Contacts of the strand formed by residues 484 - 490 (chain B) in PDB entry 4JWE
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 484 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399B LEU* 4.4 12.3 - - + -
440B VAL* 4.1 5.6 - - + -
454B LEU* 4.1 20.2 - - + -
476B PHE* 3.9 24.5 - - + -
477B ASP 3.4 13.9 - - - +
478B ILE* 3.8 22.9 - - + +
482B GLY 3.6 3.6 + - - +
483B ILE* 1.3 71.6 - - - +
485B HIS* 1.3 66.1 + - - +
486B VAL* 3.7 21.3 + - + -
499B ILE 4.0 0.7 - - - +
500B THR* 3.6 2.3 - - - -
501B ILE* 2.7 63.7 + - + +
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Residues in contact with HIS 485 (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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475B THR* 3.4 3.6 - - - +
476B PHE* 3.5 1.7 - - - -
477B ASP* 2.7 57.1 + - + +
479B ASP* 3.3 24.3 + - + +
483B ILE* 3.6 31.7 - - + +
484B LEU* 1.3 71.4 - - - +
486B VAL* 1.3 61.1 + - - +
498B LYS* 6.3 0.8 - - - +
499B ILE 3.7 4.5 - - - +
500B THR* 3.8 20.0 + - + +
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Residues in contact with VAL 486 (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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438B ILE* 4.2 6.3 - - + -
440B VAL* 4.0 18.4 - - + -
457B PHE* 3.8 21.6 - - + -
474B VAL* 4.3 4.3 - - + -
475B THR 3.3 4.3 - - - +
476B PHE* 3.7 30.7 - - + -
484B LEU* 3.7 31.2 - - + -
485B HIS* 1.3 76.1 - - - +
487B SER* 1.3 61.4 + - - +
498B LYS* 3.2 4.3 - - - +
499B ILE* 2.9 43.2 + - + -
501B ILE* 4.3 4.9 - - + -
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Residues in contact with SER 487 (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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457B PHE* 4.1 3.4 - - - -
473B GLU 4.3 1.2 + - - -
474B VAL* 3.3 7.3 - - - +
475B THR* 2.9 50.1 + - - +
485B HIS 4.2 0.6 - - - -
486B VAL* 1.3 75.0 - - - +
488B ALA* 1.3 61.3 + - - +
489B LYS* 6.3 0.2 - - - -
496B GLU* 3.7 23.8 + - - -
497B GLN 3.4 7.6 - - - -
498B LYS* 4.0 8.1 - - - -
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Residues in contact with ALA 488 (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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438B ILE* 3.8 23.8 - - + -
457B PHE* 3.8 20.2 - - + -
459B LEU* 4.0 12.0 - - + +
472B ILE* 4.1 11.9 - - + -
473B GLU 3.3 6.1 - - - -
474B VAL* 4.1 3.4 - - + -
487B SER* 1.3 74.4 - - - +
489B LYS* 1.3 58.9 + - - +
496B GLU* 3.3 6.5 - - - +
497B GLN 2.9 30.9 + - - -
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Residues in contact with LYS 489 (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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459B LEU* 4.2 3.4 - - - -
471B GLN 3.5 1.0 - - - +
472B ILE* 3.4 2.0 - - - +
473B GLU* 2.8 46.7 + - + +
488B ALA* 1.3 74.6 - - - +
490B ASP* 1.3 69.2 + - - +
491B LYS* 3.6 7.5 + - + +
494B GLY* 2.8 37.7 + - - -
495B LYS 3.4 9.4 - - - +
496B GLU* 4.0 26.2 + - + +
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Residues in contact with ASP 490 (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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459B LEU* 3.9 9.7 - - + +
460B ASP 5.8 0.2 - - - +
462B ILE* 3.6 36.2 - - + +
463B ASN 4.6 0.9 + - - -
470B PRO* 5.4 1.9 - - - +
471B GLN 3.5 8.8 + - - +
472B ILE* 3.7 17.9 - - + -
489B LYS* 1.3 72.1 - - - +
491B LYS* 1.3 55.8 + - - +
492B ASN* 2.9 22.0 + - - +
493B SER* 3.1 27.1 + - - +
494B GLY* 2.8 35.3 + - - -
495B LYS* 3.0 10.6 + - + +
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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