Contacts of the strand formed by residues 2036 - 2040 (chain A) in PDB entry 5NUG
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 PHE2036 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1901A GLY* 3.7 19.5 - - - +
1902A GLY 4.4 1.1 - - - -
1903A SER* 3.3 18.8 + - - +
1945A PHE* 5.9 0.2 - + - -
1960A PHE* 4.8 6.5 - + - -
1975A VAL* 4.0 26.2 - - + -
2014A ILE* 3.7 34.5 - - + -
2015A PHE 4.2 3.1 - - - -
2016A ILE* 3.4 45.3 - - + -
2028A LEU* 5.9 2.7 - - + -
2032A LEU* 3.3 39.0 + - + +
2033A LYS* 3.2 20.8 - - + +
2034A LYS 3.6 0.6 - - - -
2035A LEU* 1.3 77.7 - - + +
2037A ARG* 1.3 64.0 + - - +
2038A SER* 3.4 7.8 + - - -
4255A ARG* 5.3 0.7 + - - -
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Residues in contact with ARG2037 (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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1891A THR* 4.1 8.3 - - + +
1892A MET* 4.3 4.4 - - - +
1894A GLN* 4.1 22.0 - - - +
1895A ALA* 3.9 17.0 - - + +
1898A ALA* 5.9 2.0 - - - +
1900A LEU* 3.4 29.0 - - + +
1901A GLY 2.8 17.3 + - - +
1902A GLY* 3.7 2.1 - - - -
1903A SER* 2.8 28.1 + - - -
2033A LYS 6.1 0.2 - - - -
2034A LYS 6.1 0.2 - - - +
2035A LEU 4.0 1.4 + - - -
2036A PHE* 1.3 69.7 - - - +
2038A SER* 1.3 62.1 + - - +
4210A SER* 5.5 6.5 - - - -
4211A ASP* 5.2 8.9 + - - +
4214A SER* 4.1 23.9 + - - -
4218A THR* 6.1 0.6 - - - +
4250A SER* 2.6 45.9 + - - -
4251A ILE* 3.3 24.5 - - - +
4255A ARG* 6.2 1.1 - - - +
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Residues in contact with SER2038 (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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1891A THR* 3.6 14.4 - - - +
1903A SER* 3.2 21.4 + - - -
1905A PHE* 4.4 9.2 - - - -
2033A LYS* 5.0 12.5 - - - +
2036A PHE 3.4 7.5 + - - -
2037A ARG* 1.3 79.4 + - - +
2039A LEU* 1.3 65.7 + - - +
4250A SER 3.9 8.7 - - - +
4254A GLY* 4.0 3.7 - - - -
4255A ARG* 3.5 39.7 + - - +
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Residues in contact with LEU2039 (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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1887A ARG* 3.8 26.2 - - + +
1888A CYS* 3.5 44.0 - - + -
1891A THR* 3.8 18.2 - - + +
1892A MET* 4.0 17.0 - - + -
1903A SER 3.4 2.4 + - - -
1904A PRO* 4.1 10.5 - - + -
1905A PHE* 2.8 32.1 + - - -
2038A SER* 1.3 80.7 - - - +
2040A ALA* 1.3 80.4 + - - +
2041A MET* 4.1 8.1 - - + -
4249A GLN 4.7 0.7 - - - +
4254A GLY* 2.9 16.3 + - - -
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Residues in contact with ALA2040 (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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1884A LEU* 4.8 3.5 - - - +
1887A ARG* 4.3 13.7 + - - +
1905A PHE* 3.6 8.5 - - + -
2039A LEU* 1.3 89.4 - - - +
2041A MET* 1.3 70.8 + - - +
2042A THR* 4.0 5.2 - - - +
4254A GLY* 2.8 10.3 + - - +
4256A VAL 3.3 27.4 - - - +
4257A ASP* 3.9 20.9 - - - +
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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