Contacts of the helix formed by residues 1744 - 1755 (chain A) in PDB entry 5A31
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 ASP1744 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1703A ALA* 4.4 18.5 - - - +
1742A THR* 3.9 14.6 + - - -
1743A SER* 1.3 81.7 + - - +
1745A PRO* 1.3 75.1 - - + +
1746A ALA* 4.2 6.3 - - + +
1747A LEU* 3.0 33.8 + - - +
1748A LEU* 2.9 23.1 + - - +
1784A PRO* 4.7 4.2 - - - +
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Residues in contact with PRO1745 (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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1743A SER 4.2 4.5 - - - +
1744A ASP* 1.3 82.9 - - + +
1746A ALA* 1.3 63.1 + - - +
1748A LEU* 4.2 4.2 - - + +
1749A SER* 3.0 28.4 + - - -
606O GLN* 5.8 1.6 - - - +
609O ALA* 3.7 25.0 - - + +
613O GLU* 4.0 18.4 - - - +
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Residues in contact with ALA1746 (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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1744A ASP* 3.0 6.0 + - + +
1745A PRO* 1.3 80.0 - - - +
1747A LEU* 1.3 70.2 + - + +
1749A SER 3.9 0.5 - - - -
1750A PHE* 3.1 24.4 + - - +
602O PRO* 5.2 4.7 - - + +
605O LEU* 3.9 27.3 - - + +
606O GLN* 4.8 17.6 - - + +
609O ALA* 4.9 0.4 - - - +
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Residues in contact with LEU1747 (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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1703A ALA* 6.2 0.7 - - + -
1742A THR* 5.3 6.1 - - - +
1744A ASP* 3.0 24.8 + - - +
1746A ALA* 1.3 90.9 - - + +
1748A LEU* 1.3 66.4 - - - +
1750A PHE* 3.1 18.2 + - + +
1751A ALA* 3.2 10.2 + - - +
1775A LEU* 3.8 13.3 - - + +
1778A CYS* 4.8 4.9 - - + +
1779A VAL* 3.5 39.0 - - + +
1784A PRO* 4.1 39.5 - - + +
1787A LEU* 5.3 9.9 - - + -
605O LEU* 6.4 0.4 - - + -
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Residues in contact with LEU1748 (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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1739A SER* 3.6 30.3 - - - +
1740A ALA 4.6 1.3 - - - +
1742A THR 4.2 2.8 + - - +
1743A SER* 3.5 34.3 - - - -
1744A ASP 2.9 16.9 + - - +
1745A PRO* 4.2 4.0 - - + +
1747A LEU* 1.3 77.6 - - - +
1749A SER* 1.3 60.2 + - - +
1751A ALA* 3.3 16.7 + - + +
1752A GLU* 3.5 27.8 + - + +
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Residues in contact with SER1749 (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 PRO 3.0 20.4 + - - -
1746A ALA 4.0 1.3 - - - -
1748A LEU* 1.3 75.0 - - - +
1750A PHE* 1.3 65.7 + - - +
1752A GLU* 4.1 9.3 + - - -
1753A TYR* 3.1 39.4 + - - +
605O LEU* 3.8 14.3 - - - +
608O LEU* 3.1 30.5 - - - +
609O ALA* 4.7 7.9 - - - -
612O LYS* 4.4 3.9 + - - -
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Residues in contact with PHE1750 (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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1746A ALA 3.1 14.8 + - - +
1747A LEU* 3.1 14.6 + - + +
1749A SER* 1.3 77.0 - - - +
1751A ALA* 1.3 62.2 + - - +
1754A PHE* 3.0 47.6 + + + +
1755A CYS* 3.4 21.3 - - - -
1771A PHE* 3.6 31.4 - + - -
1775A LEU* 3.5 26.7 - - + -
1787A LEU* 4.0 36.8 - - + -
1791A ILE* 4.7 2.7 - - + -
601O LEU* 4.0 15.0 - - + -
605O LEU* 3.7 22.4 - - + +
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Residues in contact with ALA1751 (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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1733A PHE* 6.4 0.2 - - + -
1734A LYS* 5.5 8.7 - - + +
1739A SER* 5.1 13.5 - - - +
1747A LEU 3.2 8.2 + - - +
1748A LEU* 3.3 16.1 + - + +
1750A PHE* 1.3 78.7 - - - +
1752A GLU* 1.3 58.6 + - + +
1755A CYS* 2.9 38.7 + - + +
1756A LYS* 2.9 12.2 + - - +
1775A LEU* 4.2 12.3 - - + -
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Residues in contact with GLU1752 (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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1748A LEU* 3.5 30.5 + - + +
1749A SER* 4.1 6.5 + - - +
1750A PHE 3.4 0.4 - - - -
1751A ALA* 1.3 79.3 - - + +
1753A TYR* 1.3 89.3 + - + +
1754A PHE 3.6 0.2 + - - -
1756A LYS* 3.7 40.6 + - - +
1758A THR* 5.7 0.7 - - - +
612O LYS* 5.3 3.2 + - - -
639O GLN* 3.7 11.8 + - - -
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Residues in contact with TYR1753 (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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1749A SER* 3.1 31.9 - - - +
1750A PHE 3.3 1.2 + - - -
1751A ALA 3.3 0.4 - - - -
1752A GLU* 1.3 105.3 + - + +
1754A PHE* 1.3 73.3 + - + +
605O LEU* 5.0 0.2 - - + -
608O LEU* 4.0 14.3 - - + +
612O LYS* 3.0 29.8 + - - -
624O VAL* 5.0 7.9 - - + +
627O LEU* 3.9 15.9 - - + -
631O GLN* 3.4 24.4 + - - +
639O GLN* 3.3 13.1 + - - +
643O LEU* 3.2 33.9 - - + +
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Residues in contact with PHE1754 (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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1750A PHE* 3.0 55.7 + + + +
1753A TYR* 1.3 92.3 - - + +
1755A CYS* 1.3 64.7 + - - +
1756A LYS 3.7 2.6 + - - +
1768A LEU* 3.4 22.9 - - - +
1771A PHE* 4.5 7.9 - + + +
601O LEU* 4.6 7.0 - - + -
605O LEU* 4.4 7.6 - - + -
627O LEU* 4.2 23.8 - - + -
630O ALA* 4.6 7.6 - - + -
631O GLN* 3.5 27.6 - - + -
634O LEU* 3.6 26.7 - - + -
636O ILE* 3.6 29.8 - - + +
639O GLN* 4.0 3.5 + - - +
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Residues in contact with CYS1755 (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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1734A LYS 3.9 24.9 - - - +
1750A PHE* 3.4 39.9 - - - -
1751A ALA* 2.9 25.9 + - + +
1754A PHE* 1.3 74.1 - - - +
1756A LYS* 1.3 59.2 + - - -
1757A PRO* 3.7 2.3 - - - +
1768A LEU* 3.0 24.6 - - - +
1771A PHE* 4.1 2.5 - - - -
1772A SER* 3.9 29.4 - - - -
1775A LEU* 4.6 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