Contacts of the strand formed by residues 481 - 486 (chain A) in PDB entry 4BUR
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 MET 481 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A HIS* 4.5 2.6 - - - +
456A ASP* 3.1 39.8 + - - +
457A HIS* 4.5 2.8 + - - +
480A SER* 1.3 76.5 - - - +
482A PHE* 1.3 86.3 - - - +
483A TRP* 4.4 2.2 - - + -
493A GLU* 4.5 4.9 - - + +
494A ALA 3.3 15.0 - - - +
495A ILE* 4.6 2.0 - - + +
585A MET* 4.3 30.3 - - + -
589A ARG* 4.0 16.8 - - - +
701A NAD 3.9 58.6 - - + +
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Residues in contact with PHE 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A PHE* 3.9 26.9 - + - -
343A ILE* 5.0 6.3 - - + -
452A VAL* 5.7 2.5 - - + -
454A HIS* 3.4 49.4 - + + +
481A MET* 1.3 84.5 - - - +
483A TRP* 1.3 66.9 - - - +
492A TYR* 4.1 12.3 - + - -
493A GLU* 3.2 5.9 - - - +
494A ALA* 2.8 62.5 + - + +
495A ILE* 4.9 1.8 - - - -
496A GLY 5.1 5.6 - - - -
498A VAL* 4.3 23.6 - - + -
700A NAD 4.6 1.1 - - - -
1612A FAD 3.4 8.3 - - - +
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Residues in contact with TRP 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PRO* 3.9 24.7 - - + -
177A LYS* 3.8 17.3 - - - +
455A HIS* 4.0 18.6 - + + -
456A ASP* 4.5 6.5 - - + -
481A MET* 4.4 2.9 - - + -
482A PHE* 1.3 88.2 - - - +
484A SER* 1.3 66.3 + - - +
485A ASP* 4.1 14.1 + - - -
492A TYR* 3.2 15.3 - - - +
493A GLU* 4.2 4.9 - - + +
700A NAD 3.1 20.6 + - - +
701A NAD 3.4 85.4 - + + +
1612A FAD 3.5 41.5 + + - -
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Residues in contact with SER 484 (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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310A PHE* 4.6 5.0 + - - -
314A GLU* 2.8 29.7 + - - +
340A MET* 5.7 1.2 - - - -
483A TRP* 1.3 83.3 - - - +
485A ASP* 1.3 71.1 + - - +
486A LEU* 4.6 5.5 - - - +
491A GLY* 3.5 0.3 - - - -
492A TYR* 3.0 63.7 + - - +
700A NAD 3.7 6.6 + - - -
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Residues in contact with ASP 485 (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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177A LYS* 3.7 28.7 - - + +
314A GLU* 3.5 14.3 + - - +
317A CYS* 5.3 1.0 - - - +
483A TRP* 4.1 10.8 + - - -
484A SER* 1.3 85.5 + - - +
486A LEU* 1.3 75.2 - - - +
487A GLY 4.0 6.1 - - - +
490A VAL* 3.3 8.0 - - - +
491A GLY* 3.5 14.4 - - - -
492A TYR 4.5 0.2 + - - -
701A NAD 5.5 4.5 - - - +
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Residues in contact with LEU 486 (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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313A SER* 3.6 23.6 - - - +
314A GLU* 3.6 36.3 - - + +
317A CYS* 3.8 17.3 - - - -
340A MET* 4.7 12.1 - - + -
352A THR* 3.6 28.3 - - + -
355A LYS* 4.9 6.1 - - - +
356A VAL* 4.4 10.8 - - + +
358A ARG* 5.8 0.7 + - - -
359A GLU* 4.8 2.4 - - - +
484A SER* 4.6 7.0 - - - +
485A ASP* 1.3 87.6 - - - +
487A GLY* 1.3 63.9 + - - +
489A ASP* 4.3 0.7 + - - +
490A VAL* 3.0 40.1 + - + +
492A TYR* 5.1 4.7 - - + -
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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