Contacts of the strand formed by residues 538 - 543 (chain C) 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 ALA 538 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458C PHE* 3.8 7.8 - - - -
468C LEU 3.1 7.7 + - - +
469C ILE* 4.5 9.6 - - + -
470C VAL* 2.8 33.3 + - - +
513C ALA* 4.7 0.9 - - - +
514C ASP* 3.2 13.5 - - + +
516C TYR* 4.0 19.5 - - + -
531C ALA* 4.1 19.1 - - + -
536C ARG 3.6 5.3 + - - +
537C PRO* 1.3 76.0 - - - +
539C CYS* 1.3 58.6 - - - +
540C ILE* 4.2 0.4 - - + -
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Residues in contact with CYS 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458C PHE* 3.5 16.2 - - + -
470C VAL 3.3 4.9 - - - -
472C ILE* 3.5 32.3 - - - -
504C TYR 3.9 14.8 - - - -
505C HIS* 4.1 9.4 - - - -
508C ALA* 3.3 25.8 - - + -
514C ASP 2.7 9.9 + - - +
515C GLY* 3.4 0.5 - - - -
516C TYR* 2.8 35.1 + - - +
538C ALA* 1.3 73.4 - - - +
540C ILE* 1.3 61.9 + - - +
541C ASN 4.5 0.7 - - - -
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Residues in contact with ILE 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469C ILE* 4.1 16.8 - - + -
470C VAL 2.8 11.4 + - - +
471C ILE* 3.5 9.4 - - + -
472C ILE 2.8 31.1 + - - +
516C TYR* 3.6 22.2 - - + -
518C VAL* 3.9 10.1 - - + -
524C PHE* 3.9 13.9 - - + -
527C ALA* 4.0 13.2 - - + +
528C LEU* 3.7 46.4 - - + +
531C ALA* 4.2 4.3 - - + -
538C ALA* 5.0 0.2 - - + -
539C CYS* 1.3 76.2 - - - +
541C ASN* 1.3 58.0 + - - +
542C VAL* 3.5 20.4 + - + +
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Residues in contact with ASN 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472C ILE* 3.9 12.3 + - - +
474C ASN* 3.0 42.9 + - - +
502C GLY 5.0 0.7 - - - +
503C SER* 4.8 1.0 - - - -
504C TYR* 3.8 17.6 + - + -
505C HIS* 3.1 37.2 + - + +
516C TYR 2.8 16.8 + - - +
517C HIS* 3.2 15.1 + - - +
518C VAL* 2.9 28.1 + - - +
539C CYS* 3.9 3.5 - - - -
540C ILE* 1.3 70.5 - - - +
542C VAL* 1.3 57.9 + - - +
543C ALA 4.0 0.2 - - - -
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Residues in contact with VAL 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C LEU* 3.6 31.6 - - + -
471C ILE* 3.7 19.3 - - + -
472C ILE 2.8 15.8 + - - +
473C MET* 4.1 7.9 - - - -
474C ASN* 2.8 30.6 + - - -
518C VAL* 3.6 18.8 - - + +
524C PHE* 3.7 23.8 - - + -
540C ILE* 3.7 13.0 - - + +
541C ASN* 1.3 73.7 - - - +
543C ALA* 1.3 62.1 + - - +
544C VAL* 3.2 11.8 + - + +
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Residues in contact with ALA 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369C ALA* 5.6 0.6 - - - +
370C LEU* 3.5 22.5 + - - +
474C ASN* 3.6 11.0 - - + +
517C HIS* 4.7 13.1 - - + -
518C VAL 2.9 17.1 + - - +
519C ASP* 4.0 19.8 - - + +
541C ASN 3.9 1.2 + - - -
542C VAL* 1.3 70.4 - - - +
544C VAL* 1.3 59.6 + - - +
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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