Contacts of the helix formed by residues 562 - 573 (chain A) in PDB entry 5C8H
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 562 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471A SER* 2.9 34.4 + - - +
561A VAL* 1.3 73.0 - - - +
563A ASN* 1.3 60.9 + - - +
564A GLY* 4.3 2.9 - - - +
565A THR* 3.0 34.9 + - - +
566A LEU* 3.0 11.4 + - - +
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Residues in contact with ASN 563 (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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499A GLN* 3.0 35.1 + - - +
500A LEU* 3.5 21.0 - - + +
503A GLN* 3.7 38.0 + - - +
561A VAL 3.8 2.8 - - - +
562A ASP* 1.3 69.8 - - - +
564A GLY* 1.3 56.1 + - - +
566A LEU* 3.9 6.3 - - - +
567A THR* 2.6 39.1 + - - -
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Residues in contact with GLY 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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562A ASP* 3.2 3.9 - - - +
563A ASN* 1.3 78.9 - - - +
565A THR* 1.3 55.6 + - - +
567A THR* 3.5 5.6 + - - -
568A ASP* 3.0 37.0 + - - +
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Residues in contact with THR 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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471A SER* 4.9 0.9 + - - -
472A LEU 3.8 15.0 + - - +
473A PRO* 5.2 1.4 - - - +
474A LEU* 3.7 36.4 + - + +
477A LEU* 4.2 7.2 - - + -
561A VAL* 3.8 13.5 - - + -
562A ASP* 3.0 22.7 + - - +
564A GLY* 1.3 75.8 - - - +
566A LEU* 1.3 57.9 + - - +
568A ASP* 3.3 10.8 + - - +
569A PHE* 2.9 26.2 + - - +
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Residues in contact with LEU 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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477A LEU* 4.0 15.9 - - + -
492A PHE* 4.4 2.5 - - + -
496A ILE* 3.9 33.2 - - + +
499A GLN* 3.7 23.8 - - + +
500A LEU* 4.2 6.3 - - + -
559A ILE* 4.0 24.2 - - + -
561A VAL* 3.7 36.8 - - + +
562A ASP 3.0 13.1 + - - +
563A ASN* 3.7 12.6 - - - +
564A GLY 3.3 0.2 - - - -
565A THR* 1.3 77.5 - - - +
567A THR* 1.3 61.6 + - - +
569A PHE* 3.2 6.5 + - - +
570A LEU* 3.1 25.1 + - - +
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Residues in contact with THR 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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500A LEU* 3.7 22.5 - - + +
503A GLN* 5.3 3.3 + - - -
563A ASN 2.6 22.3 + - - -
564A GLY* 3.5 9.2 - - - -
566A LEU* 1.3 72.7 - - - +
568A ASP* 1.3 67.3 + - - +
570A LEU* 3.1 7.5 + - - +
571A GLU* 3.0 45.3 + - - +
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Residues in contact with ASP 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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474A LEU* 4.2 16.8 - - + +
564A GLY 3.0 19.3 + - - +
565A THR* 3.4 11.2 - - - +
567A THR* 1.3 77.7 - - - +
569A PHE* 1.3 63.6 + - - +
571A GLU* 3.4 11.8 + - - +
572A LYS* 3.2 46.6 + - - +
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Residues in contact with PHE 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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474A LEU* 3.6 19.0 - - + +
477A LEU* 3.9 24.2 - - + -
478A THR* 4.1 16.8 - - + -
481A LEU* 3.3 34.8 - - + -
489A ARG* 5.7 2.2 - - + -
492A PHE* 4.3 1.6 - + - -
493A ARG* 4.1 12.1 - - + -
496A ILE* 3.7 26.0 - - + -
565A THR 2.9 13.3 + - - +
566A LEU* 3.3 10.8 - - - +
567A THR 3.2 0.2 - - - -
568A ASP* 1.3 75.6 - - - +
570A LEU* 1.3 61.0 + - + +
572A LYS* 3.1 6.2 + - + +
573A GLU* 2.9 73.1 + - + +
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Residues in contact with LEU 570 (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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493A ARG* 4.1 41.5 - - + +
496A ILE* 3.8 26.7 - - + -
497A LYS* 4.6 14.6 - - + +
500A LEU* 4.0 13.0 - - + -
566A LEU 3.1 14.6 + - - +
567A THR* 3.1 7.4 + - - +
569A PHE* 1.3 77.2 - - + +
571A GLU* 1.3 63.1 + - + +
572A LYS 3.3 0.9 + - - -
573A GLU* 3.5 5.5 + - + +
574A GLU* 3.5 21.7 + - - +
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Residues in contact with GLU 571 (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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567A THR* 3.0 37.6 + - - +
568A ASP* 3.8 17.4 - - - +
570A LEU* 1.3 75.0 - - + +
572A LYS* 1.3 67.0 + - + +
574A GLU 3.5 5.3 - - - +
575A GLU 3.2 26.5 - - - +
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Residues in contact with LYS 572 (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 LEU* 3.7 25.3 - - + +
568A ASP* 3.2 35.7 + - - +
569A PHE* 3.1 12.1 + - + +
571A GLU* 1.3 84.9 + - + +
573A GLU* 1.3 61.0 + - + +
574A GLU 2.9 11.6 + - - -
575A GLU 3.9 11.7 + - - +
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Residues in contact with GLU 573 (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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478A THR* 5.5 5.0 - - - +
481A LEU* 5.8 0.5 - - - +
489A ARG* 4.2 11.9 - - - +
493A ARG* 2.7 53.5 + - - +
569A PHE* 2.9 58.9 + - + +
570A LEU* 3.5 8.7 + - + +
572A LYS* 1.3 73.4 - - + +
574A GLU* 1.3 61.9 + - - +
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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