Contacts of the helix formed by residues 474 - 492 (chain A) in PDB entry 5NP1
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 474 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433A SER 5.4 6.7 - - - -
436A LEU* 5.5 9.0 - - - -
437A MET* 6.0 5.6 - - - -
472A LEU* 3.1 6.5 - - - +
473A GLU* 1.3 76.5 - - - +
475A SER* 1.3 52.3 + - - +
476A GLN 2.7 17.3 + - - -
477A LYS* 2.7 23.6 + - - +
478A SER* 3.2 7.3 + - - -
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Residues in contact with SER 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A LEU* 6.5 0.9 - - - -
468A LYS 3.7 6.3 - - - -
469A ARG 2.8 17.8 - - - +
470A SER 3.2 25.4 - - - -
471A ASN 3.5 5.6 - - - -
472A LEU* 3.3 23.3 - - - +
473A GLU 3.4 0.4 - - - -
474A SER* 1.3 77.2 - - - +
476A GLN* 1.3 49.2 - - - +
478A SER* 3.1 10.8 - - - -
479A ASP 2.1 36.7 + - - -
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Residues in contact with GLN 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A SER 4.6 1.7 + - - -
472A LEU 3.9 4.8 + - - +
473A GLU 3.7 14.9 + - - +
474A SER 2.7 0.6 + - - -
475A SER* 1.3 74.4 - - - +
477A LYS* 1.3 54.8 + - - +
479A ASP* 3.2 9.1 - - - +
480A LEU* 2.1 42.4 + - - +
520A ASP* 4.6 14.9 - - + +
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Residues in contact with LYS 477 (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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440A SER* 5.1 4.9 - - - -
473A GLU 4.7 0.2 + - - -
474A SER* 2.7 17.5 + - - +
476A GLN* 1.3 75.0 - - - +
478A SER* 1.3 52.4 + - - +
480A LEU* 3.3 8.8 - - - +
481A LEU* 2.5 37.2 + - - +
520A ASP* 5.2 1.7 - - - +
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Residues in contact with SER 478 (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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436A LEU* 5.9 5.4 - - - -
440A SER* 4.2 21.5 - - - +
468A LYS* 5.4 4.9 - - - -
469A ARG* 4.3 11.4 - - - -
474A SER 3.2 2.7 + - - -
475A SER* 3.1 18.6 + - - -
477A LYS* 1.3 77.1 - - - +
479A ASP* 1.3 51.2 - - - +
481A LEU* 2.9 9.8 + - - +
482A LYS* 2.2 40.5 + - - +
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Residues in contact with ASP 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ARG* 3.1 18.7 + - + +
470A SER* 5.2 1.6 - - - +
475A SER 2.1 31.8 + - - +
476A GLN* 2.8 11.7 + - - +
478A SER* 1.3 65.0 - - - +
480A LEU* 1.3 52.8 + - - +
482A LYS* 2.7 9.9 + - - -
483A LEU* 2.1 43.2 + - + +
524A TRP* 5.2 5.2 - - + -
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Residues in contact with LEU 480 (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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476A GLN 2.1 30.2 + - - +
477A LYS* 3.3 10.1 - - - +
479A ASP* 1.3 65.2 - - - +
481A LEU* 1.3 52.0 + - - +
483A LEU* 3.2 8.2 - - - +
484A TRP* 2.3 40.2 + - - +
520A ASP* 4.0 23.3 - - + +
523A PHE* 5.2 7.2 - - + -
524A TRP* 4.6 6.6 - - - +
527A PHE* 4.9 0.5 - - - +
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Residues in contact with LEU 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A SER* 3.8 23.1 - - - +
443A LEU* 4.0 13.2 - - + +
444A PRO* 4.5 11.2 - - + -
477A LYS 2.5 17.6 + - - +
478A SER* 3.1 10.8 - - - +
480A LEU* 1.3 71.6 - - - +
482A LYS* 1.3 51.5 + - - +
484A TRP* 2.8 8.7 + - - +
485A ASN* 2.1 42.8 + - - +
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Residues in contact with LYS 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LEU* 5.5 0.6 - - - +
465A CYS* 4.9 13.7 - - + -
469A ARG* 3.4 26.5 - - + -
478A SER 2.2 28.2 + - - +
479A ASP* 2.7 7.4 + - - +
481A LEU* 1.3 65.2 - - - +
483A LEU* 1.3 51.9 + - - +
485A ASN* 3.1 9.5 - - - +
486A LYS* 2.2 41.4 + - - +
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Residues in contact with LEU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A ASP* 2.1 31.3 + - + +
480A LEU 3.3 3.6 - - - +
482A LYS* 1.3 65.5 - - - +
484A TRP* 1.3 50.6 + - - +
486A LYS* 3.1 5.4 + - - -
487A ILE* 2.5 33.4 + - - +
524A TRP* 3.6 26.0 - - + +
527A PHE* 2.8 36.7 - - + +
528A THR* 4.1 3.1 - - - +
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Residues in contact with TRP 484 (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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444A PRO* 5.4 10.3 - - + -
447A ARG* 5.3 3.1 - - + -
480A LEU 2.3 29.7 + - - +
481A LEU* 2.8 12.5 + - - +
483A LEU* 1.3 67.3 - - - +
485A ASN* 1.3 51.2 + - - +
487A ILE* 2.8 11.2 + - - +
488A TRP* 2.3 38.5 + - - +
527A PHE* 4.0 4.1 - - - +
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Residues in contact with ASN 485 (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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443A LEU* 5.4 11.4 - - + +
444A PRO* 6.1 0.4 - - - +
447A ARG* 4.7 6.6 - - + +
461A GLU* 6.5 1.1 - - + -
465A CYS* 6.3 2.2 - - + -
481A LEU 2.1 31.7 + - - +
482A LYS* 3.2 11.4 - - - +
484A TRP* 1.3 65.0 - - - +
486A LYS* 1.3 51.2 + - - +
488A TRP* 2.8 13.0 + - + +
489A CYS* 2.4 36.9 + - - +
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Residues in contact with LYS 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A LYS 2.2 28.6 + - - +
483A LEU* 3.1 12.6 - - - +
485A ASN* 1.3 66.6 - - - +
487A ILE* 1.3 55.6 + - - +
489A CYS* 2.7 30.7 + - - +
490A ILE* 3.0 10.0 + - - +
504A ASN* 6.2 4.5 - - + -
527A PHE 3.6 10.1 - - - +
528A THR* 5.2 4.5 - - - +
531A ALA* 6.1 7.8 - - + +
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Residues in contact with ILE 487 (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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483A LEU 2.5 16.4 + - - +
484A TRP* 2.8 15.0 + - - +
486A LYS* 1.3 70.0 - - - +
488A TRP* 1.3 53.3 + - - +
490A ILE* 2.7 35.7 + - - +
491A THR* 3.9 2.3 + - - -
527A PHE* 3.7 17.1 + - + +
530A SER* 4.7 11.4 - - - -
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Residues in contact with TRP 488 (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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447A ARG* 3.4 35.2 - - + +
484A TRP 2.3 26.3 + - - +
485A ASN* 3.0 12.1 - - - +
487A ILE* 1.3 68.0 - - - +
489A CYS* 1.3 61.3 + - - +
490A ILE 3.2 0.5 + - - -
491A THR* 4.0 2.8 + - - -
492A PHE* 3.5 16.0 + - - +
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Residues in contact with CYS 489 (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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458A CYS* 5.9 7.0 - - + -
485A ASN 2.4 24.2 + - - +
486A LYS* 2.7 18.4 + - - +
488A TRP* 1.3 69.2 - - - +
490A ILE* 1.3 61.7 + - - -
492A PHE* 2.8 29.6 + - + +
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Residues in contact with ILE 490 (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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486A LYS 3.0 5.5 + - - +
487A ILE* 2.7 26.6 + - - +
489A CYS* 1.3 70.2 - - - +
491A THR* 1.3 58.5 + - - +
492A PHE 2.9 14.4 - - - +
493A ARG* 4.6 2.8 - - - +
530A SER* 4.3 24.5 - - - +
531A ALA* 5.7 2.0 - - - +
533A ARG 5.4 1.1 - - - +
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Residues in contact with THR 491 (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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487A ILE 3.9 3.0 + - - -
488A TRP 4.0 2.8 + - - -
490A ILE* 1.3 76.5 - - - +
492A PHE* 1.3 65.9 + - - +
493A ARG* 3.0 12.9 + - - +
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Residues in contact with PHE 492 (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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452A THR* 6.2 5.2 - - - +
453A PRO 6.1 0.7 - - - +
455A VAL* 5.8 9.4 - - + -
488A TRP 3.5 10.6 + - - +
489A CYS* 2.8 35.3 + - + +
490A ILE 2.9 9.4 - - - +
491A THR* 1.3 74.8 - - - +
493A ARG* 1.3 59.2 + - - +
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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