Contacts of the strand formed by residues 460 - 464 (chain B) in PDB entry 3H8E
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 TRP 460 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B LEU* 3.9 21.4 - - + +
371B VAL* 3.1 14.8 - - + +
373B ASP* 3.5 14.8 + - - -
394B GLY* 3.2 9.1 - - - -
395B ASN* 2.8 56.3 + - + +
396B ASN* 4.0 3.0 + - - +
399B LEU* 3.7 7.0 - - - +
419B LEU* 3.9 17.3 - - + -
448B GLY* 3.5 21.1 - - - -
451B LEU* 3.7 20.9 - - + -
452B SER* 3.5 24.0 - - - -
455B ALA* 3.4 32.1 - - + -
458B TYR* 3.8 6.5 - - + -
459B ASN* 1.4 75.0 - - - +
461B ALA* 1.3 83.5 + - - +
462B HIS* 3.5 23.6 - - + -
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Residues in contact with ALA 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B VAL 2.9 6.4 + - - +
372B ILE* 3.2 8.0 - - + -
373B ASP* 2.8 32.3 + - - +
392B LEU* 4.1 6.7 - - + -
393B MET 3.2 12.6 - - - +
394B GLY* 3.9 2.7 - - - -
399B LEU* 3.8 9.8 - - + +
400B VAL* 4.5 4.3 - - + -
403B LEU* 3.6 31.4 - - + -
460B TRP* 1.3 84.1 + - - +
462B HIS* 1.3 55.1 - - - +
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Residues in contact with HIS 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ASP* 2.5 33.7 - - - +
375B ALA* 4.6 3.9 - - + +
377B LEU* 3.7 23.0 - - + +
391B GLY 3.6 0.5 - - - +
392B LEU* 3.3 5.9 - - - +
393B MET* 2.8 70.5 + - + +
444B THR 4.9 0.9 - - - -
447B ALA* 5.1 0.4 - - + -
448B GLY* 4.0 7.2 - - - -
451B LEU* 3.4 19.5 - - + +
460B TRP* 3.5 20.0 - - + -
461B ALA* 1.3 71.5 - - - +
463B MET* 1.3 75.1 + - - +
464B ASP* 4.2 19.7 - - + -
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Residues in contact with MET 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ILE* 3.8 14.8 - - + -
373B ASP 2.8 14.2 + - - +
374B ILE* 3.5 10.7 - - + -
375B ALA 2.9 27.9 + - - +
390B THR* 3.9 22.2 - - + +
391B GLY 3.3 3.4 - - - -
392B LEU* 3.7 19.3 - - + -
403B LEU* 4.8 5.6 - - - -
414B ALA* 5.4 1.1 - - + -
462B HIS* 1.3 80.9 + - - +
464B ASP* 1.3 60.8 + - - +
465B ILE* 3.6 10.4 + - + +
483B PRO* 5.3 5.6 - - + +
486B LEU* 4.0 36.6 - - + -
487B LEU* 3.8 29.8 - - + -
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Residues in contact with ASP 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B ALA 3.3 2.7 - - - -
377B LEU* 3.0 27.1 + - - +
378B THR* 2.6 39.7 + - - +
381B CYS* 3.5 26.0 - - - +
390B THR* 3.6 3.6 - - - +
391B GLY* 2.9 32.6 + - - +
393B MET* 5.6 0.4 - - + -
444B THR* 3.6 11.1 - - + +
462B HIS* 4.1 15.7 + - + -
463B MET* 1.3 69.1 - - - +
465B ILE* 1.3 58.8 + - - +
466B ALA* 3.2 12.1 + - - +
467B GLY 5.0 0.9 + - - -
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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