Contacts of the helix formed by residues 476 - 495 (chain A) in PDB entry 2WP9
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 GLU 476 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A ARG* 5.8 1.3 - - - -
470A ASN 5.0 0.4 + - - -
474A PHE 5.1 1.6 - - - +
475A ARG* 1.3 85.3 - - - +
477A GLY* 1.3 68.1 + - - +
478A ASP* 3.3 2.7 + - + +
479A ALA* 4.3 21.3 + - + +
480A MET* 2.9 29.7 + - - +
543A PHE* 2.9 37.2 - - + +
544A ASP* 4.5 3.6 - - - +
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Residues in contact with GLY 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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476A GLU* 1.3 74.5 - - - +
478A ASP* 1.3 62.8 + - - +
480A MET* 3.3 4.1 + - - +
481A ALA* 3.0 22.7 + - - +
531A ASN* 4.2 2.3 - - - +
542A ARG* 3.7 11.9 - - - -
544A ASP* 3.2 33.0 + - - +
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Residues in contact with ASP 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A GLU* 3.3 2.2 - - + +
477A GLY* 1.3 71.0 - - - +
479A ALA* 1.3 66.4 + - - +
481A ALA* 3.1 9.4 + - - +
482A LYS* 3.0 23.6 + - - +
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Residues in contact with ALA 479 (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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469A HIS 5.3 1.8 - - - +
470A ASN* 3.6 29.9 - - + +
476A GLU* 3.3 26.5 + - + +
478A ASP* 1.3 79.8 - - - +
480A MET* 1.3 52.1 + - - +
482A LYS* 3.3 7.5 + - - +
483A GLY* 2.8 31.7 + - - -
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Residues in contact with MET 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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470A ASN 3.5 12.8 - - - +
471A PHE* 3.5 25.2 - - + -
475A ARG* 3.7 18.4 - - + -
476A GLU 2.9 26.1 + - - +
477A GLY* 3.7 2.0 - - - +
479A ALA* 1.3 73.4 - - - +
481A ALA* 1.3 59.9 + - - +
483A GLY 3.3 0.2 + - - -
484A LEU* 2.9 30.1 + - - +
530A ALA* 3.7 35.0 - - - +
531A ASN* 3.3 17.5 + - - +
540A HIS* 4.7 0.2 - - - -
542A ARG* 3.5 51.8 - - + +
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Residues in contact with ALA 481 (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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477A GLY 3.0 13.5 + - - +
478A ASP* 3.1 9.8 + - - +
480A MET* 1.3 75.9 - - - +
482A LYS* 1.3 57.3 + - - +
484A LEU* 3.5 7.5 + - - +
485A GLU* 3.1 32.4 + - - +
531A ASN* 3.2 11.3 + - - +
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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
----------------------------------------------------------
470A ASN* 5.8 0.7 - - - +
478A ASP 3.0 12.9 + - - +
479A ALA* 3.6 10.1 - - - +
481A ALA* 1.3 72.9 - - - +
483A GLY* 1.3 67.7 + - - +
485A GLU* 3.1 10.3 + - + +
486A GLN* 2.9 43.0 + - + +
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Residues in contact with GLY 483 (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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466A CYS* 3.6 10.1 - - - -
470A ASN* 3.4 27.0 - - - +
471A PHE* 4.4 5.6 - - - -
479A ALA 2.8 17.5 + - - -
480A MET 3.3 1.8 + - - -
482A LYS* 1.3 74.0 - - - +
484A LEU* 1.3 61.9 + - - +
486A GLN* 3.0 7.0 + - - +
487A LEU* 2.9 27.0 + - - +
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Residues in contact with LEU 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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471A PHE* 4.3 2.2 - - - -
480A MET 2.9 17.2 + - - +
481A ALA* 3.5 7.4 - - - +
483A GLY* 1.3 73.5 - - - +
485A GLU* 1.3 68.0 + - - +
487A LEU* 3.2 9.5 + - + +
488A LYS* 3.2 36.6 + - - +
524A TYR* 4.0 17.3 - - + -
527A ALA* 3.8 18.2 - - + -
528A VAL* 3.7 35.0 - - + +
531A ASN* 3.5 22.7 - - + +
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Residues in contact with GLU 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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481A ALA 3.1 18.1 + - - +
482A LYS* 3.1 13.9 + - + +
484A LEU* 1.3 80.9 - - - +
486A GLN* 1.3 62.6 + - + +
488A LYS* 3.1 44.8 + - - +
489A VAL* 3.3 16.1 + - - +
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Residues in contact with GLN 486 (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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466A CYS* 3.5 25.0 - - - +
470A ASN* 4.0 7.3 + - - +
482A LYS* 2.9 38.2 + - + +
483A GLY* 3.0 6.9 + - - +
485A GLU* 1.3 75.7 - - + +
487A LEU* 1.3 57.5 + - - +
489A VAL* 3.1 10.8 + - - +
490A ILE* 2.8 39.1 + - + +
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Residues in contact with LEU 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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463A LEU* 4.6 11.9 - - + +
466A CYS* 3.9 22.9 - - + -
467A MET* 4.2 9.2 - - - -
471A PHE* 4.6 2.2 - - + -
483A GLY 2.9 16.3 + - - +
484A LEU* 3.2 10.3 + - + +
486A GLN* 1.3 76.2 - - - +
488A LYS* 1.3 53.4 + - - +
490A ILE* 3.2 12.4 + - + +
491A ARG* 2.6 38.8 + - - +
520A MET* 4.3 8.6 - - - +
523A ALA* 4.0 24.9 - - + +
524A TYR* 4.1 19.3 - - + -
527A ALA* 3.5 31.4 - - + -
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Residues in contact with LYS 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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484A LEU* 3.2 20.8 + - - +
485A GLU* 3.1 39.6 + - - +
487A LEU* 1.3 77.1 - - - +
489A VAL* 1.3 62.8 + - + +
491A ARG* 3.7 11.5 - - - +
492A GLU* 3.1 29.0 + - + +
524A TYR* 3.4 35.2 - - + +
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Residues in contact with VAL 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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485A GLU 3.3 11.9 + - - +
486A GLN* 3.1 11.9 + - - +
488A LYS* 1.3 78.4 - - + +
490A ILE* 1.3 64.7 + - + +
492A GLU* 3.0 17.4 + - + +
493A ARG* 3.0 28.8 + - + +
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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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459A ILE* 3.7 24.5 - - + +
462A ALA* 3.8 38.4 - - + +
463A LEU* 3.9 5.4 - - + +
466A CYS* 4.5 5.2 - - + -
486A GLN* 2.8 27.8 + - + +
487A LEU* 3.5 15.5 - - + +
489A VAL* 1.3 77.4 - - + +
491A ARG* 1.3 62.5 + - - +
493A ARG* 3.2 20.4 + - - +
494A LEU* 3.1 21.1 + - - +
520A MET* 3.0 27.8 - - + -
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Residues in contact with ARG 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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227A ILE* 6.2 0.2 - - - +
487A LEU 2.6 21.0 + - - +
488A LYS* 3.7 9.7 - - - +
489A VAL 3.1 0.2 - - - -
490A ILE* 1.3 75.7 - - - +
492A GLU* 1.3 67.6 + - - +
494A LEU* 3.5 5.6 + - + +
495A LYS* 3.4 26.5 + - + +
520A MET* 3.8 31.7 - - + +
521A GLU* 3.6 23.6 + - - -
524A TYR* 3.5 49.1 + - + +
559A TYR* 4.4 2.6 + - - -
564A GLU* 3.2 30.1 + - - -
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Residues in contact with GLU 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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488A LYS 3.1 16.0 + - - +
489A VAL* 3.0 12.1 + - + +
491A ARG* 1.3 80.8 - - - +
493A ARG* 1.3 67.4 + - + +
495A LYS* 3.3 47.6 + - - +
496A ASN* 3.9 10.8 + - - -
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Residues in contact with ARG 493 (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 GLU* 2.9 44.5 + - - +
455A ASP 5.1 0.2 + - - -
458A ALA* 3.8 36.6 + - - +
459A ILE* 3.9 18.4 - - + +
462A ALA* 4.2 18.2 - - - +
489A VAL* 3.0 30.4 + - + +
490A ILE* 3.2 19.9 + - - +
492A GLU* 1.3 74.5 - - + +
494A LEU* 1.3 52.1 + - - +
496A ASN* 2.8 36.9 + - - +
497A ALA 3.5 0.9 + - - -
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Residues in contact with LEU 494 (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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446A ARG* 3.5 9.0 + - - -
447A TRP* 3.9 19.1 - - + -
459A ILE* 3.6 19.2 - - + +
490A ILE 3.1 12.4 + - - +
491A ARG* 3.6 10.3 - - + +
492A GLU 3.2 0.2 - - - -
493A ARG* 1.3 72.4 - - - +
495A LYS* 1.3 57.1 + - + +
496A ASN 2.9 9.7 + - - -
497A ALA* 3.2 13.9 + - - +
516A LEU* 3.8 32.3 - - + +
517A ASP* 3.7 23.7 - - - +
520A MET* 3.5 39.3 - - + -
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Residues in contact with LYS 495 (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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446A ARG* 3.2 29.5 + - - +
450A ASN* 4.9 0.3 + - - -
491A ARG* 3.4 14.3 + - + +
492A GLU* 3.3 42.4 + - - +
494A LEU* 1.3 76.9 - - - +
496A ASN* 1.3 67.2 + - - +
497A ALA 3.6 0.7 - - - -
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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