Contacts of the helix formed by residues 1547 - 1552 (chain A) in PDB entry 5M64
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 ALA1547 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1230A SER 5.7 4.0 - - - +
1231A ALA* 5.8 8.1 - - - -
1545A ASP* 3.4 8.4 + - + +
1546A VAL* 1.3 79.5 - - + +
1548A ALA* 1.3 62.4 + - - +
1549A VAL 3.2 2.0 - - - -
1550A LEU* 3.1 21.4 - - - +
1551A LYS* 3.2 19.3 + - + +
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Residues in contact with ALA1548 (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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1524A VAL* 3.7 7.6 - - + -
1526A PHE* 3.6 26.0 - - + -
1545A ASP* 3.4 18.3 + - - +
1547A ALA* 1.3 77.2 - - - +
1549A VAL* 1.3 61.1 + - - +
1550A LEU 3.3 0.4 - - - -
1551A LYS* 3.9 10.3 - - + -
1552A THR* 2.4 37.8 + - + +
1553A TYR* 3.9 0.9 - - - -
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Residues in contact with VAL1549 (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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1526A PHE* 4.7 4.7 - - + -
1543A SER* 4.0 23.8 - - - +
1545A ASP* 3.3 27.1 - - - +
1546A VAL* 3.6 19.7 - - + +
1548A ALA* 1.3 79.7 - - - +
1550A LEU* 1.3 59.6 + - - +
1553A TYR* 3.1 30.8 - - + +
1554A GLY 3.3 6.8 - - - +
1557A ALA* 4.1 0.8 - - - +
1558A ALA* 3.6 22.3 + - + +
1561A THR* 3.8 26.7 - - + +
1562A ILE* 5.0 0.9 - - + -
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Residues in contact with LEU1550 (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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1546A VAL 3.1 22.0 - - - +
1547A ALA* 3.1 28.0 - - - +
1548A ALA 3.3 0.2 - - - -
1549A VAL* 1.3 78.1 - - - +
1551A LYS* 1.3 64.3 + - + +
1552A THR 3.1 2.0 - - - -
1553A TYR 3.9 0.2 + - - -
1554A GLY 3.2 27.4 + - - +
1555A VAL* 4.1 6.5 - - - +
1558A ALA* 3.7 9.9 - - + -
1590A THR* 5.1 2.7 - - + -
1593A GLY 4.5 4.9 - - - +
1594A THR* 3.1 47.8 - - + +
1595A TYR* 5.9 3.4 - - + -
182E ASP* 3.2 22.9 - - - +
183E PRO* 3.9 1.9 - - - +
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Residues in contact with LYS1551 (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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1547A ALA* 3.2 21.0 + - + +
1548A ALA* 3.8 7.8 + - + -
1550A LEU* 1.3 80.3 - - + +
1552A THR* 1.3 67.3 + - + +
183E PRO* 3.2 17.7 - - - +
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Residues in contact with THR1552 (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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1526A PHE* 3.8 13.0 - - + -
1527A GLN* 5.1 8.7 - - + +
1530A TRP* 4.1 18.7 - - + -
1548A ALA* 2.4 32.4 + - + +
1551A LYS* 1.3 95.1 - - + +
1553A TYR* 1.3 75.8 + - - +
144E ILE* 3.9 19.8 - - - +
183E PRO* 4.0 14.9 - - - +
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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