Contacts of the helix formed by residues 1737 - 1751 (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 ASN1737 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1733A ILE* 2.9 23.7 + - - +
1736A ALA* 1.3 69.7 - - - +
1738A PRO* 1.3 63.3 - - - +
1739A ALA 3.2 3.1 - - - -
1740A LEU* 3.0 15.5 + - - -
1741A TYR* 3.0 9.7 + - - -
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Residues in contact with PRO1738 (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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1736A ALA 3.1 6.6 - - - +
1737A ASN* 1.3 69.7 - - - +
1739A ALA* 1.3 56.8 - - - +
1741A TYR* 3.2 3.9 + - - +
1742A VAL* 2.8 25.8 + - - -
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Residues in contact with ALA1739 (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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1737A ASN 3.2 1.4 + - - -
1738A PRO* 1.3 75.0 - - - +
1740A LEU* 1.3 63.2 + - - +
1742A VAL* 3.2 3.0 + - - +
1743A LEU* 3.1 18.0 + - - -
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Residues in contact with LEU1740 (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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1737A ASN* 3.0 8.3 + - - +
1739A ALA* 1.3 75.1 - - - +
1741A TYR* 1.3 62.0 + - - +
1743A LEU* 3.2 4.1 + - - +
1744A ARG* 3.0 18.9 + - - -
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Residues in contact with TYR1741 (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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1736A ALA 5.8 0.2 - - - -
1737A ASN 3.0 12.8 + - - -
1738A PRO* 3.2 5.8 + - - -
1740A LEU* 1.3 75.1 - - - +
1742A VAL* 1.3 61.8 + - - +
1744A ARG* 3.1 3.7 + - - +
1745A GLU* 2.8 21.0 + - - -
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Residues in contact with VAL1742 (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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1738A PRO 2.8 14.8 + - - -
1739A ALA* 3.2 4.2 + - - +
1741A TYR* 1.3 74.2 - - - +
1743A LEU* 1.3 57.8 + - - +
1745A GLU* 3.2 2.8 + - - +
1746A ARG* 2.9 26.3 + - - -
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Residues in contact with LEU1743 (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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1492A GLY 5.7 0.2 - - - -
1739A ALA 3.1 12.5 + - - -
1740A LEU* 3.2 4.7 + - - +
1742A VAL* 1.3 76.1 - - - +
1744A ARG* 1.3 61.6 + - - +
1746A ARG* 3.2 3.4 + - - +
1747A ILE* 3.0 19.2 + - - -
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Residues in contact with ARG1744 (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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1492A GLY 4.7 7.4 - - - -
1493A THR* 4.2 27.2 - - - +
1740A LEU 3.0 13.0 + - - -
1741A TYR* 3.1 4.2 + - - +
1743A LEU* 1.3 75.1 - - - +
1745A GLU* 1.3 56.9 - - - +
1747A ILE* 3.2 2.9 + - - +
1748A ARG* 2.9 25.8 + - - -
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Residues in contact with GLU1745 (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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1741A TYR 2.8 14.7 + - - -
1742A VAL* 3.6 3.1 - - - +
1744A ARG* 1.3 75.1 - - - +
1746A ARG* 1.3 57.0 + - - +
1748A ARG* 3.2 2.8 + - - +
1749A LYS* 2.9 25.8 + - - -
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Residues in contact with ARG1746 (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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1742A VAL 2.9 13.4 + - - -
1743A LEU 3.2 4.4 + - - -
1745A GLU* 1.3 75.9 - - - +
1747A ILE* 1.3 55.8 + - - +
1749A LYS* 3.2 3.1 + - - +
1750A GLY* 2.9 25.5 + - - -
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Residues in contact with ILE1747 (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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1492A GLY 6.0 0.9 - - - -
1493A THR* 5.6 5.8 - - - +
1743A LEU 3.0 14.6 + - - -
1744A ARG* 3.2 4.0 + - - +
1746A ARG* 1.3 75.2 - - - +
1748A ARG* 1.3 57.5 + - - +
1750A GLY* 3.2 3.1 + - - -
1751A LEU* 2.9 25.3 + - - -
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Residues in contact with ARG1748 (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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1493A THR* 5.3 3.7 - - - +
1744A ARG 2.9 14.1 + - - -
1745A GLU* 3.2 3.8 + - - +
1747A ILE* 1.3 78.1 - - - +
1749A LYS* 1.3 55.9 + - - +
1751A LEU* 3.4 1.5 + - - +
1752A GLN* 2.9 23.0 + - - -
1753A LEU* 3.3 18.1 + - - +
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Residues in contact with LYS1749 (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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1745A GLU 2.9 14.4 + - - -
1746A ARG* 3.2 4.0 + - - +
1748A ARG* 1.3 75.1 - - - +
1750A GLY* 1.3 61.6 + - - +
1752A GLN* 3.0 14.5 + - - +
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Residues in contact with GLY1750 (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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1533A ARG* 4.1 18.1 - - - -
1746A ARG 2.9 14.5 + - - -
1747A ILE* 3.2 4.5 + - - -
1749A LYS* 1.3 77.3 - - - +
1751A LEU* 1.3 57.2 + - - +
1752A GLN 3.5 0.3 + - - -
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Residues in contact with LEU1751 (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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1503A TRP* 5.6 1.0 - - - -
1504A GLU* 4.9 4.5 + - - +
1533A ARG* 5.2 9.9 - - - +
1747A ILE 2.9 15.1 + - - -
1748A ARG* 3.5 3.1 - - - +
1750A GLY* 1.3 74.4 - - - +
1752A GLN* 1.3 63.0 - - - +
1753A LEU* 3.3 4.5 + - - -
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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