Contacts of the strand formed by residues 452 - 459 (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 LYS 452 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A ALA* 2.9 43.6 + - + +
450A ASP* 5.8 0.2 - - - -
451A ASN 4.7 2.2 + - - -
702A SO4 3.0 32.3 + - - -
441B LEU* 3.3 4.6 - - - -
442B GLN* 2.8 47.2 + - + +
451B ASN* 1.3 69.9 - - - +
453B SER* 1.3 74.3 + - - +
454B LEU* 3.5 3.2 + - + -
506B GLY* 3.9 31.9 - - - +
507B LEU* 3.7 37.0 - - + +
515B MET* 4.7 1.8 - - - +
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Residues in contact with SER 453 (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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449A ALA 5.1 3.8 + - - +
450A ASP* 4.8 15.4 + - - -
702A SO4 5.0 4.3 + - - -
439B HIS* 2.8 33.7 + - - -
440B VAL 3.6 5.8 - - - -
441B LEU* 3.9 4.7 - - - -
451B ASN 3.6 3.8 + - - -
452B LYS* 1.3 91.7 - - - +
454B LEU* 1.4 58.8 + - - +
455B GLY* 4.0 5.9 + - - -
456B GLN* 5.8 0.5 - - - +
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Residues in contact with LEU 454 (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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399B LEU* 3.8 29.4 - - + -
440B VAL* 2.8 19.7 + - + +
441B LEU 4.5 0.7 - - - -
442B GLN* 4.0 14.4 - - + +
452B LYS* 4.1 8.1 - - + +
453B SER* 1.4 77.8 - - - +
455B GLY* 1.3 59.1 + - - +
484B LEU* 4.1 17.7 - - + -
501B ILE* 3.9 35.5 - - + +
505B SER* 4.3 8.5 + - - -
506B GLY* 3.5 37.5 - - - +
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Residues in contact with GLY 455 (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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439B HIS* 3.6 5.3 - - - -
440B VAL* 2.9 24.8 + - - +
453B SER* 3.6 5.6 + - - -
454B LEU* 1.3 80.6 - - - +
456B GLN* 1.3 63.6 + - - +
499B ILE* 4.1 15.9 - - - -
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Residues in contact with GLN 456 (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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514A LYS* 3.9 39.3 + - + +
518A ASP* 3.4 25.3 + - - +
437B THR* 3.5 20.6 - - + +
438B ILE 3.1 14.1 - - - +
439B HIS* 4.0 17.7 - - + +
455B GLY* 1.3 76.9 - - - +
457B PHE* 1.3 65.7 + - - +
458B ASN* 5.0 1.2 - - - +
499B ILE* 3.9 9.8 - - - +
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Residues in contact with PHE 457 (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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514A LYS* 4.9 5.6 - - - +
437B THR* 3.6 1.0 - - - +
438B ILE* 2.8 71.6 + - + +
456B GLN* 1.3 75.7 - - - +
458B ASN* 1.3 71.6 + - - +
486B VAL* 3.8 18.2 - - + -
488B ALA* 3.8 17.0 - - + -
497B GLN* 3.4 47.8 - - + +
498B LYS 4.3 1.8 - - - +
499B ILE* 3.5 48.5 - - + -
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Residues in contact with ASN 458 (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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514A LYS* 4.1 21.0 + - - +
435B ALA* 5.4 1.1 - - + -
436B VAL 3.3 6.3 - - - +
437B THR* 2.7 31.9 + - - +
456B GLN* 5.0 1.4 - - - +
457B PHE* 1.3 80.0 - - - +
459B LEU* 1.3 61.6 - - - +
460B ASP* 4.1 3.7 + - + +
497B GLN* 3.5 23.2 + - - +
13C PRO* 3.6 26.2 - - + +
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Residues in contact with LEU 459 (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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435B ALA* 3.2 3.1 - - - -
436B VAL* 2.9 42.7 + - + +
438B ILE* 5.3 1.0 - - + +
457B PHE* 5.2 0.9 - - + -
458B ASN* 1.3 72.5 - - - +
460B ASP* 1.3 67.9 + - - +
462B ILE* 4.2 4.9 - - + +
472B ILE* 3.9 26.7 - - + -
488B ALA* 4.0 15.9 - - + +
490B ASP* 3.9 31.6 - - + +
495B LYS* 3.7 30.3 - - + +
496B GLU 3.8 2.0 - - - -
497B GLN* 3.8 29.6 - - + +
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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