Contacts of the strand formed by residues 1948 - 1952 (chain A) in PDB entry 2AAV
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 PHE1948 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1870A ALA* 4.6 11.9 - - + -
1875A LEU* 3.6 47.6 - - + +
1933A SER* 3.2 8.0 - - - -
1934A ILE* 2.9 37.6 + - + +
1936A VAL* 3.7 31.6 - - + -
1943A VAL* 4.3 7.6 - - + -
1945A GLY* 3.7 25.1 - - - -
1946A SER* 3.8 15.5 - - - -
1947A PRO* 1.3 75.1 - - - +
1949A THR* 1.3 65.5 + - - +
1950A ALA 4.2 0.2 - - - -
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Residues in contact with THR1949 (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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1875A LEU 3.1 8.4 + - - +
1876A THR* 3.4 10.4 + - - +
1931A ASP* 3.9 39.7 - - + +
1932A TYR 3.5 2.5 - - - -
1933A SER* 4.0 13.5 + - - +
1947A PRO* 5.4 2.9 - - - +
1948A PHE* 1.3 79.2 + - - +
1950A ALA* 1.3 62.0 + - - +
1951A ARG* 3.3 5.7 + - + +
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Residues in contact with ALA1950 (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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1874A GLY 3.4 25.1 - - - +
1875A LEU 3.2 3.7 + - - -
1876A THR 3.6 9.2 - - - -
1877A HIS 3.6 10.5 - - - +
1924A TYR* 3.5 13.9 - - - +
1930A GLY 3.4 0.3 - - - +
1931A ASP 4.7 0.7 - - - -
1932A TYR* 2.8 42.0 + - + +
1934A ILE* 3.9 4.9 - - + +
1949A THR* 1.3 69.2 - - - +
1951A ARG* 1.3 58.5 + - - +
1952A VAL* 3.1 11.4 + - + +
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Residues in contact with ARG1951 (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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1876A THR 3.0 17.9 + - - +
1877A HIS* 3.3 32.0 + - + -
1878A GLY 3.1 13.9 + - - -
1930A GLY 3.7 6.3 - - - +
1931A ASP* 3.8 22.1 + - - +
1949A THR* 3.3 5.0 + - + +
1950A ALA* 1.3 66.1 - - - +
1952A VAL* 1.3 62.7 + - - +
1953A THR* 3.5 14.2 + - - +
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Residues in contact with VAL1952 (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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1878A GLY* 3.5 12.1 - - - -
1879A VAL 3.4 22.0 - - - +
1880A VAL* 3.5 28.0 - - + +
1924A TYR* 5.4 1.3 - - - +
1926A PRO* 3.6 19.5 - - + -
1929A PRO* 3.9 5.0 - - - +
1930A GLY 3.0 29.1 + - - +
1932A TYR* 3.3 37.0 - - + -
1950A ALA* 3.5 10.5 - - + +
1951A ARG* 1.3 73.2 + - - +
1953A THR* 1.3 58.0 + - - +
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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