Contacts of the strand formed by residues 493 - 499 (chain B) in PDB entry 4P3N
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 SER 493 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491B GLY 4.1 1.2 + - - -
492B PHE* 1.3 74.3 - - - +
494B PHE* 1.3 61.4 + - - +
548B ILE* 3.7 1.0 - - - -
549B LYS* 2.8 65.0 + - - +
555B TYR* 5.1 2.8 + - - -
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Residues in contact with PHE 494 (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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483B LEU* 5.2 5.4 - - + -
484B ARG* 4.0 48.7 - - + -
487B TYR* 3.9 19.1 - + + -
488B SER* 5.5 1.6 - - - -
492B PHE 4.2 10.3 - - - -
493B SER* 1.3 78.4 - - - +
495B LYS* 1.3 63.5 + - - +
496B LEU* 4.3 17.7 - - + -
526B PHE* 4.2 21.5 - + - -
528B GLU* 4.8 12.4 - - + +
546B ILE* 3.9 18.8 - - + -
547B GLN 3.1 14.8 - - - +
548B ILE* 3.6 12.1 - - + -
555B TYR* 5.2 2.9 - - - -
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Residues in contact with LYS 495 (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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494B PHE* 1.3 75.4 - - - +
496B LEU* 1.3 67.2 + - - +
497B ASN* 5.6 1.8 + - - +
528B GLU* 5.5 1.6 - - - -
529B LYS 5.4 4.7 - - - +
545B ASP 3.8 0.5 - - - +
546B ILE* 3.4 5.4 - - - +
547B GLN* 2.5 67.3 + - + +
555B TYR* 3.6 48.7 - - + +
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Residues in contact with LEU 496 (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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480B LEU* 4.1 18.4 - - + -
483B LEU* 4.7 0.7 - - + -
494B PHE* 4.3 17.3 - - + -
495B LYS* 1.3 78.1 - - - +
497B ASN* 1.3 63.0 + - - +
523B LEU* 3.9 22.7 - - + +
526B PHE* 4.0 15.5 - - + -
528B GLU* 3.6 34.8 - - + +
529B LYS 4.6 4.3 + - - +
530B TRP* 3.5 14.5 - - + -
531B GLU* 3.1 21.9 + - - +
544B ILE* 4.6 4.7 - - + -
545B ASP 3.4 3.8 - - - +
546B ILE* 3.5 28.5 - - + -
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Residues in contact with ASN 497 (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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495B LYS* 5.6 1.5 + - - +
496B LEU* 1.3 78.0 - - - +
498B LEU* 1.3 58.4 + - - +
499B SER* 3.6 16.6 + - - +
523B LEU* 5.5 1.1 - - - -
530B TRP* 5.1 1.1 - - - -
531B GLU* 3.1 19.5 - - + +
533B ASN* 3.6 22.8 + - - +
544B ILE* 3.5 5.6 - - - +
545B ASP* 3.0 53.7 + - - +
547B GLN* 5.5 5.7 - - - +
557B GLN* 4.9 1.7 - - - +
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Residues in contact with LEU 498 (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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497B ASN* 1.3 71.2 - - - +
499B SER* 1.3 69.2 + - - +
500B THR* 4.0 18.8 - - + -
516B GLU* 4.7 2.2 - - + +
519B LEU* 4.1 30.3 - - + -
520B GLU* 3.9 21.1 - - + +
523B LEU* 3.6 20.4 - - + -
530B TRP* 3.6 33.6 - - + -
531B GLU 2.7 8.9 + - - -
532B LEU* 3.3 6.7 - - + +
533B ASN 2.7 33.1 + - - +
542B PRO* 4.9 0.7 - - + -
543B LYS 3.4 17.5 - - - +
544B ILE* 4.4 3.4 - - + +
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Residues in contact with SER 499 (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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497B ASN* 3.6 15.6 + - - -
498B LEU* 1.3 72.5 + - - +
500B THR* 1.3 61.6 + - - +
533B ASN* 3.4 8.5 + - - +
536B ASP* 3.6 17.2 + - - +
537B GLY* 3.6 18.2 - - - -
542B PRO* 3.5 5.2 - - - +
543B LYS* 2.9 59.9 + - - +
545B ASP* 4.3 0.3 + - - -
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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