Contacts of the helix formed by residues 329 - 347 (chain A) in PDB entry 1MZC
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 ASN 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A ASP* 1.3 100.9 + - - +
330A LYS* 1.3 65.7 + - - +
331A GLU* 3.3 2.9 - - - -
332A ASP* 3.1 20.0 + - + +
333A ILE* 3.0 22.2 + - + +
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Residues in contact with LYS 330 (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 LEU* 2.8 42.3 + - + +
326A GLN* 3.4 30.4 + - - +
327A CYS* 4.1 19.7 + - - +
328A ASP 3.2 1.8 - - - -
329A ASN* 1.3 75.5 - - - +
331A GLU* 1.3 61.2 + - + +
333A ILE* 3.1 3.1 + - - +
334A LEU* 2.8 31.6 + - + +
367A HIS* 3.8 37.2 - - + +
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Residues in contact with GLU 331 (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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329A ASN 3.3 0.8 - - - -
330A LYS* 1.3 81.1 - - + +
332A ASP* 1.3 57.4 + - - +
334A LEU* 3.5 18.2 + - - +
335A ASN* 3.0 29.1 + - - +
367A HIS 5.0 6.7 - - - +
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Residues in contact with ASP 332 (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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329A ASN* 3.1 22.2 + - + +
331A GLU* 1.3 75.7 - - - +
333A ILE* 1.3 73.8 + - - +
335A ASN* 3.3 7.9 + - - +
336A LYS* 3.0 60.7 + - - +
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Residues in contact with ILE 333 (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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319A TYR* 3.9 39.8 - - + +
322A MET* 4.0 21.1 - - + -
323A LEU* 3.6 25.8 - - + -
327A CYS* 3.8 18.4 - - - -
328A ASP 3.9 5.6 - - - +
329A ASN* 3.0 15.7 + - + +
330A LYS 3.6 6.5 - - - +
332A ASP* 1.3 84.4 - - - +
334A LEU* 1.3 58.8 + - - +
336A LYS* 3.2 8.8 + - + +
337A ALA* 2.9 27.9 + - - +
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Residues in contact with LEU 334 (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 LEU* 4.0 20.4 - - + +
330A LYS* 2.8 17.0 + - + +
331A GLU* 3.7 18.8 - - - +
333A ILE* 1.3 76.2 - - - +
335A ASN* 1.3 59.9 + - - +
337A ALA* 3.3 1.1 + - - +
338A LEU* 2.9 60.2 + - + +
363A LEU* 3.9 32.1 - - + +
364A GLN* 4.7 6.3 - - + +
367A HIS* 3.7 28.0 - - + +
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Residues in contact with ASN 335 (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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331A GLU 3.0 18.3 + - - +
332A ASP* 3.6 8.7 - - - +
333A ILE 3.2 0.2 - - - -
334A LEU* 1.3 79.1 - - - +
336A LYS* 1.3 64.9 + - - +
338A LEU* 3.5 8.6 + - - +
339A GLU* 2.9 56.2 + - - +
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Residues in contact with LYS 336 (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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319A TYR* 3.8 28.9 + - + +
332A ASP* 3.0 54.6 + - - +
333A ILE* 3.5 11.2 - - + +
335A ASN* 1.3 78.1 + - - +
337A ALA* 1.3 64.5 + - - +
339A GLU* 3.2 17.9 + - - +
340A LEU* 3.0 28.3 + - + +
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Residues in contact with ALA 337 (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 VAL* 4.4 6.9 - - + +
319A TYR* 3.8 28.4 - - + -
323A LEU* 4.8 3.4 - - + -
333A ILE 2.9 16.2 + - - +
334A LEU* 3.6 7.4 - - - +
335A ASN 3.3 0.2 - - - -
336A LYS* 1.3 77.3 - - - +
338A LEU* 1.3 57.1 + - - +
340A LEU* 3.3 6.1 + - - +
341A CYS* 3.0 33.6 + - - -
363A LEU* 3.7 22.0 - - + -
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Residues in contact with LEU 338 (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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334A LEU* 2.9 41.6 + - + +
335A ASN* 3.9 7.6 - - - +
337A ALA* 1.3 72.8 - - - +
339A GLU* 1.3 65.1 + - + +
341A CYS* 3.3 5.3 + - + +
342A GLU* 3.1 23.2 + - - +
360A GLY* 3.5 37.9 - - - +
363A LEU* 4.1 12.3 - - + -
364A GLN* 4.1 23.6 - - + +
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Residues in contact with GLU 339 (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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335A ASN* 2.9 50.8 + - - +
336A LYS* 3.2 18.5 + - - +
338A LEU* 1.3 75.1 - - + +
340A LEU* 1.3 60.6 + - + +
342A GLU* 3.3 7.7 + - - +
343A ILE* 2.9 36.3 + - + +
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Residues in contact with LEU 340 (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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303A GLN* 5.1 4.3 - - - +
312A ILE* 4.0 27.6 - - + +
315A LEU* 3.7 36.6 - - + -
316A VAL* 3.6 17.5 - - + -
319A TYR* 3.9 18.2 - - + -
336A LYS* 3.0 15.2 + - + +
337A ALA 3.7 3.4 - - - +
339A GLU* 1.3 76.8 - - + +
341A CYS* 1.3 60.6 + - - +
343A ILE* 3.2 19.5 + - + +
344A LEU* 2.8 36.7 + - - +
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Residues in contact with CYS 341 (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 VAL* 4.0 13.9 - - - -
337A ALA 3.0 18.5 + - - -
338A LEU* 3.6 9.6 - - - +
340A LEU* 1.3 75.8 - - - +
342A GLU* 1.3 58.0 + - - +
344A LEU* 3.4 8.7 + - - +
345A ALA* 2.9 31.8 + - - +
356A TRP* 3.7 25.7 - - - +
357A ARG* 5.4 0.9 - - - -
359A ILE* 3.7 30.3 - - - -
360A GLY* 4.0 11.2 - - - -
363A LEU* 4.2 6.7 - - - -
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Residues in contact with GLU 342 (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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338A LEU 3.1 12.4 + - - +
339A GLU* 3.4 12.1 - - - +
341A CYS* 1.3 74.3 - - - +
343A ILE* 1.3 61.8 + - + +
345A ALA* 3.2 0.7 + - - -
346A LYS* 2.9 56.8 + - - +
357A ARG* 2.5 47.5 + - - +
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Residues in contact with ILE 343 (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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312A ILE* 5.0 7.4 - - + -
339A GLU* 2.9 21.9 + - + +
340A LEU* 3.6 25.6 - - + +
342A GLU* 1.3 77.1 - - + +
344A LEU* 1.3 58.8 + - - +
346A LYS* 5.1 1.3 - - - -
347A GLU* 2.9 35.3 + - - +
348A LYS* 3.0 43.0 + - + -
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Residues in contact with LEU 344 (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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309A PRO* 4.0 12.8 - - + +
312A ILE* 3.6 34.1 - - + -
313A ALA* 4.2 2.5 - - - -
316A VAL* 3.9 10.5 - - + -
340A LEU 2.8 20.0 + - - +
341A CYS 3.7 2.7 - - - +
343A ILE* 1.3 76.7 - - - +
345A ALA* 1.3 59.9 + - - +
346A LYS 3.5 0.2 + - - -
348A LYS* 3.7 11.2 + - + +
349A ASP* 2.7 53.2 + - + +
350A THR 3.3 0.3 + - - -
356A TRP* 3.6 51.8 - - + +
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Residues in contact with ALA 345 (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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341A CYS 2.9 18.8 + - - +
342A GLU 3.8 2.7 - - - +
344A LEU* 1.3 78.1 - - - +
346A LYS* 1.3 57.2 + - - +
350A THR* 3.5 18.9 - - - +
353A LYS* 3.7 28.9 - - + +
356A TRP* 3.9 15.0 - - + +
357A ARG* 3.9 31.0 - - - +
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Residues in contact with LYS 346 (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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342A GLU* 2.9 38.8 + - - +
343A ILE* 4.6 1.3 - - - +
345A ALA* 1.3 77.4 - - - +
347A GLU* 1.3 61.8 + - + +
350A THR* 3.4 12.5 - - - +
357A ARG* 4.0 15.9 - - - +
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Residues in contact with GLU 347 (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 ILE* 2.9 20.2 + - + +
345A ALA 3.7 1.2 - - - -
346A LYS* 1.3 84.7 - - + +
348A LYS* 1.3 85.9 + - + +
349A ASP 3.6 2.0 + - - -
350A THR* 3.9 10.1 - - - +
532B ARG* 5.4 10.7 + - - +
533B GLU* 4.4 10.2 - - - +
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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