Contacts of the strand formed by residues 548 - 554 (chain A) in PDB entry 3U0Z
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 CYS 548 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483A GLU 3.7 0.2 - - - +
484A VAL* 3.5 8.0 - - - +
485A PHE* 3.0 43.2 + - + +
491A ILE* 5.1 2.2 - - + -
504A ILE* 5.7 1.1 - - - -
506A HIS 3.6 1.6 - - - -
507A GLY* 4.1 2.9 - - - -
508A VAL 3.3 36.8 - - - -
509A ALA* 4.6 6.3 - - - -
544A ALA* 4.0 10.5 - - + -
546A THR 3.8 10.1 - - - +
547A TYR* 1.3 74.7 - - - +
549A ARG* 1.3 65.1 + - - +
550A LEU* 3.7 22.5 + - + +
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Residues in contact with ARG 549 (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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426A HIS 5.2 6.7 + - - -
427A ARG 5.8 0.8 + - - -
429A GLN* 4.8 14.8 + - - +
482A PHE* 3.4 31.5 - - + -
483A GLU 3.9 3.4 - - - -
484A VAL* 4.5 12.6 - - + +
505A GLN* 2.4 78.8 + - - +
506A HIS* 2.7 36.1 + - + +
547A TYR* 5.5 4.0 - - + +
548A CYS* 1.3 75.8 - - - +
550A LEU* 1.3 63.4 + - - +
551A TYR* 5.8 0.2 + - - -
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Residues in contact with LEU 550 (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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482A PHE* 3.5 8.1 - - - -
483A GLU* 2.8 39.6 + - + +
485A PHE* 3.5 32.1 - - + -
491A ILE* 4.2 9.9 - - + -
502A TYR* 3.8 21.8 - - + -
503A PHE 3.4 4.7 - - - +
504A ILE* 3.6 35.7 - - + +
505A GLN 4.5 0.2 - - - +
527A PHE* 4.1 17.0 - - + -
548A CYS* 4.2 17.0 - - + +
549A ARG* 1.3 82.7 - - - +
551A TYR* 1.3 65.7 + - - +
552A SER 4.2 0.2 - - - -
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Residues in contact with TYR 551 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455A CYS* 4.9 18.7 - - - -
458A LEU* 5.3 9.4 - - + -
480A LEU* 3.8 38.4 - - + -
481A ARG 3.5 3.6 - - - -
482A PHE* 3.6 50.2 - + + +
502A TYR* 3.3 1.7 - - - -
503A PHE* 2.5 51.3 + - + +
505A GLN* 4.3 34.3 + - + -
549A ARG* 5.8 0.5 + - - -
550A LEU* 1.3 76.0 - - - +
552A SER* 1.3 59.9 + - - +
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Residues in contact with SER 552 (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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479A LYS 3.9 1.2 - - - +
480A LEU* 3.4 8.2 - - - -
481A ARG* 2.9 42.9 + - - +
483A GLU* 2.7 29.6 + - - -
500A LYS* 4.4 10.5 - - - +
501A MET 3.1 10.3 - - - -
502A TYR* 3.6 17.0 - - - -
550A LEU 4.2 0.2 - - - -
551A TYR* 1.3 75.4 - - - +
553A LEU* 1.3 63.0 + - - +
554A SER 4.2 0.6 + - - -
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Residues in contact with LEU 553 (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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476A MET* 3.9 37.2 - - + +
479A LYS* 3.8 26.5 - - + +
480A LEU* 4.2 11.4 - - + -
500A LYS* 4.4 1.6 - - - -
501A MET* 2.8 43.4 + - + +
503A PHE* 4.4 7.4 - - + -
532A LEU* 4.6 1.6 - - - +
552A SER* 1.3 76.8 - - - +
554A SER* 1.3 61.8 + - - +
557A ASN* 3.6 27.1 - - + +
558A PHE* 3.9 32.8 - - + +
561A VAL* 5.8 0.4 - - + -
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Residues in contact with SER 554 (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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479A LYS 5.2 0.8 + - - -
499A LYS 3.5 10.1 - - - -
500A LYS* 4.4 6.3 - - - +
552A SER 4.2 0.4 + - - -
553A LEU* 1.3 76.2 - - - +
555A VAL* 1.3 67.7 + - - +
556A ASP* 3.9 5.2 + - - +
557A ASN* 3.0 29.3 + - - +
558A PHE* 2.9 19.1 + - - +
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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