Contacts of the helix formed by residues 467 - 477 (chain A) in PDB entry 1ZD4
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 467 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ILE* 2.9 30.9 + - - +
304A GLU* 3.8 0.3 - - - -
306A TYR 3.5 13.0 + - - +
307A CYS* 3.7 13.8 - - + +
463A ASN 3.1 22.8 + - - +
464A TRP 4.5 3.6 + - - +
465A TYR 3.3 2.2 + - - -
466A ARG* 1.3 76.7 - - - +
468A MET* 1.3 68.4 + - - +
469A GLU 3.4 2.2 - - - -
470A ARG* 2.8 44.1 + - - +
471A ASN* 2.7 44.6 + - - +
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Residues in contact with MET 468 (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 TRP* 4.9 12.1 - - + -
369A PRO* 3.7 22.1 - - + +
370A LEU* 5.3 2.2 - - - +
373A ILE* 3.5 20.2 - - + -
382A GLN* 3.2 31.6 - - + +
386A GLN* 4.2 20.2 - - - +
464A TRP 5.3 0.4 - - - +
465A TYR* 3.3 37.0 - - + +
466A ARG 3.8 0.4 - - - -
467A ASN* 1.3 76.3 - - - +
469A GLU* 1.3 55.8 + - + +
471A ASN* 3.2 5.7 + - - +
472A TRP* 2.7 36.2 + - - +
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Residues in contact with GLU 469 (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 SER* 3.9 10.4 - - - -
369A PRO* 3.3 27.2 - - - +
370A LEU* 4.6 6.8 + - - +
467A ASN 3.4 0.4 - - - -
468A MET* 1.3 79.9 - - + +
470A ARG* 1.3 63.4 + - - +
472A TRP* 3.3 20.9 + - - +
473A LYS* 3.0 37.8 + - + +
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Residues in contact with ARG 470 (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 ILE* 4.1 4.4 - - - +
304A GLU* 3.5 37.3 + - - +
307A CYS* 4.1 21.6 - - + +
466A ARG 4.4 3.2 + - - -
467A ASN* 2.8 37.6 + - - +
469A GLU* 1.3 75.0 - - + +
471A ASN* 1.3 71.5 + - - +
473A LYS* 3.1 10.8 + - + +
474A TRP* 2.9 24.8 + - - +
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Residues in contact with ASN 471 (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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306A TYR 5.2 0.8 + - - -
307A CYS* 3.6 4.1 - - - +
308A MET* 3.2 52.0 + - + +
309A GLU 6.1 0.2 - - - +
334A TRP* 4.6 13.9 - - - -
337A MET* 6.0 0.2 - - - +
464A TRP 5.0 3.8 + - - -
467A ASN* 2.7 46.9 + - - +
468A MET* 3.6 5.6 - - - +
470A ARG* 1.3 70.2 - - - +
472A TRP* 1.3 63.4 + - - +
474A TRP* 3.5 8.2 + - - +
475A ALA* 3.0 25.5 + - - +
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Residues in contact with TRP 472 (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 ALA* 3.5 21.3 - - + -
364A ASN 2.9 25.2 + - - -
365A PRO 3.4 26.7 - - - -
366A ASN 4.6 4.0 - - - -
367A MET 3.7 11.7 + - - -
368A SER* 5.2 5.2 - - - -
369A PRO* 3.2 37.7 - - + -
468A MET 2.7 13.3 + - - +
469A GLU* 3.3 23.6 - - - +
471A ASN* 1.3 72.2 - - - +
473A LYS* 1.3 94.1 + - + +
475A ALA* 3.1 7.4 + - - +
476A CYS* 3.1 38.0 + - - -
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Residues in contact with LYS 473 (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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469A GLU* 3.0 23.4 + - - +
470A ARG* 3.1 10.7 + - + +
472A TRP* 1.3 100.5 - - + +
474A TRP* 1.3 67.5 + - - +
476A CYS* 3.0 23.1 + - - +
477A LYS* 3.7 7.8 + - - +
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Residues in contact with TRP 474 (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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308A MET* 3.7 24.2 - - + -
309A GLU* 3.2 73.1 + - + +
312A CYS* 4.2 17.7 - - + -
313A LYS* 5.1 1.0 - - - +
341A TYR* 4.0 11.2 - + + -
345A PHE* 3.4 62.7 - + + -
346A TYR* 4.9 7.6 - + - -
470A ARG 2.9 16.7 + - - +
471A ASN* 3.7 7.0 - - - +
473A LYS* 1.3 75.2 - - - +
475A ALA* 1.3 63.3 + - - +
477A LYS* 3.1 44.9 + - + +
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Residues in contact with ALA 475 (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 TYR* 3.6 36.6 - - + +
345A PHE* 4.4 2.7 - - - -
363A ALA* 4.1 15.7 - - + +
471A ASN 3.0 17.5 + - - +
472A TRP* 3.1 5.4 + - - +
474A TRP* 1.3 72.1 - - + +
476A CYS* 1.3 52.9 + - - +
477A LYS 2.9 5.2 - - - -
478A SER* 2.7 38.8 + - - +
479A LEU* 3.6 6.2 + - - +
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Residues in contact with CYS 476 (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 ALA* 4.4 5.2 - - - -
365A PRO* 4.5 7.6 - - - -
472A TRP* 3.1 54.1 + - - -
473A LYS* 3.0 14.2 + - - +
475A ALA* 1.3 76.5 - - - +
477A LYS* 1.3 59.6 + - - +
478A SER 3.2 0.7 + - - -
479A LEU* 3.4 38.1 + - + +
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Residues in contact with LYS 477 (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 GLU* 5.2 3.4 + - - -
345A PHE* 4.7 4.0 - - + -
473A LYS* 4.0 6.5 - - - +
474A TRP* 3.2 41.8 - - + +
475A ALA 2.8 0.6 + - - -
476A CYS* 1.3 78.9 - - + +
478A SER* 1.3 57.0 + - - +
479A LEU 3.5 0.4 + - - -
480A GLY 4.6 2.3 + - - -
481A ARG* 3.9 21.4 + - - +
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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