Contacts of the strand formed by residues 467 - 475 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400A LYS* 4.5 18.5 - - - +
459A PHE* 3.2 6.3 - - - -
460A ASP* 2.7 42.1 + - + +
462A ASP* 3.0 23.0 + - - +
465A LYS* 3.5 10.1 - - - +
466A ASP* 1.3 72.6 - - - +
468A PHE* 1.3 64.0 + - - +
469A LEU* 5.1 3.8 - - + -
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Residues in contact with PHE 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A GLN* 5.7 1.7 - - - +
457A GLU* 3.5 27.1 - - + -
458A LEU 3.8 7.4 - - - -
459A PHE* 4.2 12.8 - + + -
466A ASP 3.8 1.6 + - - -
467A ASP* 1.3 71.6 - - - +
469A LEU* 1.3 67.7 + - - +
470A GLY* 3.2 39.3 - - - -
471A SER* 3.5 15.5 - - - -
493A GLU* 3.5 33.2 - - + -
494A VAL* 4.2 6.0 - - + +
375B ILE* 3.7 23.3 - - + -
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Residues in contact with LEU 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A LEU* 4.0 20.4 - - + +
398A GLN* 3.5 35.6 + - + +
412A SER* 5.4 1.8 - - - -
414A PRO* 3.8 25.6 - - + -
434A LEU* 5.7 0.4 - - + -
458A LEU* 2.7 25.8 + - + +
459A PHE 3.6 20.6 - - - +
460A ASP* 3.8 30.7 - - + +
467A ASP* 5.0 4.0 - - + -
468A PHE* 1.3 79.3 - - - +
470A GLY* 1.3 55.8 + - - +
491A LEU* 3.6 16.8 - - - +
494A VAL* 3.4 16.1 - - - +
496A LYS 4.8 1.4 - - - +
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Residues in contact with GLY 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A GLU* 3.7 0.2 - - - -
458A LEU* 2.9 29.5 + - - +
468A PHE* 3.2 21.8 - - - -
469A LEU* 1.3 79.9 - - - +
471A SER* 1.3 59.3 + - - -
491A LEU* 4.1 10.5 - - - -
492A ASP 3.5 4.0 - - - -
494A VAL* 3.5 19.3 - - - +
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Residues in contact with SER 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A ILE 3.2 12.3 - - - -
457A GLU* 4.2 2.7 - - - -
468A PHE* 3.5 5.2 - - - -
470A GLY* 1.3 73.3 - - - -
472A LEU* 1.3 65.7 + - - +
473A MET* 5.3 7.5 - - - +
491A LEU* 3.7 6.9 - - - +
492A ASP* 2.7 53.1 + - - +
493A GLU* 4.1 5.4 - - - +
375B ILE* 3.6 31.2 - - - +
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Residues in contact with LEU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A LEU 3.6 1.2 - - - +
455A GLU* 3.6 1.0 - - - -
456A ILE* 2.9 43.5 + - + +
471A SER* 1.3 80.4 - - - +
473A MET* 1.3 74.6 + - - +
474A ILE* 4.0 20.9 - - + -
489A PHE* 3.5 40.8 - - + -
490A THR 4.2 13.7 - - - +
491A LEU* 4.6 5.8 - - + -
492A ASP* 5.1 4.3 - - + +
499A LEU* 4.1 15.5 - - + -
501A LEU* 4.0 23.6 - - + -
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Residues in contact with MET 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A GLU* 3.5 27.6 - - - +
454A LEU 3.4 5.2 - - - -
455A GLU* 3.4 39.7 - - - +
471A SER* 5.3 7.6 - - - +
472A LEU* 1.3 87.1 - - - +
474A ILE* 1.3 67.1 + - - +
475A ASP 4.1 0.9 + - - -
492A ASP* 6.1 2.0 - - + +
375B ILE* 4.7 11.9 - - - +
376B ALA* 4.6 13.2 - - + -
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Residues in contact with ILE 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A GLU* 3.1 6.9 - - - -
454A LEU* 2.7 57.7 + - + +
456A ILE* 6.0 0.7 - - + -
472A LEU* 4.0 23.8 - - + -
473A MET* 1.3 81.7 - - - +
475A ASP* 1.3 65.1 + - - +
476A LEU 3.5 0.2 + - - -
478A GLU* 5.1 7.2 - - - +
479A VAL* 3.7 28.9 - - + -
485A LEU* 5.5 2.5 - - + -
489A PHE* 3.7 40.2 - - + -
501A LEU* 5.5 1.6 - - + -
503A LEU* 4.8 8.1 - - + -
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Residues in contact with ASP 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A GLY* 4.9 6.4 - - - -
452A GLN 3.8 8.0 + - - +
453A GLU* 4.2 15.4 - - + +
473A MET 4.1 1.6 + - - -
474A ILE* 1.3 73.6 - - - +
476A LEU* 1.3 64.3 + - - +
477A ILE* 2.9 38.2 - - - +
478A GLU* 3.2 32.2 + - - +
479A VAL* 3.2 20.4 + - - +
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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