Contacts of the helix formed by residues 563 - 569 (chain A) in PDB entry 2DFS
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 GLY 563 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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448A SER* 4.9 0.4 - - - -
520A ASP* 2.8 12.6 + - - -
562A GLU* 1.3 76.4 - - - +
564A PHE* 1.3 63.6 + - - +
565A LEU 3.5 2.0 - - - -
566A GLU* 3.8 9.3 + - - +
567A LYS* 3.2 40.9 + - - +
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Residues in contact with PHE 564 (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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448A SER* 3.7 12.1 - - - -
449A PHE* 3.6 58.8 - + + -
452A PHE* 4.1 21.8 - + + -
509A LEU* 4.0 14.4 - - + +
520A ASP* 3.6 1.8 + - - +
523A TRP* 3.4 32.8 - + + -
548A PHE* 4.2 15.7 - + - -
559A TYR* 4.4 7.9 - - + -
560A GLN 3.2 29.8 - - - -
561A CYS* 3.1 19.5 + - - +
562A GLU 3.5 1.0 - - - -
563A GLY* 1.3 77.6 - - - +
565A LEU* 1.4 63.9 + - - +
567A LYS* 4.0 1.6 - - - +
568A ASN* 3.2 24.6 + - - +
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Residues in contact with LEU 565 (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 LEU* 3.6 18.4 - - + -
512A GLU* 4.1 25.8 - - + +
513A CYS* 3.8 21.3 - - - +
518A GLY 4.2 4.3 - - - +
519A SER* 3.7 38.6 - - - +
520A ASP* 2.9 33.1 + - - +
523A TRP* 3.9 14.1 - - + -
563A GLY 3.5 0.2 - - - -
564A PHE* 1.4 75.8 - - - +
566A GLU* 1.4 68.3 + - + +
568A ASN* 3.4 2.6 + - - +
569A LYS* 3.3 32.5 + - - +
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Residues in contact with GLU 566 (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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398A ASN* 2.8 25.6 + - - +
405A LYS* 5.0 1.9 + - - -
520A ASP* 5.6 0.4 + - - -
563A GLY* 3.8 9.6 + - - +
564A PHE 3.5 0.6 - - - -
565A LEU* 1.4 78.4 - - + +
567A LYS* 1.3 62.6 + - + +
569A LYS* 2.6 55.1 + - - +
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Residues in contact with LYS 567 (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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247A SER* 4.5 14.3 - - - -
251A PHE* 3.6 42.8 - - + -
405A LYS* 4.0 5.3 + - - +
448A SER* 2.8 23.4 + - - -
449A PHE* 3.8 26.1 - - + -
450A GLU* 2.6 39.2 + - - +
562A GLU 5.3 0.4 + - - -
563A GLY* 3.2 25.8 + - - +
564A PHE 4.0 2.0 - - - +
566A GLU* 1.3 77.1 - - + +
568A ASN* 1.3 60.9 + - - +
569A LYS 4.0 2.8 - - - +
636A VAL* 3.4 17.7 - - - +
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Residues in contact with ASN 568 (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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449A PHE* 3.6 13.5 - - + -
509A LEU* 3.7 22.4 - - + +
510A ASP* 2.7 26.7 + - - +
513A CYS* 3.6 21.8 - - - -
564A PHE 3.2 16.8 + - - +
565A LEU 3.7 4.5 - - - +
566A GLU 3.3 0.2 - - - -
567A LYS* 1.3 77.4 - - - +
569A LYS* 1.3 61.1 + - - +
570A ASP 3.4 0.5 + - - -
635A THR* 3.6 6.8 - - - +
636A VAL* 2.9 28.6 + - - +
637A GLY* 2.8 34.1 + - - -
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Residues in contact with LYS 569 (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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394A LEU* 6.2 1.2 - - - +
398A ASN* 2.8 40.8 + - + +
405A LYS* 2.8 23.2 + - - -
513A CYS* 4.7 16.6 - - + +
565A LEU* 3.3 26.7 + - - +
566A GLU* 2.6 46.5 + - - +
568A ASN* 1.3 73.9 - - - +
570A ASP* 1.4 58.2 + - - +
571A THR 3.9 1.1 - - - +
633A LYS* 4.3 20.9 - - - +
635A THR* 4.9 2.9 - - - -
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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