Contacts of the helix formed by residues 504 - 513 (chain A) in PDB entry 1SKW
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 504 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499A GLU* 2.8 11.5 + - - +
503A GLY* 1.3 74.0 - - - +
505A ILE* 1.3 66.9 + - - +
506A HIS* 2.9 7.8 + - - +
507A THR* 2.7 47.9 + - - -
508A LYS* 3.0 11.4 + - - +
518A ARG* 2.9 36.5 + - - -
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Residues in contact with ILE 505 (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 LEU* 4.1 22.4 - - + -
496A TYR* 3.3 61.0 - - + +
499A GLU* 3.8 22.1 + - + -
500A ILE* 3.6 36.3 + - + +
504A ASP* 1.3 72.3 + - - +
506A HIS* 1.3 74.0 + - + +
508A LYS* 3.5 5.4 + - + +
509A ASN* 2.8 38.1 + - - +
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Residues in contact with HIS 506 (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 LEU* 3.9 25.6 - - + +
504A ASP* 2.9 9.3 + - - +
505A ILE* 1.3 87.8 - - + +
507A THR* 1.3 67.4 - - - +
509A ASN* 3.1 8.9 + - - +
510A GLN* 2.8 21.9 + - - +
518A ARG* 3.9 36.1 - - + +
521A ALA* 3.7 5.4 - - - +
522A LYS* 3.8 49.7 + - + +
525A ILE* 4.4 10.0 - - + +
526A TYR* 4.5 11.1 + + - -
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Residues in contact with THR 507 (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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504A ASP* 2.7 33.7 + - - -
506A HIS* 1.3 71.7 - - - +
508A LYS* 1.3 57.5 + - - +
510A GLN* 2.7 29.7 + - - +
511A ILE* 2.9 21.4 + - - +
518A ARG* 4.3 12.5 - - - +
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Residues in contact with LYS 508 (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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495A GLU* 4.5 11.3 + - - +
496A TYR* 4.9 9.8 - - + +
499A GLU* 2.7 50.1 + - + +
504A ASP 3.0 12.1 + - - +
505A ILE* 3.6 17.7 - - + +
507A THR* 1.3 76.6 - - - +
509A ASN* 1.3 61.9 + - - +
511A ILE* 3.1 13.4 + - - +
512A ALA* 2.9 29.5 + - + +
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Residues in contact with ASN 509 (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 LEU* 5.0 0.6 - - - +
496A TYR* 3.0 35.6 + - - -
505A ILE* 2.8 34.4 + - - +
506A HIS* 3.1 9.9 + - - +
508A LYS* 1.3 79.0 - - - +
510A GLN* 1.3 57.2 + - - +
512A ALA* 3.9 1.4 - - - +
513A ALA* 2.9 32.9 + - - +
521A ALA* 4.1 12.3 - - + +
524A PHE* 5.6 2.2 - - + -
525A ILE* 4.3 19.2 - - + +
555A PHE* 3.1 29.0 - - + -
559A THR* 4.9 1.4 + - - -
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Residues in contact with GLN 510 (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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506A HIS 2.8 12.2 + - - +
507A THR* 2.7 17.1 + - - +
509A ASN* 1.3 77.3 - - - +
511A ILE* 1.3 56.7 + - + +
513A ALA 2.4 22.6 - - - +
514A GLU* 4.3 0.9 - - - -
515A LEU* 3.6 16.7 + - - +
516A PRO 5.2 1.3 - - - +
517A THR 4.3 14.4 - - - +
518A ARG* 4.3 7.9 - - + -
521A ALA* 3.7 16.8 - - + +
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Residues in contact with ILE 511 (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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507A THR* 2.9 21.9 + - - +
508A LYS* 3.5 12.8 - - - +
510A GLN* 1.3 79.8 - - + +
512A ALA* 1.3 66.3 + - - +
513A ALA 3.2 3.9 + - - -
514A GLU* 4.1 13.0 + - - +
558A ASN* 5.2 0.2 - - - +
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Residues in contact with ALA 512 (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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508A LYS* 2.9 18.0 + - + +
509A ASN* 3.9 1.8 - - - +
511A ILE* 1.3 79.4 - - - +
513A ALA* 1.3 59.8 + - - +
514A GLU* 3.7 7.6 - - - +
554A LYS 3.1 21.9 - - - +
555A PHE* 3.8 15.3 - - + -
558A ASN* 3.5 29.9 - - + +
559A THR* 3.7 18.4 - - - +
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Residues in contact with ALA 513 (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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509A ASN 2.9 14.8 + - - +
510A GLN 2.4 27.3 - - - +
511A ILE 3.9 0.2 - - - -
512A ALA* 1.3 77.0 - - - +
514A GLU* 1.3 53.0 + - - +
515A LEU* 2.4 20.4 + - + +
521A ALA* 6.0 1.1 - - + -
524A PHE* 4.4 15.0 - - + -
551A LEU* 4.5 9.2 - - + +
554A LYS 4.7 0.4 - - - -
555A PHE* 3.8 28.7 - - + +
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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