Contacts of the helix formed by residues 410 - 425 (chain A) in PDB entry 2Z1Z
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 HIS 410 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A THR* 3.3 27.3 + - - -
68A GLU* 2.8 24.9 + - - -
337A PHE* 4.3 0.7 - - - -
409A GLY* 1.3 75.7 - - - +
411A ARG* 1.3 64.9 + - - +
412A GLU* 4.4 7.0 - - + +
413A ASN* 3.0 41.7 + - - +
414A ILE* 3.2 9.2 + - - +
88B ILE* 3.4 44.7 + - + +
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Residues in contact with ARG 411 (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 PHE* 3.4 48.8 + - + +
340A GLU* 3.5 21.5 - - - +
341A ASN* 2.8 31.6 + - - -
344A ILE* 3.7 24.7 - - - +
409A GLY 3.4 2.6 + - - -
410A HIS* 1.3 71.0 - - - +
412A GLU* 1.3 61.1 + - - +
414A ILE* 3.5 2.0 + - - +
415A LEU* 3.0 45.6 + - + +
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Residues in contact with GLU 412 (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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410A HIS* 3.4 6.3 - - + +
411A ARG* 1.3 78.4 - - - +
413A ASN* 1.3 60.4 + - - +
415A LEU* 3.4 9.9 + - + +
416A GLU* 2.9 31.9 + - - +
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Residues in contact with ASN 413 (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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59A ILE* 3.6 36.0 - - + +
409A GLY* 4.7 4.3 - - - -
410A HIS* 3.0 53.4 + - - +
412A GLU* 1.3 78.4 - - - +
414A ILE* 1.3 56.8 + - + +
416A GLU* 4.6 0.7 - - - -
417A ALA* 2.9 28.8 + - - +
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Residues in contact with ILE 414 (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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61A LEU* 3.5 31.0 - - + -
341A ASN* 3.7 36.1 - - + +
344A ILE* 4.2 14.6 - - + -
345A ILE* 3.8 29.4 - - + -
407A ALA 3.8 11.7 - - - +
409A GLY* 3.8 18.2 - - - +
410A HIS 3.2 14.1 + - - +
411A ARG 4.0 4.7 - - - +
413A ASN* 1.3 72.5 - - - +
415A LEU* 1.3 61.9 + - - +
417A ALA* 3.9 4.2 - - - +
418A CYS* 2.9 31.5 + - - +
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Residues in contact with LEU 415 (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 ILE* 4.1 28.5 - - + -
411A ARG* 3.0 42.6 + - + +
412A GLU* 3.7 9.6 - - + +
414A ILE* 1.3 75.1 - - - +
416A GLU* 1.3 51.2 + - - +
418A CYS* 3.1 8.1 + - + +
419A ARG* 2.7 35.9 + - - +
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Residues in contact with GLU 416 (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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59A ILE* 3.7 7.9 - - + -
412A GLU 2.9 18.9 + - - +
413A ASN* 3.9 2.9 - - - +
415A LEU* 1.3 72.5 - - - +
417A ALA* 1.3 66.4 + - - +
418A CYS 3.0 1.1 - - - -
419A ARG* 2.7 52.8 + - - +
420A ARG* 2.9 53.2 + - - +
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Residues in contact with ALA 417 (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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59A ILE* 3.8 16.3 - - + +
61A LEU* 3.7 30.3 - - + -
387A VAL* 4.1 17.9 - - + -
413A ASN 2.9 22.9 + - - +
414A ILE* 4.0 3.6 - - - +
416A GLU* 1.3 72.3 - - - +
418A CYS* 1.3 57.5 + - - +
420A ARG* 3.3 4.5 + - - +
421A PHE* 3.0 35.2 + - + -
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Residues in contact with CYS 418 (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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61A LEU* 6.2 0.2 - - - -
344A ILE* 4.0 11.9 - - + -
345A ILE* 3.9 25.1 - - - -
348A THR* 3.0 34.1 + - + -
414A ILE 2.9 23.1 + - - +
415A LEU* 3.2 7.4 - - + +
417A ALA* 1.3 78.3 - - - +
419A ARG* 1.3 59.0 + - - +
421A PHE* 3.2 14.7 + - - +
422A LYS* 2.9 37.2 + - - +
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Residues in contact with ARG 419 (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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415A LEU 2.7 18.2 + - - +
416A GLU* 2.7 46.7 + - - +
418A CYS* 1.3 72.4 - - - +
420A ARG* 1.3 69.3 + - - +
422A LYS* 3.3 15.4 + - + +
423A GLN* 2.9 54.9 + - - +
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Residues in contact with ARG 420 (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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57A GLN* 2.5 39.2 + - - +
59A ILE* 3.5 17.1 - - - +
385A THR* 2.9 48.3 + - + +
386A HIS* 3.5 13.6 + - - +
387A VAL* 3.8 7.5 - - + +
416A GLU* 2.9 61.0 + - - +
417A ALA* 3.4 9.6 - - - +
418A CYS 3.2 0.4 - - - -
419A ARG* 1.3 80.0 - - - +
421A PHE* 1.3 67.7 + - - +
423A GLN* 3.4 6.6 + - + +
424A LEU* 3.0 24.3 + - - +
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Residues in contact with PHE 421 (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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61A LEU* 4.4 2.7 - - + -
345A ILE* 5.2 1.1 - - + -
348A THR* 4.2 10.8 - - - +
349A PHE* 3.4 42.2 - + + -
352A LEU* 3.8 7.0 - - + +
381A ILE* 3.7 30.7 - - + -
385A THR* 4.6 4.7 - - + -
387A VAL* 3.7 27.1 - - + -
389A THR* 4.4 6.3 - - + -
405A VAL* 4.3 20.4 - - + -
417A ALA* 3.0 29.0 + - + -
418A CYS* 3.7 18.8 - - - +
420A ARG* 1.3 74.9 - - - +
422A LYS* 1.3 57.3 + - - +
424A LEU* 4.4 4.0 - - - -
425A TYR* 3.0 44.8 + + + +
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Residues in contact with LYS 422 (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 ASP* 5.2 0.8 + - - +
348A THR* 3.7 36.5 - - - +
351A SER* 4.1 15.3 + - - +
352A LEU* 4.3 16.8 - - + +
418A CYS* 2.9 21.5 + - - +
419A ARG* 3.5 16.6 - - + +
420A ARG 3.1 0.2 - - - -
421A PHE* 1.3 72.2 - - - +
423A GLN* 1.3 60.0 + - - +
425A TYR 2.8 25.8 - - - +
426A LYS 4.2 3.1 - - - +
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Residues in contact with GLN 423 (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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419A ARG* 2.9 37.9 + - - +
420A ARG* 3.9 7.4 - - - +
422A LYS* 1.3 72.2 - - - +
424A LEU* 1.3 64.8 + - - +
425A TYR 4.1 2.1 - - - +
426A LYS* 5.4 3.3 - - - +
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Residues in contact with LEU 424 (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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380A GLU* 4.7 7.2 - - - +
381A ILE* 4.4 12.8 - - + -
384A LYS* 3.7 34.8 - - + -
385A THR* 3.5 26.7 - - + -
420A ARG 3.0 17.8 + - - +
421A PHE* 3.6 4.9 - - - +
422A LYS 3.3 0.2 - - - -
423A GLN* 1.3 77.1 - - - +
425A TYR* 1.3 100.1 + - + +
426A LYS* 4.2 2.3 + - - -
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Residues in contact with TYR 425 (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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349A PHE* 4.5 7.9 - + - -
352A LEU* 3.4 23.0 - - + +
354A TYR* 3.5 31.9 - + + +
369A PHE* 3.6 29.1 - + - -
377A VAL* 4.0 1.7 - - - +
380A GLU* 3.7 19.4 + - - -
381A ILE* 3.3 28.5 - - + +
421A PHE* 3.0 32.7 + + + +
422A LYS 2.8 14.9 - - - +
423A GLN 4.1 2.1 - - - +
424A LEU* 1.3 107.5 - - + +
426A LYS* 1.3 70.4 + - - +
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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