Contacts of the helix formed by residues 361 - 374 (chain A) in PDB entry 1Z6T
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 TYR 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A ARG* 3.4 44.4 - - + +
354A ARG 5.0 2.0 - - - -
355A LYS 4.2 11.4 - - - -
356A SER 4.8 1.1 - - - -
357A SER* 3.6 30.5 + - - -
359A TYR* 3.4 32.7 + + - +
360A ASP* 1.3 71.7 - - - +
362A GLU* 1.3 66.8 + - - +
363A ALA 3.3 1.8 - - - -
364A LEU* 2.9 11.4 + - + -
365A ASP* 2.8 42.9 + - - +
440A LEU* 3.6 17.6 - - + +
443A ASP* 2.5 31.7 + - + -
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Residues in contact with GLU 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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348A LYS* 4.0 30.1 - - + +
352A ARG* 6.4 0.2 - - - -
360A ASP* 3.4 10.8 - - + -
361A TYR* 1.3 81.0 - - - +
363A ALA* 1.3 61.9 + - - +
365A ASP* 3.8 4.9 - - - +
366A GLU* 3.2 24.3 + - - +
465B GLN 4.5 11.6 - - - +
466B ARG* 5.1 12.9 - - - +
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Residues in contact with ALA 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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316A GLU 3.4 25.8 - - - +
317A CYS 4.3 9.2 - - - +
318A LYS* 4.6 8.3 - - + -
323A VAL* 3.9 15.8 - - + +
345A LEU* 4.7 3.8 - - + +
348A LYS* 3.9 15.0 - - - +
360A ASP 4.8 2.3 + - - +
361A TYR 3.3 0.2 - - - -
362A GLU* 1.3 76.9 - - - +
364A LEU* 1.3 61.7 + - - +
366A GLU* 3.4 2.4 + - - +
367A ALA* 3.0 30.8 + - - +
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Residues in contact with LEU 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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322A LEU* 3.9 18.8 - - + -
323A VAL* 3.6 22.2 - - + +
326A LEU* 3.8 24.9 - - + -
359A TYR* 3.9 19.5 + - + +
360A ASP 5.1 0.8 + - - -
361A TYR* 2.9 13.2 + - + +
363A ALA* 1.3 79.6 - - - +
365A ASP* 1.3 58.6 + - - +
367A ALA* 3.4 1.1 + - - +
368A MET* 2.9 37.5 + - + +
440A LEU* 3.2 53.2 - - + +
441A GLN* 5.3 0.4 - - + -
444A PHE* 5.6 0.4 - - + -
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Residues in contact with ASP 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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350A PHE* 3.6 28.6 - - + -
352A ARG* 2.9 54.7 + - - +
361A TYR* 2.8 32.1 + - - +
362A GLU* 3.8 5.6 + - - +
364A LEU* 1.3 72.3 - - - +
366A GLU* 1.3 58.1 + - - +
369A SER* 2.8 30.6 + - - -
444A PHE* 3.3 20.2 - - - +
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Residues in contact with GLU 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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344A GLN* 3.7 19.0 - - - +
345A LEU* 4.5 8.1 - - + -
347A ASN 4.2 0.7 - - - +
348A LYS* 3.5 23.3 - - + +
349A GLN* 3.2 26.4 + - - +
350A PHE* 3.0 31.5 + - - +
362A GLU 3.2 15.8 + - - +
363A ALA 3.9 3.8 - - - +
365A ASP* 1.3 80.4 - - - +
367A ALA* 1.3 56.4 + - - +
369A SER* 3.2 7.4 + - - -
370A ILE* 2.9 48.4 + - + +
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Residues in contact with ALA 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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323A VAL* 3.8 16.6 - - + -
326A LEU* 4.1 17.7 - - + +
327A ILE* 3.8 29.4 - - + -
330A LEU* 4.7 1.9 - - - +
345A LEU* 4.5 2.3 - - + +
363A ALA 3.0 17.7 + - - +
364A LEU 3.8 3.1 - - - +
366A GLU* 1.3 74.0 - - - +
368A MET* 1.3 65.6 + - - +
370A ILE* 3.5 3.1 + - - +
371A SER* 3.0 25.9 + - - -
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Residues in contact with MET 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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326A LEU* 3.7 20.4 - - + +
364A LEU* 2.9 30.5 + - + +
365A ASP 3.7 3.4 - - - +
367A ALA* 1.3 75.6 - - - +
369A SER* 1.3 59.2 + - - +
371A SER* 3.7 2.4 - - - -
372A VAL* 2.8 35.7 + - + +
383A TYR* 3.5 29.4 - - + +
423A LEU* 3.6 20.9 - - + -
441A GLN* 3.7 30.7 - - + +
444A PHE* 3.6 41.7 - - + -
445A LEU* 4.9 0.7 - - + -
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Residues in contact with SER 369 (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 PHE* 3.9 19.8 - - - +
365A ASP 2.8 19.2 + - - -
366A GLU* 3.6 12.8 + - - -
368A MET* 1.3 76.0 - - - +
370A ILE* 1.3 57.2 + - - +
372A VAL* 3.6 3.1 + - - +
373A GLU* 3.0 29.5 + - - +
444A PHE* 3.6 16.9 - - - -
448A LYS* 6.0 2.3 - - - +
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Residues in contact with ILE 370 (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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327A ILE* 4.9 3.4 - - + -
330A LEU* 3.3 22.9 - - + -
341A TYR* 3.8 17.5 - - + +
344A GLN* 3.5 48.7 - - + +
345A LEU* 4.2 14.1 - - + +
366A GLU* 2.9 43.7 + - + +
367A ALA* 3.9 4.7 - - - +
369A SER* 1.3 75.8 - - - +
371A SER* 1.3 62.3 + - - +
373A GLU* 3.3 6.9 + - - +
374A MET* 3.2 26.0 + - + +
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Residues in contact with SER 371 (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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326A LEU* 4.4 13.0 + - - +
329A ALA* 5.9 0.3 - - - +
330A LEU* 4.0 24.3 + - - +
367A ALA 3.0 19.4 + - - -
368A MET* 3.7 3.4 - - - -
370A ILE* 1.3 77.5 - - - +
372A VAL* 1.3 63.7 + - - +
374A MET* 3.2 12.1 + - - +
375A LEU* 3.5 13.6 + - - +
421A LYS* 4.4 13.0 + - - +
423A LEU* 3.8 28.7 - - - +
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Residues in contact with VAL 372 (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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368A MET* 2.8 26.7 + - + +
369A SER* 4.0 4.5 - - - +
371A SER* 1.3 72.4 - - - +
373A GLU* 1.3 64.0 + - - +
375A LEU* 3.1 34.3 + - + +
380A LYS* 3.6 12.5 - - + +
383A TYR* 3.7 33.9 - - + -
384A THR* 5.8 2.9 - - - +
423A LEU* 4.3 8.5 - - + -
444A PHE* 4.2 12.3 - - + -
445A LEU* 5.2 0.9 - - + -
448A LYS* 4.1 25.4 - - + +
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Residues in contact with GLU 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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369A SER 3.0 19.7 + - - +
370A ILE* 3.4 9.6 - - - +
371A SER 3.3 0.2 - - - -
372A VAL* 1.3 78.9 - - - +
374A MET* 1.3 73.7 + - + +
375A LEU 4.0 0.3 - - - +
377A GLU* 4.9 0.2 - - - +
380A LYS* 2.8 42.9 + - - +
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Residues in contact with MET 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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330A LEU* 3.7 17.7 - - + -
334A PHE* 3.6 34.2 - - + -
337A ARG* 3.7 13.2 - - - +
340A TYR* 4.0 26.0 - - + +
341A TYR* 3.6 23.1 - - + +
344A GLN* 4.6 6.5 - - - +
370A ILE* 3.2 15.6 + - + +
371A SER 3.8 6.3 - - - +
372A VAL 3.2 1.0 - - - -
373A GLU* 1.3 98.9 - - + +
375A LEU* 1.3 64.3 + - - +
376A ARG* 3.5 2.6 + - - -
421A LYS* 4.7 5.6 + - - +
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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