Contacts of the helix formed by residues 458 - 464 (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 PHE 458 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A PHE* 4.0 14.6 - + - -
266A PRO* 3.6 24.9 - - + -
392A GLU* 4.1 2.0 - - - -
395A LEU* 3.4 38.1 - - + -
396A GLU* 3.5 29.8 - - + +
399A LEU* 4.0 17.3 - - + -
402A THR* 4.0 13.0 - - + -
403A PHE* 3.7 29.8 - + - -
453A PHE* 3.5 19.5 - + + -
457A GLY* 1.3 75.3 - - - -
459A ARG* 1.3 64.6 + - - +
461A PRO* 3.5 7.1 - - + +
462A LEU* 3.1 37.4 + - + +
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Residues in contact with ARG 459 (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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301A PRO* 3.3 54.3 + - + +
302A GLU* 5.1 0.8 - - - +
303A ILE* 5.6 2.6 - - - +
388A PRO* 6.4 2.0 - - - +
392A GLU* 3.8 27.5 - - + +
396A GLU* 4.2 2.8 + - - +
456A SER 4.3 7.4 + - - +
457A GLY 3.5 2.8 - - - -
458A PHE* 1.3 78.4 - - - +
460A GLY* 1.3 62.9 + - - +
462A LEU* 3.6 1.7 - - - +
463A ASN* 2.5 38.5 + - - +
466A ARG* 5.0 0.6 - - - +
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Residues in contact with GLY 460 (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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293A GLY* 4.5 4.9 - - - -
299A ALA* 4.9 5.5 + - - +
300A PRO 4.7 1.3 + - - -
306A TYR* 3.3 45.1 - - - -
456A SER 4.9 2.8 + - - -
457A GLY 4.9 0.4 + - - -
459A ARG* 1.3 77.4 - - - +
461A PRO* 1.3 72.7 - - - +
463A ASN* 3.1 18.5 + - - +
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Residues in contact with PRO 461 (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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265A PHE* 3.7 20.0 - - + -
293A GLY 3.5 19.3 - - - +
294A TYR* 3.2 46.2 - - + +
299A ALA* 5.9 0.2 - - + -
453A PHE* 4.5 4.9 - - + -
457A GLY 3.6 12.3 - - - +
458A PHE* 3.5 19.7 - - + +
460A GLY* 1.3 87.4 - - - +
462A LEU* 1.3 56.4 + - - +
464A TRP* 2.9 35.9 + - + +
465A TYR* 4.4 0.5 + - - -
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Residues in contact with LEU 462 (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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265A PHE* 3.7 24.9 - - + -
385A PHE* 3.3 42.1 - - + +
391A ALA* 3.4 13.9 - - + -
392A GLU* 2.9 37.7 - - + +
395A LEU* 4.3 3.1 - - + -
458A PHE* 3.1 28.4 + - + +
459A ARG 3.6 3.8 - - - +
461A PRO* 1.3 77.8 - - - +
463A ASN* 1.3 61.8 + - - +
465A TYR* 3.2 22.6 + - + +
466A ARG* 3.7 21.8 + - - +
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Residues in contact with ASN 463 (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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301A PRO 3.0 19.5 + - - -
302A GLU 3.7 2.6 + - - -
303A ILE* 3.0 42.0 - - - +
306A TYR* 3.4 21.3 - - + -
459A ARG* 2.5 30.8 + - - +
460A GLY 3.2 11.2 - - - +
461A PRO 3.0 1.2 + - - -
462A LEU* 1.3 71.7 - - - +
464A TRP* 1.3 57.2 + - - +
465A TYR 2.9 5.6 - - - -
466A ARG* 2.8 39.2 + - - +
467A ASN* 3.1 17.5 + - - -
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Residues in contact with TRP 464 (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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263A HIS 5.5 1.3 - - - -
291A MET* 3.9 40.4 - - + -
292A LYS 3.2 28.2 + - - -
294A TYR* 4.0 12.7 - + - -
306A TYR* 3.4 23.5 - + - +
308A MET* 4.1 11.7 - - + -
311A LEU* 3.4 40.2 - - + -
334A TRP* 3.1 78.9 - + + +
338A LEU* 4.8 1.8 - - + -
460A GLY 3.4 10.1 - - - -
461A PRO* 2.9 28.6 + - + +
463A ASN* 1.3 76.8 - - - +
465A TYR* 1.3 58.0 + - + +
467A ASN* 4.5 6.5 + - - +
468A MET* 5.3 0.5 - - - +
471A ASN* 5.0 3.6 + - - -
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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