Contacts of the helix formed by residues 565 - 573 (chain A) in PDB entry 4HBN
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 565 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564A PHE* 1.3 70.7 - - - +
566A GLU* 1.3 51.3 + - - +
567A GLU* 2.5 5.1 + - - -
568A SER* 2.2 56.9 + - - +
569A ILE* 2.9 14.0 + - + +
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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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564A PHE* 2.7 24.0 + - + +
565A ASP* 1.3 70.7 - - - +
567A GLU* 1.3 53.0 + - - +
569A ILE* 4.2 12.3 - - + -
570A LEU* 2.7 64.2 + - + +
581A ILE* 6.0 1.4 - - - +
585A ASN* 5.6 4.2 + - - -
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Residues in contact with GLU 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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565A ASP 2.5 5.5 + - - -
566A GLU* 1.3 76.8 + - - +
568A SER* 1.3 56.4 + - - +
570A LEU* 3.9 5.3 - - - +
571A GLY* 3.1 24.6 + - - -
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Residues in contact with SER 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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565A ASP* 2.2 45.7 + - - +
567A GLU* 1.3 68.8 - - - +
569A ILE* 1.3 66.6 + - - +
571A GLY* 3.1 3.2 + - - -
572A GLU* 3.1 27.8 + - - +
802A PO4 2.2 42.6 + - - -
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Residues in contact with ILE 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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564A PHE* 3.9 29.8 - - + -
565A ASP* 2.9 16.2 + - + +
566A GLU* 3.8 13.9 - - + +
568A SER* 1.3 76.6 - - - +
570A LEU* 1.3 75.0 + - + +
572A GLU* 3.2 23.4 + - - +
573A LEU* 3.4 20.7 + - + +
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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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566A GLU* 2.7 52.2 + - + +
567A GLU* 3.9 6.1 - - - +
569A ILE* 1.3 79.5 - - + +
571A GLY* 1.3 58.6 + - - +
573A LEU* 2.8 34.3 + - + +
578A ARG* 3.0 46.9 + - + -
581A ILE* 4.9 16.4 - - + -
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Residues in contact with GLY 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 GLU 3.1 14.9 + - - -
568A SER* 3.1 4.2 + - - -
570A LEU* 1.3 76.1 - - - +
572A GLU* 1.3 60.0 + - - +
573A LEU 3.3 8.3 - - - +
578A ARG* 4.2 6.1 + - - -
802A PO4 5.3 2.0 - - - -
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Residues in contact with GLU 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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568A SER* 3.1 19.6 + - - +
569A ILE* 3.4 16.1 - - - +
571A GLY* 1.3 77.3 - - - +
573A LEU* 1.3 64.2 + - + +
802A PO4 2.6 38.5 + - - +
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Residues in contact with LEU 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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569A ILE* 3.6 19.3 - - + +
570A LEU* 2.8 25.2 + - + +
571A GLY 3.3 4.9 - - - +
572A GLU* 1.3 85.6 - - + +
574A SER* 1.3 66.2 + - - +
577A LEU* 4.0 23.8 - - + -
578A ARG* 2.9 18.9 + - + -
581A ILE* 3.5 32.1 - - + -
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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