Contacts of the strand formed by residues 481 - 487 (chain A) in PDB entry 3HS0
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 LEU 481 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A ASN* 4.7 12.8 - - + +
442A PHE 3.5 4.3 - - - -
443A ASN* 3.2 26.9 - - - +
479A GLN* 3.0 12.2 - - - +
480A ASN* 1.3 81.8 - - + +
482A VAL* 1.3 65.0 + - - +
483A THR* 4.3 16.6 + - - +
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Residues in contact with VAL 482 (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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441A ASN* 3.5 1.6 - - - -
442A PHE* 2.8 47.9 + - + +
457A PHE* 4.1 14.6 - - + -
473A GLN* 3.9 16.6 - - + +
474A PRO 3.7 20.0 - - - +
475A ARG* 3.9 17.7 - - + -
479A GLN* 3.6 32.5 - - - +
481A LEU* 1.3 80.2 - - - +
483A THR* 1.3 66.8 + - - +
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Residues in contact with THR 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A PRO* 4.6 10.5 - - + -
440A VAL 3.1 11.7 - - - +
441A ASN* 2.7 21.3 + - - +
473A GLN* 4.1 10.8 - - - +
481A LEU* 4.3 10.6 + - - +
482A VAL* 1.3 78.0 - - - +
484A MET* 1.3 74.9 + - - +
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Residues in contact with MET 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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438A LEU 3.3 1.0 - - - +
439A PRO* 3.7 3.3 - - - +
440A VAL* 2.8 43.8 + - + +
442A PHE* 3.4 20.2 - - + -
459A TYR* 3.6 34.5 - - + -
473A GLN* 3.8 26.0 - - - +
482A VAL 4.2 0.2 + - - -
483A THR* 1.3 80.6 - - - +
485A ASN* 1.3 74.5 + - - +
486A LEU* 5.5 4.5 - - + -
498A PHE* 3.4 38.8 - - + -
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Residues in contact with ASN 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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437A ASN* 3.0 51.7 + - - +
438A LEU 3.5 4.1 + - - +
439A PRO* 4.7 2.1 - - + +
484A MET* 1.3 84.4 - - - +
486A LEU* 1.3 65.1 + - - +
487A HIS* 4.0 5.5 + - - +
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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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427A ILE* 6.0 0.4 - - + -
437A ASN* 3.6 0.3 - - - -
438A LEU* 2.8 48.5 + - + +
440A VAL* 4.2 10.5 - - + -
459A TYR* 5.6 5.8 - - + +
461A ILE* 3.8 27.4 - - + -
469A LYS* 4.1 25.1 - - - +
484A MET* 5.4 4.5 - - + -
485A ASN* 1.3 76.4 - - - +
487A HIS* 1.3 74.9 + - - +
488A ILE* 3.5 10.8 + - + +
492A LEU* 5.2 6.1 - - + -
496A PHE* 4.1 23.3 - - + -
498A PHE* 4.3 12.8 - - + -
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Residues in contact with HIS 487 (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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435A GLY* 4.2 18.6 - - - -
436A ASP 3.8 3.0 + - - -
437A ASN* 3.2 25.9 + - - +
469A LYS* 4.7 8.0 + - - +
485A ASN* 4.0 6.5 + - - +
486A LEU* 1.3 82.4 - - - +
488A ILE* 1.3 71.7 + - - +
489A THR* 3.5 33.6 + - + +
492A LEU* 5.0 2.9 - - - +
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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