Contacts of the helix formed by residues 1724 - 1731 (chain A) in PDB entry 2H04
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 LEU1724 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1720A ASP* 3.3 12.9 + - + +
1721A ILE* 3.1 41.8 + - + +
1722A ALA 4.3 0.5 - - - +
1723A LEU* 1.3 77.8 - - - +
1725A PRO* 1.3 77.6 - - + +
1726A GLU* 3.4 31.6 - - + +
1727A ASN* 3.0 25.5 + - - +
1728A ARG* 3.6 5.9 + - - +
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Residues in contact with PRO1725 (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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1723A LEU 3.5 4.7 - - - +
1724A LEU* 1.3 91.4 - - + +
1726A GLU* 1.3 61.8 + - - +
1727A ASN 3.1 1.4 + - - -
1728A ARG* 3.2 53.9 + - - +
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Residues in contact with GLU1726 (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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1724A LEU* 3.4 32.2 - - + +
1725A PRO* 1.3 73.9 - - - +
1727A ASN* 1.3 71.3 + - - +
1728A ARG 3.4 0.6 + - - -
1729A GLY 4.9 1.4 + - - -
1730A LYS* 3.6 18.7 + - - +
1755A SER* 3.3 26.6 + - - +
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Residues in contact with ASN1727 (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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1721A ILE* 2.8 35.3 + - - +
1722A ALA 4.1 6.1 - - - +
1724A LEU* 3.0 22.7 + - - +
1726A GLU* 1.3 89.2 + - - +
1728A ARG* 1.3 59.5 + - - +
1729A GLY 3.3 2.7 - - - -
1730A LYS* 2.9 53.3 + - - +
1731A ASN* 3.3 11.8 + - - -
1757A TYR* 3.4 33.4 - - + +
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Residues in contact with ARG1728 (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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1722A ALA 5.4 0.7 - - - -
1723A LEU 4.5 7.6 + - - +
1724A LEU 3.6 4.9 + - - +
1725A PRO* 3.2 52.7 + - - +
1726A GLU 3.4 0.6 - - - -
1727A ASN* 1.3 77.9 - - - +
1729A GLY* 1.3 60.2 + - - +
1730A LYS 3.1 0.9 + - - -
1731A ASN* 3.6 23.8 + - - +
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Residues in contact with GLY1729 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1726A GLU 4.9 1.6 + - - -
1727A ASN 3.3 0.6 - - - -
1728A ARG* 1.3 77.4 - - - +
1730A LYS* 1.3 58.9 + - - +
1731A ASN 3.3 5.4 - - - -
1779A LEU* 3.5 19.1 - - - +
1781A GLY* 5.8 1.2 - - - -
1782A THR* 4.5 3.3 - - - +
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Residues in contact with LYS1730 (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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1726A GLU* 3.6 13.9 + - - +
1727A ASN* 2.9 42.7 + - - +
1729A GLY* 1.3 80.0 - - - +
1731A ASN* 1.3 58.8 + - - +
1746A LEU* 6.4 0.2 - - - +
1755A SER* 4.2 23.2 - - - +
1757A TYR* 3.8 32.0 + - + +
1758A ILE* 5.9 0.2 - - - -
1759A ASN* 4.1 5.6 + - - +
1776A GLN* 2.7 27.7 + - - -
1779A LEU* 4.1 2.9 - - - +
1782A THR* 4.0 20.2 - - + +
1785A ASP* 5.0 6.7 - - - +
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Residues in contact with ASN1731 (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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1722A ALA 2.9 29.3 + - - -
1727A ASN 3.3 15.0 + - - -
1728A ARG* 3.6 17.1 + - - +
1729A GLY* 3.3 1.4 - - - -
1730A LYS* 1.3 81.0 - - - +
1732A ARG* 1.3 66.6 + - - +
1733A TYR* 4.2 9.1 - - - +
1734A ASN* 5.0 3.9 + - + -
1737A LEU* 3.5 23.3 - - + +
1757A TYR* 2.9 26.9 + - - -
1759A ASN* 3.1 12.0 + - - +
1776A GLN* 3.7 2.0 - - - -
1779A LEU* 4.2 5.0 - - - +
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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