Contacts of the helix formed by residues 455 - 471 (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 ASP 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A GLU* 1.3 72.6 + - - +
456A PRO* 1.3 72.3 - - - +
457A VAL* 2.9 31.8 + - - +
458A ALA* 3.2 24.4 + - + +
459A ILE* 3.5 13.0 + - - +
493A ARG* 5.1 0.2 + - - -
498A ARG* 3.5 27.4 + - - +
44B GLU 5.7 0.9 - - - +
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Residues in contact with PRO 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A TRP* 4.4 8.1 - - + -
454A GLU 3.4 9.1 - - - +
455A ASP* 1.3 91.0 - - - +
457A VAL* 1.3 64.0 + - + +
459A ILE* 3.3 9.8 + - + -
460A ARG* 3.0 26.1 + - - +
497A ALA* 4.6 0.9 - - + -
498A ARG* 3.6 25.8 - - + +
500A ASP* 5.9 1.1 - - - +
509A GLN* 4.6 13.2 - - - +
513A CYS* 4.0 20.6 - - - -
516A LEU* 3.4 28.1 - - + +
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Residues in contact with VAL 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ASP* 2.9 19.8 + - - +
456A PRO* 1.3 81.0 - - + +
458A ALA* 1.3 62.8 + - - +
460A ARG* 3.4 23.0 + - - +
461A LYS* 3.1 41.6 + - + +
509A GLN* 5.7 5.4 - - - +
44B GLU* 3.8 51.4 - - + +
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Residues in contact with ALA 458 (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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455A ASP* 3.2 21.4 + - + +
457A VAL* 1.3 78.9 - - - +
459A ILE* 1.3 64.1 + - - +
461A LYS* 3.4 7.6 + - - +
462A ALA* 3.1 24.3 + - - +
493A ARG* 3.8 17.9 + - - +
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Residues in contact with ILE 459 (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* 4.3 7.0 - - + +
455A ASP 3.5 11.6 + - - +
456A PRO* 3.3 9.1 + - + +
457A VAL 3.2 0.4 - - - -
458A ALA* 1.3 78.3 - - - +
460A ARG* 1.3 58.9 + - - +
462A ALA* 3.3 4.9 + - - +
463A LEU* 2.9 27.0 + - - +
490A ILE* 3.7 24.5 - - + +
493A ARG* 3.9 31.9 - - + +
494A LEU* 3.6 46.7 - - + +
497A ALA* 4.0 17.5 - - + -
516A LEU* 4.4 5.6 - - + -
520A MET* 4.5 5.2 - - + -
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Residues in contact with ARG 460 (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 PRO* 3.0 19.7 + - - +
457A VAL* 3.8 29.3 + - - +
458A ALA 3.4 0.2 - - - -
459A ILE* 1.3 78.7 - - - +
461A LYS* 1.3 59.7 + - + +
463A LEU* 3.4 3.9 + - + +
464A GLN* 3.0 55.1 + - + +
512A GLU* 4.0 33.6 + - - +
513A CYS* 5.6 0.8 - - - +
516A LEU* 3.7 33.6 - - + +
519A LEU* 4.5 12.9 - - + +
44B GLU* 5.8 1.4 + - - +
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Residues in contact with LYS 461 (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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210A GLN* 4.5 3.4 + - - +
457A VAL* 3.1 28.0 + - + +
458A ALA* 3.9 6.5 - - - +
460A ARG* 1.3 80.3 - - + +
462A ALA* 1.3 58.1 + - - +
464A GLN* 3.4 11.3 + - - +
465A GLU* 2.9 32.2 + - - +
44B GLU* 3.5 34.7 + - - -
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Residues in contact with ALA 462 (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 ALA 3.1 16.9 + - - +
459A ILE 3.7 4.0 - - - +
461A LYS* 1.3 74.1 - - - +
463A LEU* 1.3 66.0 + - - +
465A GLU* 3.3 9.9 + - - +
466A CYS* 2.9 25.5 + - - +
490A ILE* 3.8 17.3 - - + +
493A ARG* 4.2 17.5 - - - +
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Residues in contact with LEU 463 (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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208A ILE* 3.4 26.7 - - + +
459A ILE 2.9 17.3 + - - +
460A ARG* 3.5 5.2 - - - +
461A LYS 3.3 0.2 - - - -
462A ALA* 1.3 77.7 - - - +
464A GLN* 1.3 67.3 + - + +
466A CYS* 3.3 4.0 + - - +
467A MET* 3.2 20.1 + - + +
487A LEU* 4.6 3.4 - - + +
490A ILE* 3.9 10.3 - - + +
516A LEU* 4.4 11.0 - - + -
519A LEU* 3.8 12.8 - - + +
520A MET* 3.5 55.0 - - + +
523A ALA* 3.9 21.3 - - + -
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Residues in contact with GLN 464 (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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207A ARG* 2.9 39.0 + - - +
208A ILE 3.3 10.3 - - - +
209A TYR 3.3 23.6 + - - +
210A GLN* 3.7 17.6 + - + +
460A ARG* 3.0 45.4 + - + +
461A LYS* 3.8 10.1 - - - +
463A LEU* 1.3 77.7 - - + +
465A GLU* 1.3 65.5 + - - +
467A MET* 3.4 1.9 + - - +
468A GLN* 3.1 23.4 + - - +
519A LEU* 5.1 0.8 - - + +
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Residues in contact with GLU 465 (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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210A GLN* 3.3 28.4 - - - +
461A LYS 2.9 16.0 + - - +
462A ALA* 3.9 8.4 - - - +
464A GLN* 1.3 77.3 - - - +
466A CYS* 1.3 64.7 + - - +
469A HIS* 3.1 57.1 + - + +
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Residues in contact with CYS 466 (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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462A ALA 2.9 19.2 + - - +
463A LEU 3.4 5.6 - - - +
464A GLN 3.2 0.2 - - - -
465A GLU* 1.3 78.0 - - - +
467A MET* 1.3 63.3 + - - +
469A HIS* 5.1 0.4 - - - -
470A ASN* 3.1 41.5 + - - +
471A PHE* 4.8 2.7 - - - -
483A GLY* 3.6 23.1 - - - -
486A GLN* 3.5 27.1 - - - +
487A LEU* 3.9 22.4 - - + -
490A ILE* 4.5 4.0 - - + -
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Residues in contact with MET 467 (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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208A ILE* 3.5 37.5 - - + +
209A TYR* 3.4 24.6 - - + +
463A LEU 3.2 14.4 + - - +
464A GLN 3.9 0.9 - - - +
465A GLU 3.3 0.2 - - - -
466A CYS* 1.3 76.9 - - - +
468A GLN* 1.3 58.5 + - - +
471A PHE* 2.9 56.5 + - + -
487A LEU* 4.2 12.6 - - - -
523A ALA* 3.9 28.9 - - + +
526A THR* 3.6 36.3 - - + -
527A ALA 4.8 0.4 - - - +
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Residues in contact with GLN 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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209A TYR* 3.7 13.5 - - - +
210A GLN* 2.9 48.8 + - + +
211A SER* 3.0 22.7 + - - +
241A PHE* 4.7 6.9 - - - -
464A GLN 3.1 16.0 + - - +
465A GLU 3.7 4.0 - - - +
466A CYS 3.3 0.2 - - - -
467A MET* 1.3 77.9 - - - +
469A HIS* 1.3 65.3 + - + +
472A SER* 3.1 38.8 + - - -
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Residues in contact with HIS 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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210A GLN* 4.3 6.2 + - - -
465A GLU* 3.1 48.4 + - + +
466A CYS* 4.2 2.0 - - - +
468A GLN* 1.3 93.0 - - + +
470A ASN* 1.3 74.0 + - - +
472A SER* 5.0 2.4 + - - -
474A PHE 5.5 2.6 - - - +
479A ALA* 5.3 1.9 - - - +
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Residues in contact with ASN 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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466A CYS* 3.1 28.0 + - - +
469A HIS* 1.3 91.4 - - - +
471A PHE* 1.3 81.7 - - + +
472A SER 3.7 1.3 - - - -
474A PHE 5.4 1.3 - - - -
475A ARG* 3.9 10.5 - - - +
476A GLU 5.0 0.3 + - - -
479A ALA* 3.6 37.3 - - - +
480A MET* 3.5 14.7 + - - +
482A LYS* 5.8 0.3 - - - +
483A GLY* 3.4 21.0 - - - +
486A GLN* 4.0 9.3 + - - +
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Residues in contact with PHE 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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209A TYR* 2.7 31.2 + - - +
241A PHE* 3.9 0.5 - - - -
466A CYS* 4.7 2.2 - - - -
467A MET* 2.9 45.7 + - + +
470A ASN* 1.3 92.3 - - + +
472A SER* 1.3 61.2 + - - +
475A ARG* 2.9 24.7 + - - +
480A MET* 3.5 45.8 - - + -
483A GLY* 4.4 11.2 - - - -
484A LEU 4.3 1.6 - - - -
487A LEU* 4.6 1.3 - - + -
526A THR* 5.0 2.2 - - + -
527A ALA* 3.3 39.9 - - + -
530A ALA* 3.7 24.2 - - + -
531A ASN* 4.3 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