Contacts of the helix formed by residues 355 - 368 (chain A) in PDB entry 2Y4T
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 MET 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A ILE* 5.6 1.8 - - - -
350A TYR* 2.7 41.0 + - + +
351A LEU* 4.6 0.2 - - - +
353A GLU* 3.4 34.1 - - + +
354A GLU* 1.3 70.6 - - - +
356A TYR* 1.3 58.9 + - - +
357A ASP 3.3 2.7 - - - -
358A GLU* 3.1 40.4 + - + +
359A ALA* 3.0 26.9 + - - +
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Residues in contact with TYR 356 (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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351A LEU* 3.9 25.8 + - + -
354A GLU* 3.3 52.1 + - + +
355A MET* 1.3 68.0 - - - +
357A ASP* 1.3 64.9 + - - +
359A ALA* 3.6 4.7 - - - +
360A ILE* 3.0 30.3 + - - +
383A ALA* 3.8 7.4 - - - +
386A LEU* 3.3 57.3 - - + +
387A LEU* 3.7 30.5 - - + -
390A SER* 4.3 16.4 - - - -
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Residues in contact with ASP 357 (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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355A MET 3.3 0.4 - - - -
356A TYR* 1.3 77.7 - - - +
358A GLU* 1.3 67.5 + - + +
360A ILE* 2.9 31.6 - - + +
361A GLN* 3.0 15.3 + - - +
387A LEU* 3.5 27.3 - - - +
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Residues in contact with GLU 358 (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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350A TYR* 3.4 38.5 - - + +
355A MET* 3.1 45.2 + - + +
357A ASP* 1.3 84.7 - - + +
359A ALA* 1.3 60.2 + - - +
361A GLN* 3.9 18.0 - - - +
362A ASP* 3.3 20.4 + - - +
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Residues in contact with ALA 359 (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 ALA* 3.9 10.4 - - - +
350A TYR* 3.8 16.8 - - + +
351A LEU* 3.7 30.1 - - + +
355A MET 3.0 16.0 + - - +
356A TYR 3.6 5.4 - - - +
357A ASP 3.2 0.2 - - - -
358A GLU* 1.3 74.7 - - - +
360A ILE* 1.3 60.5 + - - +
362A ASP* 3.2 4.5 + - - +
363A TYR* 2.9 35.3 + - + -
383A ALA* 4.5 2.9 - - + -
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Residues in contact with ILE 360 (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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356A TYR 3.0 20.6 + - - +
357A ASP* 2.9 32.5 - - + +
359A ALA* 1.3 71.1 - - - +
361A GLN* 1.3 60.6 + - - +
362A ASP 2.9 2.0 + - - -
363A TYR* 3.0 7.8 + - - +
364A GLU* 2.7 63.2 + - - +
380A LEU* 4.3 12.1 - - + +
383A ALA* 3.6 22.4 - - + +
384A GLN* 4.2 29.4 - - - +
387A LEU* 5.6 3.6 - - + -
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Residues in contact with GLN 361 (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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346A ARG* 5.9 0.3 + - - -
357A ASP* 3.0 17.2 + - - +
358A GLU* 3.9 20.3 - - - +
360A ILE* 1.3 79.2 - - + +
362A ASP* 1.3 63.8 + - - +
364A GLU* 3.8 10.8 - - - +
365A THR* 3.1 30.7 + - + +
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Residues in contact with ASP 362 (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 LEU* 3.9 26.7 - - + +
346A ARG* 2.7 58.8 + - - +
347A ALA* 3.9 5.6 + - + -
350A TYR* 3.7 3.4 - - - -
358A GLU 3.3 14.1 + - - +
359A ALA 3.2 8.0 + - - +
360A ILE 3.0 0.8 - - - -
361A GLN* 1.3 86.8 - - - +
363A TYR* 1.3 64.6 + - - +
364A GLU 3.1 1.6 - - - -
365A THR* 3.3 9.1 - - - +
366A ALA* 3.0 24.3 + - - +
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Residues in contact with TYR 363 (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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344A LYS* 4.2 24.8 + - + -
347A ALA* 3.4 26.4 - - + +
348A GLU* 4.0 18.0 + - - +
351A LEU* 4.3 17.2 - - + +
359A ALA 2.9 26.9 + - - +
360A ILE* 3.7 4.5 - - - +
362A ASP* 1.3 75.7 - - - +
364A GLU* 1.3 56.1 + - - +
366A ALA* 3.4 4.1 - - + +
367A GLN* 3.0 20.3 + - - +
375A GLN 4.6 6.6 + - - -
376A ILE* 3.3 34.3 - - + +
379A GLY* 3.6 38.2 - - - -
380A LEU* 4.1 22.2 - - + -
383A ALA* 4.5 4.5 - - + -
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Residues in contact with GLU 364 (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 ILE* 2.7 45.8 + - - +
361A GLN* 3.8 10.1 - - - +
363A TYR* 1.3 69.8 - - - +
365A THR* 1.3 56.3 + - - +
366A ALA 2.9 4.0 - - - -
367A GLN* 2.7 31.0 + - - +
368A GLU* 3.1 12.7 + - - +
380A LEU* 3.5 27.1 - - + +
384A GLN* 5.3 1.2 - - - +
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Residues in contact with THR 365 (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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337A PRO 5.2 3.4 + - - +
343A LEU* 3.8 22.0 - - + +
361A GLN* 3.1 19.2 + - + +
362A ASP* 3.3 18.6 - - - +
364A GLU* 1.3 78.2 - - - +
366A ALA* 1.3 56.1 + - - +
368A GLU* 3.7 22.8 + - - +
369A HIS* 3.1 29.3 + - - -
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Residues in contact with ALA 366 (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 VAL* 4.0 12.1 - - + +
343A LEU* 3.7 23.6 - - + -
344A LYS* 5.0 3.4 - - + -
362A ASP 3.0 17.0 + - - +
363A TYR* 3.4 9.6 - - - +
364A GLU 2.9 0.4 - - - -
365A THR* 1.3 77.2 - - - +
367A GLN* 1.3 62.5 + - - +
368A GLU 3.2 2.2 - - - -
369A HIS* 3.1 15.9 + - - +
370A ASN 3.2 10.2 + - - -
376A ILE* 3.7 22.5 - - + +
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Residues in contact with GLN 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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363A TYR 3.0 12.0 + - - +
364A GLU* 2.7 20.5 + - - +
366A ALA* 1.3 67.9 - - - +
368A GLU* 1.3 60.9 + - - +
369A HIS 3.3 0.2 - - - -
370A ASN 3.0 22.3 - - - +
371A GLU* 3.7 24.2 - - - +
373A ASP 6.2 0.4 - - - +
376A ILE* 4.0 16.0 - - + +
377A ARG* 4.4 18.4 - - - +
380A LEU* 3.7 27.4 - - - +
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Residues in contact with GLU 368 (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 3.1 12.3 + - - +
365A THR* 3.7 26.9 + - - +
367A GLN* 1.3 78.2 - - - +
369A HIS* 1.3 69.6 + - + +
371A GLU* 3.4 17.6 - - - +
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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