Contacts of the strand formed by residues 478 - 483 (chain A) in PDB entry 1OZ2
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 ARG 478 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A PRO* 5.7 8.6 - - - +
396A TYR* 3.6 12.1 - - - +
447A HIS* 3.0 9.6 + - - -
475A GLU* 2.9 65.7 + - - +
477A HIS* 1.3 79.9 - - + +
479A ILE* 1.3 64.9 + - - +
493A TRP* 3.4 45.7 + - + +
494A ILE* 3.2 14.8 - - - +
495A ASP* 3.3 26.9 - - - +
496A ALA 4.1 1.3 - - - +
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Residues in contact with ILE 479 (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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447A HIS* 3.4 33.2 - - + +
449A PHE* 3.8 24.9 - - + -
455A LEU* 4.2 9.6 - - + -
471A VAL* 4.4 13.9 - - + -
473A ASP 3.7 6.7 - - - +
474A VAL* 4.2 5.2 - - + -
478A ARG* 1.3 71.1 - - - +
480A LYS* 1.3 59.9 + - - +
481A ILE* 3.7 23.1 - - + -
493A TRP* 3.4 6.6 - - - -
494A ILE* 2.9 47.1 + - + +
496A ALA* 4.8 4.0 - - + -
501A ILE* 3.8 24.0 - - + -
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Residues in contact with LYS 480 (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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21A MES 3.1 26.7 + - - -
471A VAL* 3.6 5.7 - - - -
472A GLU* 2.8 45.9 + - + +
473A ASP* 2.9 33.5 + - + +
479A ILE* 1.3 74.0 - - - +
481A ILE* 1.3 59.7 + - - +
491A ASP* 4.2 22.1 + - + +
492A PHE* 3.4 17.0 - - - +
493A TRP* 3.5 37.1 - - + +
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Residues in contact with ILE 481 (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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455A LEU* 4.1 26.5 - - + -
457A ALA* 4.2 4.0 - - + -
469A ALA* 3.9 19.3 - - + -
470A SER 3.6 3.1 - - - +
472A GLU* 4.6 0.4 - - - -
479A ILE* 3.7 26.5 - - + -
480A LYS* 1.3 73.4 - - - +
482A HIS* 1.3 66.2 + - - +
483A PHE* 4.2 8.0 + - + -
490A TYR 4.6 0.2 - - - +
491A ASP* 3.1 9.7 - - - +
492A PHE* 2.8 62.6 + - + +
494A ILE* 3.8 22.2 - - + -
501A ILE* 4.3 9.2 - - + -
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Residues in contact with HIS 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ALA* 3.4 2.1 - - - -
470A SER* 2.8 44.3 + - - +
472A GLU* 3.5 28.5 - - + +
480A LYS 3.9 0.6 + - - -
481A ILE* 1.3 75.4 - - - +
483A PHE* 1.3 77.4 + - - +
484A ASP* 3.5 12.7 + - - -
485A GLY* 4.2 4.2 + - - -
486A TRP 3.0 28.2 + - - -
487A SER 4.5 0.2 - - - -
488A HIS* 3.3 27.6 + + - -
491A ASP* 2.8 24.9 + - - +
526A ALA* 4.9 2.3 - - + +
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Residues in contact with PHE 483 (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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23A MES 3.4 32.1 - - - -
457A ALA* 3.6 28.7 - - + -
458A VAL 3.6 21.1 - - - -
459A ASP* 3.8 13.0 - - - -
460A ARG 4.8 1.1 - - - -
467A ARG* 3.5 25.1 - - + -
468A VAL 3.7 6.7 - - - +
469A ALA* 4.1 5.4 - - + -
481A ILE* 4.2 2.9 - - + -
482A HIS* 1.3 81.5 + - - +
484A ASP* 1.3 66.3 + - - +
485A GLY 3.2 0.5 + - - -
486A TRP* 3.0 40.2 + - + +
487A SER 5.9 0.2 + - - -
490A TYR* 4.8 9.8 - - + +
491A ASP* 4.3 2.2 + - - +
492A PHE* 3.5 27.6 - + - -
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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