Contacts of the helix formed by residues 480 - 490 (chain D) in PDB entry 5ZR1
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 480 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478D ARG* 4.2 1.2 - - - +
479D ASP* 1.3 81.8 - - + +
481D ALA* 1.3 63.1 + - - +
482D THR* 3.6 17.5 + - - +
483D ALA* 3.3 24.4 + - - +
484D ALA* 3.5 11.3 + - - +
142E ASP* 3.1 22.7 - - - +
144E ALA* 4.5 7.4 - - + -
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Residues in contact with ALA 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480D ASN* 1.3 75.6 - - - +
482D THR* 1.3 64.2 + - + +
484D ALA* 3.6 3.6 + - - +
485D PHE* 3.1 25.8 + - - +
70E TRP* 5.1 17.3 - - + +
142E ASP* 3.2 14.7 + - - +
144E ALA* 5.6 0.2 - - - +
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Residues in contact with THR 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480D ASN* 3.6 17.2 + - - +
481D ALA* 1.3 78.5 - - + +
483D ALA* 1.3 62.6 + - - +
485D PHE* 3.3 6.3 + - - +
486D TYR* 2.9 54.7 + - - +
55H C 4.9 5.5 + - - -
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Residues in contact with ALA 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478D ARG* 3.5 25.3 + - + +
479D ASP* 4.9 1.8 - - + +
480D ASN* 3.3 19.5 + - - +
482D THR* 1.3 80.3 + - - +
484D ALA* 1.3 62.6 + - - +
486D TYR* 4.0 10.8 - - + +
487D ALA* 3.3 22.9 + - - +
54H A 4.0 17.9 - - - +
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Residues in contact with ALA 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478D ARG* 3.8 13.1 - - + +
480D ASN 3.5 17.5 + - - +
481D ALA* 4.0 4.9 - - - +
482D THR 3.3 0.6 - - - -
483D ALA* 1.3 78.9 - - - +
485D PHE* 1.3 61.1 + - - +
487D ALA* 3.8 3.2 + - - +
488D SER* 3.5 20.1 + - - -
140E ASP* 4.0 21.7 - - - +
141E LEU 4.3 5.4 - - - +
142E ASP* 3.9 18.2 - - + -
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Residues in contact with PHE 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C ASN* 5.8 2.2 - - - -
140C ARG* 4.6 21.8 - - - -
481D ALA 3.1 18.0 + - - +
482D THR* 3.6 6.5 - - - +
483D ALA 3.3 0.2 - - - -
484D ALA* 1.3 77.0 - - - +
486D TYR* 1.3 81.3 + + - +
487D ALA 3.2 0.4 - - - -
488D SER* 2.8 24.8 + - - -
489D ASN* 2.9 36.4 - - - +
140E ASP* 6.6 0.2 - - - -
15G T 4.0 29.6 - + + -
16G T 3.9 22.7 - - + -
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Residues in contact with TYR 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D THR* 2.9 38.6 + - - +
483D ALA* 4.0 9.2 - - - +
484D ALA 3.5 0.4 - - - -
485D PHE* 1.3 95.2 - + - +
487D ALA* 1.3 60.6 + - - +
489D ASN* 3.5 7.1 + - - +
490D TYR* 3.5 19.4 + - - +
53H A 6.2 1.1 - - + -
54H A 4.1 19.7 - + + +
55H C 3.5 77.5 + + + +
56H A 4.7 11.0 + - - -
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Residues in contact with ALA 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478D ARG* 3.5 40.6 - - - +
483D ALA 3.3 12.9 + - - +
484D ALA* 4.1 5.2 - - - +
485D PHE 3.2 0.6 - - - -
486D TYR* 1.3 76.6 - - - +
488D SER* 1.3 63.0 + - - +
489D ASN 3.3 0.2 - - - -
490D TYR* 3.3 21.7 + - - +
492D PHE* 3.5 16.9 - - + -
53H A 4.8 4.3 - - - +
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Residues in contact with SER 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C PRO 3.9 5.9 - - - +
138C ASN* 3.3 44.1 + - - +
140C ARG* 5.9 1.3 - - - -
484D ALA 3.5 11.3 + - - -
485D PHE* 2.8 30.5 + - - -
487D ALA* 1.3 78.1 - - - +
489D ASN* 1.3 60.2 + - - +
490D TYR 3.4 3.7 - - - +
140E ASP* 6.3 4.7 - - - -
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Residues in contact with ASN 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C PRO* 4.9 14.7 - - - +
138C ASN* 4.4 10.7 - - - +
141C MET* 5.9 0.8 - - - +
485D PHE* 2.9 34.3 + - - +
486D TYR* 3.5 8.8 + - - +
487D ALA 3.3 0.6 - - - -
488D SER* 1.3 78.9 + - - +
490D TYR* 1.3 63.3 + - - +
491D GLN* 3.9 2.6 + - - +
439E LYS* 4.5 12.1 + - - +
16G T 3.5 44.6 + - - +
17G T 4.0 21.1 - - + +
55H C 6.4 0.4 - - - +
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Residues in contact with TYR 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C PRO 5.7 0.3 - - - +
486D TYR 3.5 14.2 + - - +
487D ALA* 3.3 19.2 + - - +
488D SER 3.4 4.4 - - - +
489D ASN* 1.3 80.4 - - - +
491D GLN* 1.3 69.5 + - - +
492D PHE* 3.6 38.6 + + + -
437E MET* 3.9 9.8 - - + +
439E LYS* 5.1 18.2 - - - +
51H A 3.6 2.6 - - - +
52H T 3.0 86.7 + + + +
53H A 4.7 11.9 - - + +
54H A 6.2 1.6 - - - -
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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