Contacts of the strand formed by residues 472 - 476 (chain A) in PDB entry 1U8C
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 472 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A PRO* 4.3 4.7 - - - +
454A LEU* 4.3 3.1 - - - +
460A THR 4.4 1.8 + - - +
461A CYS* 2.0 55.4 - - + -
470A VAL* 3.2 20.2 + - - -
471A SER* 1.3 81.6 + - - +
473A PHE* 1.3 67.5 + - - +
474A ASN* 5.1 0.4 - - - +
514A LEU* 3.4 17.9 - - - -
539A ILE* 4.2 9.4 - - + -
540A ALA 3.1 10.5 - - - +
541A TYR* 3.7 2.7 - - - +
2458A NAG 4.8 10.2 + - + +
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Residues in contact with PHE 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A VAL* 3.3 26.7 - - + -
450A TYR* 5.6 0.2 - - - -
451A PRO* 3.1 25.6 - - + -
454A LEU* 3.3 40.2 - - + -
471A SER 4.8 0.7 - - - -
472A CYS* 1.3 79.9 - - - +
474A ASN* 1.3 62.4 + - - +
475A VAL* 3.8 15.7 - - + -
499A LEU* 4.2 7.0 - - + -
511A ALA* 4.3 9.2 - - + -
539A ILE* 3.8 0.2 - - - -
540A ALA* 2.6 73.5 + - + +
541A TYR 4.2 11.4 - - - -
555A ILE* 5.6 1.6 - - + -
557A ILE* 4.2 20.6 - - + -
2458A NAG 5.3 1.1 - - - -
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Residues in contact with ASN 474 (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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449A VAL* 3.1 9.4 - - - +
450A TYR* 2.4 70.2 + - + +
472A CYS* 5.1 0.5 - - - +
473A PHE* 1.3 76.9 + - - +
475A VAL* 1.3 64.2 + - - +
537A GLU* 3.5 23.3 + - - +
538A LEU 2.7 18.9 + - - -
539A ILE* 2.9 38.1 - - - +
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Residues in contact with VAL 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LEU* 3.6 26.9 - - + -
448A GLU 3.5 4.3 - - - +
449A VAL* 4.6 1.1 - - + +
473A PHE* 3.8 22.0 - - + -
474A ASN* 1.3 79.9 - - - +
476A ARG* 1.3 62.7 + - - +
477A PHE* 4.0 3.8 - - + -
497A LEU* 3.7 20.2 - - + -
499A LEU* 5.0 0.7 - - + -
513A PHE* 4.4 18.8 - - + -
536A GLU 4.3 0.4 - - - +
537A GLU* 3.6 6.9 - - - +
538A LEU* 3.0 41.4 + - + +
540A ALA* 4.6 4.5 - - + -
557A ILE* 4.1 14.6 - - + -
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Residues in contact with ARG 476 (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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446A GLY 4.2 0.2 - - - -
447A LEU* 3.6 3.8 + - - -
448A GLU* 2.8 39.3 + - + +
450A TYR* 6.2 4.6 - - + +
475A VAL* 1.3 75.5 - - - +
477A PHE* 1.3 58.8 + - - +
478A CYS* 3.6 4.2 + - + +
535A CYS* 3.9 36.7 - - + +
536A GLU 4.0 4.0 - - - +
537A GLU* 4.2 26.4 + - + +
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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
------------------------------------------------------------
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