Contacts of the strand formed by residues 467 - 475 (chain B) in PDB entry 4NPJ
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 ASP 467 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400B LYS 5.2 8.2 - - - +
459B PHE* 3.2 5.6 - - - -
460B ASP* 2.8 44.2 + - + +
462B ASP* 2.8 24.5 - - - +
465B LYS* 3.3 10.7 - - - +
466B ASP* 1.3 72.7 - - - +
468B PHE* 1.3 65.0 + - - +
469B LEU* 4.0 3.8 - - + +
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Residues in contact with PHE 468 (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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375A ILE* 3.8 20.9 - - + -
398B GLN* 4.0 10.4 + - - -
457B GLU* 3.5 27.4 - - + -
458B LEU 3.7 9.9 - - - -
459B PHE* 3.9 15.5 - + + -
465B LYS* 5.9 1.2 - - - +
466B ASP 3.9 1.6 + - - -
467B ASP* 1.3 74.1 - - - +
469B LEU* 1.3 65.5 + - - +
470B GLY* 3.2 42.2 - - - -
471B SER* 3.4 16.2 - - - -
493B GLU* 3.7 26.0 - - + -
494B VAL* 4.2 4.7 - - + +
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Residues in contact with LEU 469 (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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397B LEU* 4.3 18.0 - - + +
398B GLN* 3.9 36.9 + - + +
399B GLY 5.3 1.8 - - - +
412B SER* 4.0 14.1 - - - +
414B PRO* 4.0 20.0 - - + -
458B LEU* 2.8 20.8 + - + +
459B PHE* 3.7 22.9 - - - +
460B ASP* 3.7 20.9 - - + +
467B ASP* 4.4 4.0 - - + +
468B PHE* 1.3 79.8 - - - +
470B GLY* 1.3 57.5 + - - +
491B LEU* 3.8 12.8 - - - +
494B VAL* 3.6 20.9 - - - +
496B LYS 4.6 2.1 - - - +
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Residues in contact with GLY 470 (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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456B ILE 4.9 0.2 - - - -
457B GLU* 3.6 0.2 - - - -
458B LEU* 2.9 30.0 + - - +
468B PHE* 3.2 22.6 - - - -
469B LEU* 1.3 81.2 - - - +
471B SER* 1.3 59.2 + - - -
491B LEU* 4.4 10.0 - - - +
492B ASP 3.5 10.1 - - - -
494B VAL* 3.6 10.4 - - - +
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Residues in contact with SER 471 (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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375A ILE* 3.4 28.8 + - - +
456B ILE 3.2 12.3 - - - -
457B GLU* 4.1 1.3 - - - -
468B PHE* 3.4 3.8 - - - -
470B GLY* 1.3 75.2 - - - -
472B LEU* 1.3 64.8 + - - +
473B MET* 6.4 1.8 - - - -
491B LEU* 3.7 6.8 - - - -
492B ASP* 2.9 34.0 + - - +
493B GLU* 3.4 26.5 - - - +
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Residues in contact with LEU 472 (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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454B LEU 3.6 1.1 - - - +
455B GLU* 3.4 3.8 - - - +
456B ILE* 2.8 43.7 + - + +
471B SER* 1.3 80.8 + - - +
473B MET* 1.3 66.7 + - - +
474B ILE* 3.9 15.0 - - + -
489B PHE* 3.7 42.0 - - + -
490B THR 4.4 11.9 - - - +
491B LEU* 4.6 6.7 - - + -
492B ASP* 4.6 9.0 - - - +
499B LEU* 3.8 25.4 - - + -
501B LEU* 3.8 18.4 - - + -
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Residues in contact with MET 473 (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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375A ILE* 3.9 22.2 - - + +
376A ALA* 4.2 9.4 - - + -
453B GLU* 3.8 39.7 - - + +
454B LEU 3.4 3.6 - - - +
455B GLU* 3.9 25.6 - - + +
471B SER* 6.4 1.3 - - - -
472B LEU* 1.3 79.1 - - - +
474B ILE* 1.3 61.6 + - - +
475B ASP* 4.3 2.6 + - - +
492B ASP* 4.6 8.2 + - - +
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Residues in contact with ILE 474 (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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453B GLU* 3.3 7.6 - - - +
454B LEU* 2.9 52.5 + - + +
456B ILE* 5.6 0.2 - - + -
472B LEU* 3.9 35.0 - - + -
473B MET* 1.3 78.0 - - - +
475B ASP* 1.3 66.7 + - - +
476B LEU 3.3 0.7 + - - -
478B GLU* 5.8 2.5 - - + +
479B VAL* 3.8 26.0 - - + -
485B LEU* 5.3 3.4 - - + -
489B PHE* 4.0 28.3 - - + -
501B LEU* 4.1 12.1 - - + -
503B LEU* 4.5 6.5 - - + -
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Residues in contact with ASP 475 (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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451B GLY* 5.3 6.2 - - - -
452B GLN 4.0 2.6 - - - +
453B GLU* 3.2 22.5 - - - +
473B MET 5.2 2.3 - - - +
474B ILE* 1.3 73.2 - - - +
476B LEU* 1.3 66.9 + - - +
477B ILE* 4.4 12.6 - - + +
478B GLU* 3.2 41.9 + - + +
479B VAL* 3.3 12.5 + - - +
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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