Contacts of the helix formed by residues 395 - 405 (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 GLY 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A VAL* 1.3 76.6 - - - +
396A ASP* 1.3 66.1 - - - -
397A ILE* 3.0 4.8 + - - +
398A ASN* 2.9 22.0 + - - +
479A TRP* 3.6 29.7 - - - -
1611A TDM 3.8 18.6 - - - -
1612A FAD 4.4 1.0 - - - +
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Residues in contact with ASP 396 (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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264A ARG* 4.9 0.3 + - - -
395A GLY* 1.3 70.8 - - - -
397A ILE* 1.3 50.4 + - - +
399A LEU* 2.9 9.6 + - - +
400A ASN* 2.8 45.5 + - - +
474A ASN* 4.3 5.9 + - - -
478A GLY* 4.1 11.6 - - - -
479A TRP* 3.3 31.7 + - - -
482A ASP* 4.1 5.9 - - - +
544A ILE* 6.5 0.9 - - + -
547A ASP 5.2 1.6 - - - +
549A PRO* 4.0 28.0 - - - +
1611A TDM 2.8 33.2 + - - +
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Residues in contact with ILE 397 (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* 4.3 16.2 - - + -
392A ILE* 3.8 8.7 - - + -
393A ASP* 3.6 30.5 - - - +
394A VAL 4.1 3.1 - - - +
395A GLY* 3.0 5.8 + - - +
396A ASP* 1.3 75.8 - - - +
398A ASN* 1.3 60.4 + - - +
400A ASN* 4.4 4.7 - - + +
401A ALA* 2.7 41.2 + - + +
444A LEU* 3.8 32.1 - - + +
445A ALA 4.9 0.4 - - - -
446A GLY* 4.4 17.5 - - - +
472A PHE* 3.5 42.4 - - + -
1611A TDM 4.3 3.0 + - - +
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Residues in contact with ASN 398 (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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245A TYR* 2.9 34.4 + - + +
265A VAL* 3.3 21.3 - - + +
392A ILE* 3.7 4.7 - - - +
393A ASP 2.8 20.2 + - - -
394A VAL* 3.2 5.9 - - - -
395A GLY 2.9 33.7 + - - +
397A ILE* 1.3 77.0 - - - +
399A LEU* 1.3 57.6 + - - +
401A ALA* 4.8 0.2 - - - -
402A ASN* 3.0 31.0 + - - +
415A THR* 3.4 14.3 + - - +
1612A FAD 3.3 16.5 - - - +
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Residues in contact with LEU 399 (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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264A ARG* 3.6 29.8 - - + +
265A VAL* 4.0 10.4 - - - +
266A ALA 5.0 0.2 - - - +
395A GLY 4.0 0.4 + - - -
396A ASP* 2.9 8.9 + - - +
398A ASN* 1.3 76.9 - - - +
400A ASN* 1.3 81.9 + - - +
402A ASN* 3.4 3.3 + - - +
403A ARG* 3.1 62.4 + - - +
479A TRP* 3.7 26.2 - - + -
549A PRO* 3.7 22.7 - - + +
550A LEU 4.4 4.7 - - - +
551A PRO* 5.6 2.5 - - + -
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Residues in contact with ASN 400 (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* 3.5 27.1 - - + +
374A TYR* 3.8 14.8 - - - -
377A LEU* 3.4 19.7 - - + -
396A ASP* 2.8 36.1 + - - +
397A ILE* 4.2 6.7 - - + +
399A LEU* 1.3 87.8 - - - +
401A ALA* 1.3 57.0 + - - +
403A ARG* 3.3 2.2 + - - -
404A HIS* 2.9 39.4 + - + +
472A PHE* 5.8 0.6 - - - -
549A PRO* 3.7 15.8 - - - +
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Residues in contact with ALA 401 (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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245A TYR* 5.5 0.9 - - + +
248A LYS* 3.5 2.5 - - - -
377A LEU* 3.8 7.2 - - - +
392A ILE* 3.9 28.5 - - + -
397A ILE* 2.7 33.6 + - + +
398A ASN* 4.3 1.6 - - - +
400A ASN* 1.3 69.9 - - - +
402A ASN* 1.3 65.3 + - - +
404A HIS 4.5 0.2 - - - +
405A LEU* 3.0 43.3 + - + +
444A LEU* 4.4 3.1 - - + -
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Residues in contact with ASN 402 (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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245A TYR* 3.5 27.9 - - + +
248A LYS* 2.6 47.3 + - - +
258A TYR* 5.0 1.4 + - - -
261A SER* 3.0 25.8 + - - -
265A VAL* 3.5 11.4 + - + -
266A ALA* 3.5 14.3 + - - +
267A GLN* 3.4 22.3 + - - +
398A ASN 3.0 21.4 + - - +
399A LEU 3.5 4.4 + - - +
400A ASN 3.3 0.2 - - - -
401A ALA* 1.3 76.7 - - - +
403A ARG* 1.3 57.1 + - - +
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Residues in contact with ARG 403 (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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248A LYS* 4.7 1.3 + - - -
264A ARG 4.1 2.8 + - - -
266A ALA 2.8 27.6 + - - +
267A GLN* 4.1 12.7 + - + +
356A TRP* 3.5 30.4 - - + -
359A TYR* 5.7 0.6 - - - -
360A LEU* 3.6 35.2 - - + +
364A GLU* 5.0 0.3 - - - +
399A LEU* 3.1 47.2 + - - +
400A ASN* 3.8 4.0 - - - +
402A ASN* 1.3 79.7 - - - +
404A HIS* 1.3 67.4 + - + +
405A LEU 3.9 2.3 - - - +
549A PRO* 4.4 0.8 - - - +
550A LEU* 2.6 47.5 + - - +
552A ALA* 3.6 20.0 - - - +
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Residues in contact with HIS 404 (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 LEU* 3.9 35.6 - - + +
363A LEU* 4.5 2.4 - - + +
364A GLU* 2.7 42.1 + - + +
374A TYR* 3.4 35.5 - + + -
377A LEU* 3.6 32.5 - - + -
381A ASN* 2.9 21.4 + - - +
400A ASN* 2.9 35.4 + - - +
403A ARG* 1.3 78.9 - - + +
405A LEU* 1.3 67.2 + - - +
406A LYS* 3.3 6.9 + - - +
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Residues in contact with LEU 405 (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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248A LYS* 3.0 26.4 + - - -
253A ASP* 3.2 3.5 - - - +
377A LEU* 4.1 16.2 - - + +
380A VAL* 4.1 13.0 - - + -
381A ASN* 3.6 14.1 - - - +
390A TYR* 3.7 48.0 - - + -
392A ILE* 4.2 8.1 - - + -
401A ALA* 3.0 36.8 + - + +
403A ARG 4.6 1.0 - - - +
404A HIS* 1.3 76.9 - - - +
406A LYS* 1.3 61.1 + - - +
407A LEU* 3.6 21.3 - - + -
444A LEU* 4.1 5.2 - - + -
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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