Contacts of the helix formed by residues 475 - 489 (chain A) in PDB entry 1WCN
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 475 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464A ILE* 3.2 35.6 - - + +
468A ALA* 4.3 19.4 - - - +
473A LEU 5.3 0.5 - - - +
474A THR* 1.3 77.0 - - - +
476A GLU* 1.3 66.2 + - + +
479A GLY 3.2 8.5 + - - -
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Residues in contact with GLU 476 (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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474A THR* 4.2 4.1 - - - -
475A ASP* 1.3 78.6 - - + +
477A LYS* 1.3 66.6 + - - +
479A GLY* 3.1 10.4 + - - -
480A ALA* 3.1 13.3 + - - +
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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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439A GLY* 3.0 30.1 + - - -
441A ASP* 5.8 2.6 + - - -
444A LEU* 3.7 21.8 - - - +
472A GLY 4.1 14.2 + - - +
473A LEU* 3.3 17.6 - - + +
474A THR* 3.0 25.8 + - - +
476A GLU* 1.3 78.6 - - - +
478A ALA* 1.3 53.6 + - - +
480A ALA* 3.0 5.3 + - - +
481A LEU* 2.6 51.6 + - + +
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Residues in contact with ALA 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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464A ILE* 3.6 34.1 - - + +
467A LEU* 4.4 3.4 - - + -
468A ALA* 5.2 0.7 - - - +
473A LEU* 3.6 28.6 - - + +
474A THR 2.7 22.8 + - - +
477A LYS* 1.3 72.4 - - - +
479A GLY* 1.3 63.8 + - - +
481A LEU* 4.3 2.7 - - - -
482A ILE* 2.9 30.3 + - - +
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Residues in contact with GLY 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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464A ILE* 3.4 26.6 - - - +
475A ASP 3.2 5.2 + - - -
476A GLU* 3.1 8.6 + - - -
478A ALA* 1.3 79.6 - - - +
480A ALA* 1.3 54.8 + - - +
482A ILE* 4.5 1.2 - - - +
483A MET* 2.6 48.0 + - - +
486A ARG* 5.6 0.8 + - - -
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Residues in contact with ALA 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 GLU 3.1 9.6 + - - +
477A LYS* 3.0 9.3 + - - +
479A GLY* 1.3 76.1 - - - +
481A LEU* 1.3 61.3 + - + +
483A MET* 2.9 11.9 + - + +
484A ALA* 2.5 40.1 + - - +
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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
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437A LEU* 3.8 3.0 - - + +
438A GLU 3.9 5.2 - - - +
439A GLY* 3.1 33.9 - - - +
440A VAL* 2.9 38.6 - - + +
444A LEU* 5.1 2.5 - - + -
459A LEU* 3.6 13.4 - - + +
467A LEU* 5.7 0.7 - - + -
473A LEU* 4.5 7.4 - - + -
477A LYS* 2.6 50.6 + - + +
478A ALA* 4.0 6.5 - - - +
480A ALA* 1.3 80.7 - - + +
482A ILE* 1.3 64.2 + - + +
484A ALA* 3.0 13.3 + - + +
485A ALA 3.1 9.4 + - - -
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Residues in contact with ILE 482 (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 LEU* 3.3 20.0 - - + +
462A GLN 3.2 13.2 - - - +
463A GLY* 3.3 30.5 - - - -
464A ILE* 3.3 9.2 - - + +
467A LEU* 2.9 37.9 - - + -
478A ALA* 2.9 18.4 + - - +
479A GLY* 4.5 1.6 - - - +
481A LEU* 1.3 75.9 - - - +
483A MET* 1.3 58.5 + - - +
485A ALA* 3.4 2.9 + - - +
486A ARG* 2.7 72.0 + - - +
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Residues in contact with MET 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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479A GLY* 2.6 55.0 + - - +
480A ALA* 2.9 10.4 + - + +
482A ILE* 1.3 75.5 - - - +
484A ALA* 1.3 54.0 + - - +
486A ARG* 4.0 20.9 - - + +
487A ASN* 2.4 54.0 + - - +
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Residues in contact with ALA 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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437A LEU* 3.8 22.4 - - + -
438A GLU* 4.5 7.4 - - + +
480A ALA 2.5 26.0 + - - +
481A LEU* 3.0 9.8 + - + +
483A MET* 1.3 74.2 - - - +
485A ALA* 1.3 61.7 + - - +
487A ASN* 3.8 7.5 - - - +
488A ILE* 3.2 30.8 + - + +
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Residues in contact with ALA 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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437A LEU* 3.9 0.6 - - - +
456A LEU* 3.1 51.6 - - + +
459A LEU* 3.6 23.1 - - + -
460A ALA* 4.1 2.9 - - - +
481A LEU 3.1 3.0 + - - -
482A ILE 3.8 2.9 - - - +
484A ALA* 1.3 77.2 - - - +
486A ARG* 1.3 57.3 + - - +
488A ILE 3.3 0.2 + - - -
489A CYS* 2.6 41.4 + - - +
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Residues in contact with ARG 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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460A ALA* 2.6 43.6 + - + +
461A GLU* 4.5 3.2 + - - +
462A GLN 3.3 11.3 + - - -
463A GLY* 5.0 4.4 - - - -
464A ILE* 5.8 2.6 - - - +
479A GLY* 6.3 0.6 - - - -
482A ILE* 2.7 50.8 + - - +
483A MET* 3.7 19.0 - - + +
485A ALA* 1.3 78.3 - - - +
487A ASN* 1.3 57.3 + - - +
490A TRP* 2.4 75.8 + - + +
491A PHE* 4.8 1.1 - - + -
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Residues in contact with ASN 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 MET* 2.4 52.0 + - - +
484A ALA* 3.8 8.3 - - - +
486A ARG* 1.3 74.2 - - - +
488A ILE* 1.3 54.1 + - + +
491A PHE* 3.2 31.6 - - + +
492A GLY* 2.5 36.1 + - - +
495A ALA 4.7 12.0 - - - +
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Residues in contact with ILE 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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433A ASP* 6.1 3.1 - - + -
437A LEU* 3.3 32.5 - - + -
456A LEU* 3.7 14.6 - - + -
484A ALA* 3.2 11.9 + - - +
486A ARG 3.2 0.2 - - - -
487A ASN* 1.3 78.6 - - + +
489A CYS* 1.3 62.8 + - - +
492A GLY* 3.2 22.8 - - - +
493A ASP* 4.7 13.7 - - - +
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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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433A ASP* 5.7 1.3 - - - -
456A LEU* 3.1 29.6 - - - -
457A GLU* 3.0 63.6 - - + +
460A ALA* 4.3 1.3 - - + -
485A ALA 2.6 20.1 + - - +
486A ARG* 4.3 0.7 - - - -
488A ILE* 1.3 77.0 - - - +
490A TRP* 1.3 74.0 + - + +
492A GLY* 5.2 0.3 - - - -
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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