Contacts of the helix formed by residues 2030 - 2037 (chain A) in PDB entry 5DZZ
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 SER2030 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2019A ALA 5.4 0.4 - - - -
2020A GLY* 4.6 3.6 - - - -
2021A ALA 4.6 0.7 - - - -
2029A TYR* 1.3 76.1 - - - +
2031A LEU* 1.3 58.7 + - - +
2032A VAL* 3.3 14.4 - - - +
2033A GLU* 3.2 33.3 + - - +
2034A ALA* 3.0 28.1 + - - +
2059A ILE 5.4 0.4 - - - -
2061A PRO* 3.7 25.2 - - - +
2062A HIS* 4.3 3.3 + - - -
2077A LEU* 3.9 20.5 - - - +
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Residues in contact with LEU2031 (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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2018A ILE* 4.4 5.8 - - + +
2019A ALA 4.5 0.8 + - - +
2020A GLY* 3.7 29.1 - - - +
2030A SER* 1.3 74.9 - - - +
2032A VAL* 1.3 61.1 + - - +
2034A ALA* 4.2 2.1 - - - +
2035A LYS* 3.4 15.2 + - - +
2040A ILE* 4.0 19.9 - - + +
2045A THR* 3.6 21.8 + - + +
2048A LEU* 3.7 44.2 - - + -
2049A LEU* 3.7 27.6 - - + +
2052A GLN* 3.4 28.3 - - - +
2077A LEU* 5.7 0.2 - - - +
2201A LEU* 6.0 0.4 - - + -
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Residues in contact with VAL2032 (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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2030A SER* 3.3 12.8 - - - +
2031A LEU* 1.3 76.8 - - - +
2033A GLU* 1.3 69.9 + - + +
2035A LYS* 3.5 7.5 + - - +
2036A ARG* 3.3 50.4 + - - +
2045A THR* 4.6 4.3 - - + -
2049A LEU* 5.6 2.2 - - + +
2076A ASP 3.9 12.6 - - - +
2077A LEU* 3.7 30.4 + - + +
2078A ILE* 5.1 0.4 - - - -
2079A ASP* 3.4 36.6 - - - +
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Residues in contact with GLU2033 (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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2029A TYR* 3.4 18.3 - - + +
2030A SER* 3.2 33.9 + - - +
2032A VAL* 1.3 78.2 - - + +
2034A ALA* 1.3 59.9 + - - +
2036A ARG* 3.2 19.8 + - - +
2037A LYS* 3.0 41.9 + - - +
2062A HIS* 3.3 26.7 + - - -
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Residues in contact with ALA2034 (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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2021A ALA* 4.0 12.3 - - + -
2029A TYR* 4.2 5.5 - - + +
2030A SER 3.0 16.6 + - - +
2031A LEU 4.2 0.4 - - - +
2033A GLU* 1.3 77.1 - - - +
2035A LYS* 1.3 57.2 + - - +
2037A LYS* 3.5 1.4 + - - -
2038A LYS 3.1 2.9 + - - -
2039A LEU* 2.6 53.6 + - + +
2040A ILE* 3.2 31.8 + - + -
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Residues in contact with LYS2035 (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 LEU 3.4 11.5 + - - +
2032A VAL 3.6 7.4 - - - +
2033A GLU 3.1 0.6 - - - -
2034A ALA* 1.3 78.3 - - - +
2036A ARG* 1.3 66.8 + - - +
2038A LYS* 2.9 23.4 + - - +
2040A ILE* 3.4 18.1 - - - +
2042A PRO* 3.6 32.5 - - + +
2045A THR* 3.4 33.9 - - + +
2079A ASP* 3.0 38.9 + - - +
2082A ASP* 4.7 6.0 + - - +
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Residues in contact with ARG2036 (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 VAL* 3.3 50.0 + - + +
2033A GLU* 3.2 18.3 + - - +
2035A LYS* 1.3 89.3 - - - +
2037A LYS* 1.3 60.5 + - + +
2038A LYS* 3.1 11.3 + - - +
2076A ASP* 4.0 14.1 + - - +
2079A ASP* 5.1 4.2 + - - +
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Residues in contact with LYS2037 (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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2029A TYR* 3.5 43.9 - - + +
2033A GLU* 3.0 25.8 + - - +
2034A ALA 4.0 3.8 - - - +
2035A LYS 3.2 0.2 - - - -
2036A ARG* 1.3 78.3 - - + +
2038A LYS* 1.3 70.3 - - - +
2039A LEU* 3.3 21.2 + - + +
2205A LYS* 6.0 7.1 - - - +
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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