Contacts of the helix formed by residues 1964 - 1972 (chain E) in PDB entry 3NBN
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 THR1964 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1934E HIS* 3.3 1.2 - - - -
1955E ALA 3.2 18.1 + - - -
1956E ASN* 4.1 14.6 + - - +
1957E ILE 3.2 8.7 + - - -
1958E GLN* 4.7 5.3 - - - +
1963E ARG* 1.3 72.9 - - - +
1965E PRO* 1.3 64.0 - - - +
1966E LEU* 3.2 17.0 + - + +
1967E HIS* 2.7 54.1 + - + +
1968E ALA 3.4 1.6 + - - -
1987E THR* 5.0 0.9 - - - +
1988E ASP 4.8 1.7 + - - +
1991E ALA* 3.4 28.7 - - + -
1999E PRO* 5.5 0.7 - - + -
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Residues in contact with PRO1965 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1931E THR* 4.1 2.0 - - + -
1933E LEU* 3.3 36.1 - - + -
1934E HIS* 3.1 52.2 - - + +
1937E ALA* 3.5 6.2 - - + +
1954E ASP 5.5 0.2 - - - +
1955E ALA* 3.8 14.1 - - - +
1957E ILE* 3.5 9.4 - - + +
1964E THR* 1.3 85.8 - - - +
1966E LEU* 1.3 51.7 + - - +
1968E ALA* 2.8 5.4 + - + +
1969E ALA* 2.7 32.2 + - - +
1981E LEU* 4.0 5.4 - - + -
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Residues in contact with LEU1966 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1964E THR* 3.0 13.7 + - + +
1965E PRO* 1.3 76.7 - - - +
1967E HIS* 1.3 52.5 + - - +
1969E ALA* 3.2 6.8 + - - +
1970E VAL* 2.8 40.0 + - + +
1978E PHE* 3.7 34.3 - - + +
1981E LEU* 3.9 22.9 - - + +
1982E ILE* 4.9 5.4 - - + +
1987E THR* 4.5 12.3 - - + -
1988E ASP 4.0 17.7 - - - +
1989E LEU* 4.2 15.7 - - + -
1999E PRO* 3.3 33.4 - - + -
2015E LEU* 4.4 8.7 - - + -
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Residues in contact with HIS1967 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1963E ARG* 3.4 17.2 - - + +
1964E THR* 2.7 47.3 + - + +
1966E LEU* 1.3 75.4 - - - +
1968E ALA* 1.3 54.5 + - - +
1970E VAL* 4.6 0.4 - - - +
1971E SER* 3.0 29.7 + - - -
1991E ALA 3.2 25.7 + - - -
1992E ARG 3.9 5.4 - - - -
1993E MET* 3.2 33.2 - - + -
1997E THR 2.6 24.7 + - - -
1998E THR 4.1 0.2 - - - -
1999E PRO* 3.3 24.6 - - + +
2002E LEU* 3.4 13.6 - - + +
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Residues in contact with ALA1968 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1930E GLU* 4.9 5.2 - - - +
1934E HIS* 3.7 30.7 - - + +
1937E ALA* 3.8 2.7 - - + -
1938E ARG* 4.2 10.9 - - + +
1959E ASP* 6.0 0.4 - - - +
1963E ARG* 4.0 17.4 - - - +
1964E THR 3.4 1.6 + - - +
1965E PRO* 2.8 15.7 + - + +
1967E HIS* 1.3 76.8 - - - +
1969E ALA* 1.3 60.1 + - - +
1971E SER* 3.2 2.8 + - - -
1972E ALA* 2.9 33.3 + - - +
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Residues in contact with ALA1969 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1937E ALA* 3.6 18.7 - - + +
1965E PRO 2.7 14.4 + - - +
1966E LEU* 3.4 8.3 - - - +
1968E ALA* 1.3 70.1 - - - +
1970E VAL* 1.3 66.0 + - - +
1972E ALA 3.3 4.5 + - - -
1974E ALA* 3.1 26.5 + - - +
1977E VAL* 4.5 2.9 - - + -
1978E PHE* 3.9 18.2 - - + +
1981E LEU* 3.8 24.9 - - + -
2011E MET* 4.2 2.5 - - - +
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Residues in contact with VAL1970 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1966E LEU* 2.8 24.0 + - + +
1967E HIS 3.9 4.3 - - - +
1969E ALA* 1.3 70.5 - - - +
1971E SER* 1.3 64.9 + - - +
1973E ASP* 3.0 15.2 + - - -
1978E PHE* 4.2 23.1 - - + -
1999E PRO* 3.9 24.2 - - + +
2002E LEU* 4.0 12.8 - - + -
2003E ALA* 3.6 35.0 - - + +
2006E LEU* 4.5 2.2 - - + +
2008E VAL* 4.1 10.7 - - + +
2011E MET* 4.0 18.9 - - - +
2015E LEU* 4.9 2.7 - - + -
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Residues in contact with SER1971 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D ASN* 3.4 34.6 + - - +
350D GLY 4.5 0.9 - - - -
358D GLU* 5.4 0.7 + - - -
1963E ARG* 3.0 41.0 + - - -
1967E HIS 3.0 12.1 + - - -
1968E ALA 3.2 3.6 + - - -
1970E VAL* 1.3 76.1 - - - +
1972E ALA* 1.3 57.4 + - - +
1973E ASP 3.4 3.6 + - - -
2002E LEU* 3.8 6.4 - - - +
2006E LEU* 3.6 23.1 - - - +
26F ARG* 4.9 6.6 + - - -
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Residues in contact with ALA1972 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D GLY* 3.9 21.4 - - - +
1937E ALA 4.1 4.0 - - - +
1938E ARG* 3.4 34.0 - - - +
1940E SER* 5.3 2.1 + - - -
1968E ALA 2.9 16.5 + - - +
1969E ALA 4.0 2.7 - - - +
1970E VAL 3.1 0.8 - - - -
1971E SER* 1.3 76.4 - - - +
1973E ASP* 1.3 68.2 + - - +
1974E ALA* 2.9 6.3 + - + +
26F ARG* 5.0 4.8 + - - +
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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