Contacts of the helix formed by residues 503 - 511 (chain D) in PDB entry 2UZ1
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 SER 503 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510C ALA* 2.9 21.1 + - - +
511C PHE* 5.1 0.4 - - - -
502D GLY* 1.3 70.0 - - - -
504D TYR* 1.3 57.9 + - - +
505D HIS* 3.1 24.0 + - - -
506D GLY* 3.1 20.0 + - - -
507D VAL* 3.0 27.4 + - - +
541D ASN* 4.8 0.4 - - - -
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Residues in contact with TYR 504 (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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48C ARG* 2.9 36.3 + - - -
511C PHE* 4.1 18.4 - + - -
448D ASP* 3.3 41.6 + - + +
451D VAL* 3.9 4.9 - - + -
452D GLY* 5.2 0.9 - - - -
455D ILE* 3.7 24.8 - - + +
458D PHE* 4.9 0.5 - - - -
472D ILE* 3.4 26.0 - - + -
474D ASN* 3.6 22.4 - - - -
476D GLN* 5.8 1.1 - - - -
499D LEU* 4.8 5.0 + - - +
501D ASN 3.9 13.1 + - - -
502D GLY 4.1 8.7 - - - -
503D SER* 1.3 68.4 - - - +
505D HIS* 1.3 59.9 + - - +
507D VAL* 3.1 8.6 + - - +
508D ALA* 2.9 27.4 + - - +
539D CYS* 4.0 3.4 - - - -
541D ASN* 3.8 11.4 + - - +
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Residues in contact with HIS 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503D SER* 3.1 22.6 + - - -
504D TYR* 1.3 77.4 + - - +
506D GLY* 1.3 63.0 + - - +
508D ALA* 3.3 3.6 + - - +
509D ALA* 2.8 30.5 + - - +
515D GLY* 4.0 8.1 - - - -
516D TYR 3.5 34.5 - - - +
517D HIS* 3.6 31.0 - + + +
539D CYS* 3.9 13.1 - - - +
541D ASN* 3.1 25.1 + - + +
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Residues in contact with GLY 506 (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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506C GLY 4.7 0.3 - - - +
510C ALA* 3.6 13.8 - - - +
503D SER* 3.1 22.7 + - - -
505D HIS* 1.3 77.9 - - - +
507D VAL* 1.3 58.3 + - - +
509D ALA* 3.7 7.1 - - - +
510D ALA* 3.0 28.4 + - - +
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Residues in contact with VAL 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C VAL* 3.8 21.1 - - + +
510C ALA* 3.8 15.3 - - + -
511C PHE* 3.5 35.4 - - + -
455D ILE* 3.7 28.9 - - + -
458D PHE* 5.1 0.2 - - + -
503D SER 3.0 18.6 + - - +
504D TYR* 3.1 8.9 + - - +
506D GLY* 1.3 72.9 - - - +
508D ALA* 1.3 64.6 + - - +
510D ALA* 3.1 15.0 + - - +
511D PHE* 3.2 27.0 + - + -
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Residues in contact with ALA 508 (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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458D PHE* 4.0 27.7 - - + -
504D TYR 2.9 8.9 + - - +
505D HIS 3.3 6.7 + - - +
507D VAL* 1.3 75.1 - - - +
509D ALA* 1.3 62.2 + - - +
511D PHE* 3.0 12.0 + - - +
512D GLY 3.2 0.2 + - - -
513D ALA* 3.0 30.5 + - + +
514D ASP 4.8 1.6 - - - +
539D CYS* 3.4 33.9 - - + -
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Residues in contact with ALA 509 (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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505D HIS 2.8 21.0 + - - +
506D GLY* 3.7 7.6 - - - +
507D VAL 3.2 0.2 - - - -
508D ALA* 1.3 74.0 - - - +
510D ALA* 1.3 57.1 + - - +
512D GLY* 2.9 19.6 + - - -
513D ALA 3.3 14.8 + - - +
515D GLY* 5.0 5.8 - - - +
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Residues in contact with ALA 510 (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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502C GLY* 3.7 1.0 - - - -
503C SER* 2.9 39.4 + - - +
506C GLY* 3.6 9.4 - - - -
507C VAL* 3.5 32.1 - - + +
506D GLY 3.0 17.6 + - - +
507D VAL 3.1 5.6 + - - +
509D ALA* 1.3 76.0 - - - +
511D PHE* 1.3 58.2 + - - +
512D GLY 3.3 0.6 + - - -
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Residues in contact with PHE 511 (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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452C GLY* 5.9 2.0 - - - -
455C ILE* 4.2 17.0 - - + -
501C ASN* 2.8 26.0 + - - -
502C GLY* 4.2 11.0 - - - -
504C TYR* 4.1 22.4 - + - -
507C VAL* 3.6 26.9 - - + -
48D ARG* 4.8 2.0 - - - -
455D ILE 4.0 11.4 - - - -
456D GLY* 4.0 15.0 - - - -
458D PHE* 3.8 18.8 - - + +
459D ASP* 3.5 41.7 - - + +
462D VAL* 3.3 10.6 - - - +
507D VAL* 3.2 30.8 + - + -
508D ALA 3.0 9.6 + - - +
510D ALA* 1.3 78.0 - - - +
512D GLY* 1.3 57.7 + - - +
513D ALA 3.5 0.7 - - - -
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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