Contacts of the strand formed by residues 1931 - 1935 (chain A) in PDB entry 4M6W
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 ARG1931 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1861A MET* 5.8 4.0 - - + -
1893A ARG* 5.7 11.6 - - - +
1894A ILE 3.2 11.3 + - - +
1895A CYS* 3.2 16.8 - - + -
1896A VAL* 3.0 25.6 + - - +
1929A GLY* 3.1 32.1 + - - -
1930A ILE* 1.3 72.6 - - - +
1932A ILE* 1.3 59.6 + - - +
86B LYS* 4.4 17.8 - - - +
109B VAL* 4.3 24.2 - - + +
113B GLY* 3.5 25.9 + - - -
114B MET* 4.3 9.4 + - - +
115B VAL* 4.9 14.3 - - + +
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Residues in contact with ILE1932 (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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1896A VAL* 3.3 20.4 - - + +
1898A VAL* 3.4 27.4 - - + -
1922A LEU* 4.8 14.8 - - + -
1925A LEU* 5.3 9.2 - - + -
1926A ILE* 4.5 20.2 - - + -
1930A ILE 3.9 10.3 - - - +
1931A ARG* 1.3 76.2 - - - +
1933A LEU* 1.3 89.9 + - - +
1934A PHE* 3.6 29.4 - - + -
105B GLN* 4.3 2.6 - - - +
109B VAL* 4.6 10.3 - - - +
115B VAL* 4.9 11.8 - - + +
116B LEU 4.6 6.9 + - - +
117B LEU* 5.4 4.0 - - + -
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Residues in contact with LEU1933 (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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1895A CYS* 3.1 35.2 - - - -
1896A VAL 2.9 6.1 + - - -
1897A ILE* 3.4 16.6 - - + -
1898A VAL 2.8 24.7 + - - -
1931A ARG* 5.2 0.4 - - + -
1932A ILE* 1.3 81.9 - - - +
1934A PHE* 1.3 62.7 + - - +
1944A LEU* 4.2 21.3 - - + -
1948A LEU* 4.3 18.8 - - + -
105B GLN* 3.4 29.6 - - + +
109B VAL* 3.7 28.3 - - + -
110B LEU* 3.9 12.1 - - + -
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Residues in contact with PHE1934 (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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1868A GLN* 6.2 2.7 - - + -
1898A VAL* 3.5 33.9 - - + +
1900A LYS* 6.4 0.7 - - - -
1918A TYR* 4.6 11.2 - - - -
1922A LEU* 4.9 15.7 - - + -
1932A ILE* 3.6 28.3 - - + -
1933A LEU* 1.3 74.5 - - - +
1935A SER* 1.3 61.9 - - - +
1940A GLU* 3.6 7.4 - - - +
1944A LEU* 3.9 3.5 - - - +
93B LYS* 5.1 8.7 - - - +
101B PHE* 4.1 15.6 - + + -
105B GLN* 2.8 38.3 + - - +
116B LEU 3.8 11.9 - - - -
117B LEU* 5.1 3.1 - - + -
118B PRO* 3.4 42.8 - - + -
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Residues in contact with SER1935 (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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1897A ILE* 3.8 15.9 - - - -
1898A VAL 3.0 7.3 + - - +
1899A GLU* 3.5 6.5 - - - +
1900A LYS* 3.0 33.4 + - - +
1934A PHE* 1.3 74.1 - - - +
1936A SER* 1.3 58.3 + - - +
1937A CYS 2.6 29.3 + - - -
1940A GLU* 3.5 7.3 - - - +
1941A THR* 2.7 21.1 + - - -
1944A LEU* 3.9 9.9 - - - -
93B LYS* 6.0 0.2 - - - -
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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