Contacts of the helix formed by residues 1721 - 1735 (chain A) in PDB entry 6AH0
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 GLY1721 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1604A LEU* 6.6 0.2 - - - -
1719A PHE 3.0 1.0 + - - -
1720A PRO* 1.3 71.3 - - - +
1722A SER* 1.3 62.3 + - - +
1723A LYS 3.3 2.2 - - - +
1724A PRO* 3.8 6.4 - - - +
1725A LEU* 3.4 17.8 + - - -
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Residues in contact with SER1722 (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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1718A TRP* 6.1 0.4 - - - +
1719A PHE* 2.9 17.0 + - - +
1720A PRO 3.2 3.2 + - - -
1721A GLY* 1.3 78.4 - - - +
1723A LYS* 1.3 56.8 + - - +
1725A LEU* 4.0 0.9 - - - -
1726A ILE* 3.1 24.1 + - - -
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Residues in contact with LYS1723 (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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1718A TRP* 6.0 1.2 - - - +
1719A PHE 4.0 5.5 + - - +
1721A GLY 3.3 0.8 - - - +
1722A SER* 1.3 74.3 - - - +
1724A PRO* 1.3 59.0 - - - +
1726A ILE* 3.2 1.3 + - - +
1727A GLN* 2.8 30.3 + - - -
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Residues in contact with PRO1724 (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 GLY* 3.8 8.5 - - - +
1722A SER 3.6 0.4 - - - -
1723A LYS* 1.3 72.4 - - - +
1725A LEU* 1.3 61.0 + - - +
1727A GLN* 4.2 0.8 - - - -
1728A GLN* 3.3 19.1 + - - -
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Residues in contact with LEU1725 (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 GLY 3.4 13.3 + - - -
1722A SER 4.0 2.7 - - - -
1723A LYS 3.1 0.6 - - - -
1724A PRO* 1.3 77.2 - - - +
1726A ILE* 1.3 57.1 + - - +
1728A GLN* 3.4 1.6 + - - -
1729A ALA* 2.8 27.5 + - - -
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Residues in contact with ILE1726 (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 SER 3.1 16.0 + - - -
1723A LYS* 3.7 2.0 - - - +
1725A LEU* 1.3 74.4 - - - +
1727A GLN* 1.3 57.0 + - - +
1729A ALA* 4.4 1.1 - - - +
1730A MET* 2.8 29.6 + - - -
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Residues in contact with GLN1727 (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 LYS 2.8 16.7 + - - -
1724A PRO* 4.2 0.9 - - - -
1726A ILE* 1.3 75.1 - - - +
1728A GLN* 1.3 62.0 + - - +
1730A MET* 3.6 0.7 + - - -
1731A ALA* 3.2 18.7 + - - -
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Residues in contact with GLN1728 (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 PRO 3.3 14.6 + - - -
1725A LEU 3.8 2.0 - - - -
1726A ILE 3.2 0.2 - - - -
1727A GLN* 1.3 73.8 - - - +
1729A ALA* 1.3 65.2 + - - +
1731A ALA* 3.2 2.5 + - - +
1732A LYS* 3.0 20.1 + - - -
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Residues in contact with ALA1729 (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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1725A LEU 2.8 16.8 + - - -
1726A ILE* 3.7 1.3 - - - +
1728A GLN* 1.3 76.1 - - - +
1730A MET* 1.3 56.5 + - - +
1732A LYS* 3.2 2.9 + - - +
1733A ILE* 2.9 25.8 + - - -
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Residues in contact with MET1730 (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 ILE 2.8 15.2 + - - -
1727A GLN 4.1 0.7 - - - -
1729A ALA* 1.3 77.7 - - - +
1731A ALA* 1.3 61.8 + - - +
1733A ILE* 3.8 1.3 - - - +
1734A MET* 2.9 22.7 + - - -
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Residues in contact with ALA1731 (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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1727A GLN 3.2 14.9 + - - -
1728A GLN* 3.2 3.3 + - - +
1730A MET* 1.3 76.6 - - - +
1732A LYS* 1.3 61.4 + - - +
1734A MET* 4.0 1.1 - - - +
1735A LYS* 3.1 19.2 + - - -
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Residues in contact with LYS1732 (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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1728A GLN 3.0 13.8 + - - -
1729A ALA* 3.7 3.1 - - - +
1731A ALA* 1.3 77.4 - - - +
1733A ILE* 1.3 61.0 + - - +
1735A LYS* 3.2 3.9 + - - +
1736A ALA* 3.1 20.3 + - - -
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Residues in contact with ILE1733 (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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1729A ALA 2.9 15.4 + - - -
1730A MET* 3.8 1.3 - - - +
1732A LYS* 1.3 75.5 - - - +
1734A MET* 1.3 62.0 + - - +
1737A ASN* 2.9 32.8 + - - +
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Residues in contact with MET1734 (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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1730A MET 2.9 15.9 + - - -
1731A ALA* 4.0 1.8 - - - +
1733A ILE* 1.3 75.5 - - - +
1735A LYS* 1.3 58.0 + - - +
1736A ALA 3.7 0.5 + - - -
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Residues in contact with LYS1735 (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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1731A ALA 3.1 13.6 + - - -
1732A LYS* 3.2 5.8 + - - +
1733A ILE 3.1 0.8 - - - -
1734A MET* 1.3 77.7 - - - +
1736A ALA* 1.3 54.7 + - - +
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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