Contacts of the strand formed by residues 458 - 466 (chain B) in PDB entry 5N4D
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 PHE 458 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B ASN* 3.1 27.1 + - + -
453B LEU* 3.7 20.2 - - + -
454B ASP 3.4 22.7 - - - -
455B PRO 3.2 10.5 + - - +
456B ASP* 3.1 2.6 - - - +
457B ASP* 1.3 85.9 - - + +
459B GLU* 1.3 60.4 + - - +
478B VAL* 4.6 4.5 - - + -
479B ARG 3.3 7.9 - - - +
480B HIS* 3.7 33.9 - + + -
481B LYS* 3.8 11.0 + - - -
512B LEU* 3.3 62.4 - - + -
515B LEU* 4.2 3.6 - - + -
516B GLN* 3.5 24.5 - - + -
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Residues in contact with GLU 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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424B ASN* 4.4 2.0 - - - +
458B PHE* 1.3 74.7 - - - +
460B SER* 1.3 64.0 + - - +
461B THR* 3.6 26.7 + - + +
477B ILE 3.7 1.6 - - - +
478B VAL* 3.3 5.4 - - - +
479B ARG* 2.9 78.5 + - + +
481B LYS* 4.0 23.0 - - + +
485B PHE* 4.9 2.1 - - - -
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Residues in contact with SER 460 (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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402B VAL* 5.2 10.0 - - - +
423B PHE* 3.8 36.7 - - - +
424B ASN* 4.2 13.1 + - - +
459B GLU* 1.3 76.2 - - - +
461B THR* 1.3 69.5 + - - +
476B PHE* 5.6 3.1 - - - -
477B ILE 3.3 8.7 - - - -
478B VAL* 3.9 6.7 - - - -
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Residues in contact with THR 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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459B GLU* 3.6 29.2 + - + +
460B SER* 1.3 80.0 - - - +
462B GLN* 1.3 61.6 + - - +
463B VAL* 4.2 10.7 - - - +
475B MET 3.8 0.2 - - - +
476B PHE* 3.3 9.6 - - - +
477B ILE* 2.8 42.8 + - - +
485B PHE* 5.0 9.4 - - + -
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Residues in contact with GLN 462 (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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379B ASN* 2.9 33.2 + - - +
380B VAL* 4.1 3.4 - - - +
381B LYS* 2.5 31.9 + - + +
461B THR* 1.3 76.9 - - - +
463B VAL* 1.3 65.3 + - - +
464B TRP* 4.5 16.4 + - - +
474B PRO* 3.6 31.2 - - + +
475B MET 3.3 12.0 - - - +
476B PHE* 3.6 24.8 - - + -
526B SER* 5.1 0.4 + - - -
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Residues in contact with VAL 463 (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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461B THR* 4.3 14.4 - - - +
462B GLN* 1.3 78.3 - - - +
464B TRP* 1.3 62.9 + - - +
474B PRO* 3.2 2.9 - - - +
475B MET* 2.7 51.4 + - + +
477B ILE* 3.9 17.3 - - + -
559B PHE* 3.8 28.0 - - + -
565B TYR* 3.6 27.4 - - + +
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Residues in contact with TRP 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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379B ASN* 3.5 28.7 - - + -
462B GLN* 4.5 17.2 + - - +
463B VAL* 1.3 82.8 - - - +
465B TYR* 1.3 60.0 + - - +
472B LYS* 3.9 26.7 - - + -
473B ILE 3.4 12.1 - - - -
474B PRO* 3.5 46.1 - - + +
533B PHE* 4.0 11.4 - + - -
559B PHE* 3.8 16.0 - - - -
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Residues in contact with TYR 465 (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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464B TRP* 1.3 73.0 - - - +
466B GLU* 1.3 71.9 + - - +
467B SER 4.6 0.2 - - - -
472B LYS* 3.4 8.3 - - - -
473B ILE* 2.9 76.4 + - + +
475B MET* 3.9 23.8 - - + -
525B PRO* 3.5 20.3 - - + +
527B ILE* 3.7 1.6 - - - +
552B ASP* 2.7 33.2 + - - +
555B ALA* 3.8 11.0 - - + -
556B ALA* 3.5 25.1 - - + -
559B PHE* 3.4 35.0 - + + -
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Residues in contact with GLU 466 (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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465B TYR* 1.3 84.4 - - - +
467B SER* 1.3 72.1 + - - +
468B LYS 5.6 0.2 - - - +
470B GLY* 3.4 30.2 + - - +
471B THR 3.4 3.8 - - - +
472B LYS* 2.8 28.2 + - - +
555B ALA* 4.0 6.8 - - - +
559B PHE* 5.2 1.2 - - - -
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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