Contacts of the helix formed by residues 2033 - 2044 (chain A) in PDB entry 3ZBF
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 ASP2033 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2032A GLY* 1.3 75.7 - - - -
2034A LEU* 1.3 64.8 + - - +
2035A LEU* 3.1 17.0 + - - +
2036A THR* 2.6 41.8 + - - -
2037A TYR* 3.1 18.9 + - - +
2083A ARG* 3.7 23.0 - - - +
2085A CYS 3.2 11.7 - - - +
2086A LEU* 3.5 10.1 - - + +
3000A VGH 3.5 27.2 - - + +
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Residues in contact with LEU2034 (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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2032A GLY 3.8 0.2 + - - -
2033A ASP* 1.3 72.0 - - - +
2035A LEU* 1.3 56.1 + - - +
2037A TYR* 3.0 3.5 + - + +
2038A LEU* 2.8 52.4 + - + +
2059A LEU* 4.7 10.3 - - + -
2063A ILE* 5.1 2.5 - - + -
2082A ALA* 3.0 36.3 + - + +
2085A CYS* 2.6 27.3 + - + +
2086A LEU* 4.3 0.2 - - - +
2087A VAL* 4.0 18.2 - - + -
2098A VAL* 3.7 21.1 - - + -
2150A LEU* 4.3 4.0 - - + -
2154A ILE* 3.9 26.5 - - + -
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Residues in contact with LEU2035 (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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2033A ASP* 3.1 11.3 + - - +
2034A LEU* 1.3 79.0 - - - +
2036A THR* 1.3 57.6 + - - +
2038A LEU* 3.7 3.5 - - - +
2039A ARG* 3.1 73.8 + - - +
2082A ALA* 3.5 7.8 + - + -
2083A ARG* 3.9 28.5 - - + +
2127A TRP* 6.1 2.9 - - + -
2153A GLU* 3.8 20.0 - - - +
2158A GLY* 3.6 21.5 - - - +
2159A HIS 5.3 0.4 - - - +
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Residues in contact with THR2036 (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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2031A GLY 5.4 3.8 - - - +
2033A ASP* 2.6 34.6 + - - -
2034A LEU 3.3 0.2 - - - -
2035A LEU* 1.3 73.6 - - - +
2037A TYR* 1.3 67.7 + - - +
2039A ARG* 4.0 6.5 - - - +
2040A LYS* 3.0 47.5 + - + +
3000A VGH 4.0 19.6 - - + +
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Residues in contact with TYR2037 (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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2031A GLY* 4.0 15.2 + - - +
2033A ASP 3.1 12.7 + - - +
2034A LEU* 3.0 14.0 + - + +
2036A THR* 1.3 76.4 - - - +
2038A LEU* 1.3 64.2 + - + +
2040A LYS* 4.8 1.8 - - - -
2041A ALA* 3.2 7.4 + - - +
2051A LEU* 4.0 13.9 - - + -
2059A LEU* 5.4 2.7 - - + -
2087A VAL* 3.7 33.0 - - + -
2089A VAL* 3.3 24.7 + - - +
2090A LYS 3.7 13.7 - - - -
2091A ASP 2.8 18.2 + - - -
2092A TYR* 2.6 58.1 + + - -
2096A ARG* 3.0 31.6 + - - -
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Residues in contact with LEU2038 (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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2034A LEU* 2.8 42.0 + - + +
2035A LEU* 3.7 4.7 - - - +
2037A TYR* 1.3 78.7 - - + +
2039A ARG* 1.3 62.2 + - - +
2041A ALA* 3.2 7.1 + - - +
2042A ARG 3.1 17.3 + - - -
2051A LEU* 3.9 13.7 - - + -
2056A LEU* 4.0 10.5 - - + -
2059A LEU* 4.2 6.7 - - + -
2082A ALA* 4.4 8.5 - - + -
2153A GLU 3.6 24.9 - - - +
2154A ILE* 3.7 15.3 - - + +
2157A LEU* 3.7 40.4 - - + +
2158A GLY* 3.9 5.4 - - - +
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Residues in contact with ARG2039 (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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2035A LEU* 3.1 46.1 + - - +
2036A THR* 3.3 6.9 + - - +
2038A LEU* 1.3 73.2 - - - +
2040A LYS* 1.3 65.5 + - + +
2042A ARG* 3.2 7.1 + - - +
2043A MET* 3.1 50.6 + - + +
2157A LEU 3.8 10.3 - - - +
2158A GLY* 2.7 31.9 + - - +
2159A HIS 4.4 1.0 - - - -
2160A GLN* 4.4 22.2 + - - +
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Residues in contact with LYS2040 (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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2036A THR* 3.0 36.5 + - + +
2037A TYR* 5.3 1.1 - - - -
2039A ARG* 1.3 77.3 - - + +
2041A ALA* 1.3 64.2 + - - +
2043A MET* 4.9 2.9 - - - -
2044A ALA* 3.2 28.1 + - - +
2050A LEU* 4.5 0.2 - - - +
2092A TYR* 3.2 22.7 - - + +
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Residues in contact with ALA2041 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2037A TYR 3.2 6.5 + - - +
2038A LEU 3.3 9.9 - - - +
2040A LYS* 1.3 79.4 - - - +
2042A ARG* 1.3 61.0 + - - +
2044A ALA 4.0 3.8 + - - -
2048A GLY 4.4 0.5 - - - +
2049A PRO* 3.4 4.3 - - - +
2050A LEU* 3.0 41.3 + - + +
2051A LEU* 3.5 23.1 - - + +
2092A TYR* 3.5 27.1 + - + -
2157A LEU* 4.3 2.9 - - + -
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Residues in contact with ARG2042 (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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2038A LEU 3.1 5.7 + - - +
2039A ARG* 3.7 10.3 - - - +
2040A LYS 3.2 0.2 - - - -
2041A ALA* 1.3 78.3 - - - +
2043A MET* 1.3 94.3 + - + +
2044A ALA 3.8 0.5 + - - -
2045A THR 4.6 9.2 - - - +
2048A GLY 5.2 0.2 - - - -
2049A PRO* 4.6 13.0 - - + +
2156A THR 3.5 2.3 + - - -
2157A LEU* 3.0 48.4 + - + +
2158A GLY 3.4 19.8 + - - -
2159A HIS* 3.4 36.5 + - - +
2184A ARG* 5.3 5.8 - - - +
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Residues in contact with MET2043 (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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2039A ARG* 3.1 36.3 + - + +
2040A LYS* 3.3 4.2 + - - +
2042A ARG* 1.3 119.8 - - + +
2044A ALA* 1.3 62.7 + - - +
2045A THR* 3.6 2.6 - - - -
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Residues in contact with ALA2044 (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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2040A LYS 3.2 11.0 + - - +
2041A ALA 4.0 1.0 + - - +
2042A ARG 3.6 1.6 - - - -
2043A MET* 1.3 79.2 - - - +
2045A THR* 1.3 68.5 + - - +
2050A LEU* 3.2 38.4 - - + -
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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