - - + -
373B ALA* 1.3 79.8 - - + +
375B GLN* 1.3 60.0 - - - +
377B LEU* 3.6 3.1 + - - +
378B ARG 3.2 18.5 + - - -
400B ASN* 3.9 19.5 - - - -
403B ARG* 6.3 0.4 - - - -
404B HIS* 3.3 29.3 + - + +
547B ASP* 4.7 9.3 + - + +
548B ARG 4.1 5.5 + - - -
549B PRO* 3.7 27.2 - - + +
550B LEU 4.7 1.4 + - - -
575B GLU* 4.3 3.6 + - - -
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Residues in contact with GLN 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B LEU 2.9 26.1 + - - +
364B GLU 3.7 14.6 - - - +
366B LYS* 3.8 22.2 - - - +
371B LEU* 4.4 0.4 - - + -
372B GLN* 2.8 59.3 + - - +
373B ALA 3.4 0.4 - - - -
374B TYR* 1.3 76.3 - - - +
376B VAL* 1.3 60.8 + - - +
377B LEU 3.3 0.2 - - - -
378B ARG* 3.2 11.4 + - - +
379B ALA 2.8 24.9 + - - -
519B ILE* 3.3 21.7 - - + +
522B LEU* 3.4 25.4 - - + +
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Residues in contact with VAL 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LEU* 3.9 17.5 - - + -
372B GLN 3.3 16.1 + - - +
373B ALA* 3.6 7.6 - - - +
374B TYR 3.4 0.2 - - - -
375B GLN* 1.3 78.4 - - - +
377B LEU* 1.3 55.6 + - - +
379B ALA* 3.2 5.7 + - - +
380B VAL* 3.0 25.7 + - + +
470B VAL* 3.7 20.9 - - + -
472B PHE* 3.5 25.4 - - + -
522B LEU* 3.9 9.2 - - + +
526B PHE* 4.1 8.5 - - + -
542B ALA* 3.7 25.8 - - + -
544B ILE* 4.0 6.7 - - + -
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B ALA 3.1 19.7 + - - +
374B TYR 4.0 2.0 - - - +
375B GLN 3.3 0.2 - - - -
376B VAL* 1.3 72.2 - - - +
378B ARG* 1.3 61.3 + - - +
380B VAL* 3.4 8.8 + - + +
381B ASN* 3.0 34.0 + - - +
397B ILE* 4.2 5.2 - - + -
400B ASN* 3.4 45.1 - - + +
401B ALA* 3.9 5.8 - - - +
404B HIS* 3.7 21.1 - - + -
405B LEU* 4.2 14.2 - - + +
444B LEU* 3.9 27.4 - - + -
472B PHE* 4.0 21.3 - - + -
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Residues in contact with ARG 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B GLU* 3.2 39.5 + - + +
365B ASP* 5.0 5.5 + - - +
366B LYS 3.0 26.9 + - - -
367B GLN* 4.1 14.6 - - - +
374B TYR 3.2 14.1 + - - +
375B GLN* 3.2 16.1 + - - +
377B LEU* 1.3 75.7 - - - +
379B ALA* 1.3 59.1 + - - +
381B ASN* 3.2 15.2 + - + +
382B LYS* 2.9 54.2 + - + +
519B ILE* 3.7 15.2 + - - +
522B LEU* 3.8 25.4 - - - +
523B PRO* 4.6 12.5 - - - +
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Residues in contact with ALA 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B GLN 2.8 13.7 + - - +
376B VAL 3.2 10.1 + - - +
378B ARG* 1.3 83.1 - - - +
380B VAL* 1.3 60.4 + - - +
382B LYS* 3.3 13.6 + - - +
383B ILE* 3.3 18.4 + - - +
522B LEU* 4.0 16.4 - - + -
523B PRO* 6.0 0.7 - - + -
526B PHE* 3.6 37.4 - - + +
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Residues in contact with VAL 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B VAL* 3.0 19.7 + - + +
377B LEU* 3.5 15.5 - - + +
378B ARG 3.3 0.2 - - - -
379B ALA* 1.3 72.8 - - - +
381B ASN* 1.3 66.5 + - - +
383B ILE* 3.2 9.0 + - - +
384B ALA* 3.0 23.9 + - - +
390B TYR* 3.7 30.7 - - + +
405B LEU* 4.1 11.4 - - + -
442B PHE* 3.9 15.0 - - + -
444B LEU* 4.2 21.1 - - + -
470B VAL* 4.3 9.6 - - + -
472B PHE* 5.4 0.2 - - + -
526B PHE* 3.8 18.8 - - + -
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Residues in contact with ASN 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B GLU* 4.7 4.9 + - - -
377B LEU 3.0 18.7 + - - +
378B ARG* 3.2 16.9 + - + +
380B VAL* 1.3 76.5 - - - +
382B LYS* 1.3 63.5 + - + +
384B ALA* 3.4 20.1 + - - +
390B TYR* 5.0 2.8 + - - -
404B HIS* 2.9 24.8 + - - +
405B LEU* 3.7 12.9 - - - +
406B LYS* 3.5 44.6 + - + +
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Residues in contact with LYS 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B ASP* 5.8 1.8 + - - -
378B ARG* 2.9 42.8 + - - +
379B ALA* 3.8 7.4 - - - +
380B VAL 3.2 0.4 - - - -
381B ASN* 1.3 79.8 - - + +
383B ILE* 1.3 64.5 + - + +
384B ALA 3.5 1.0 - - - +
527B GLU* 4.9 4.2 - - - +
530B LYS* 5.5 1.4 - - - +
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Residues in contact with ILE 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B ALA 3.3 8.4 + - - +
380B VAL 3.2 11.2 + - - +
382B LYS* 1.3 78.4 - - + +
384B ALA* 1.3 58.0 + - - +
440B GLN* 3.0 19.6 + - - -
442B PHE* 3.9 22.9 - - + -
468B ILE* 4.2 17.0 - - + -
526B PHE* 3.6 58.3 - - + +
527B GLU* 3.6 22.9 - - - +
529B ALA* 4.8 0.7 - - + -
530B LYS* 3.0 37.7 + - + +
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Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B VAL 3.0 16.0 + - - +
381B ASN* 3.4 16.1 + - - +
382B LYS 3.5 0.9 - - - +
383B ILE* 1.3 78.0 - - - +
385B GLU* 1.3 66.7 + - - +
386B PRO* 3.9 2.4 - - - +
390B TYR* 3.2 27.4 - - - +
440B GLN* 3.3 6.1 - - - +
442B PHE* 4.2 7.0 - - + -
530B LYS* 5.0 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
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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