Contacts of the helix formed by residues 2064 - 2073 (chain B) 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 THR2064 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2055B LYS 4.0 0.3 + - - -
2056B ASP* 3.8 18.0 + - - -
2057B MET 3.4 8.9 + - - -
2058B GLN* 4.4 2.0 - - - +
2062B GLU 3.7 4.2 + - - -
2063B GLU* 1.3 73.8 - - - +
2065B PRO* 1.3 74.4 - - - +
2066B LEU* 3.5 16.1 + - + +
2067B PHE* 2.7 43.3 + - + +
2068B LEU* 3.4 4.2 + - - +
2087B ASN 4.2 4.6 + - - +
2090B ILE* 3.7 39.0 - - + +
2091B THR 4.5 1.1 + - - +
2098B PRO* 4.8 4.9 - - + -
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Residues in contact with PRO2065 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2031B SER* 5.0 0.9 - - - +
2033B LEU* 3.9 26.7 - - + +
2034B HIS* 3.1 48.2 - - + +
2037B ALA* 3.6 10.7 - - + +
2054B ASN 4.7 2.7 - - - +
2055B LYS 3.3 17.7 - - - +
2057B MET* 3.6 7.4 - - + +
2064B THR* 1.3 89.8 - - - +
2066B LEU* 1.3 63.5 + - - +
2067B PHE 2.9 1.0 + - - -
2068B LEU* 3.3 3.2 + - + -
2069B ALA 3.1 18.4 + - - -
2081B LEU* 4.2 10.1 - - + -
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Residues in contact with LEU2066 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2055B LYS 5.0 0.2 + - - -
2064B THR* 3.7 13.7 - - + +
2065B PRO* 1.3 80.3 - - - +
2067B PHE* 1.3 63.4 + - - +
2069B ALA* 3.3 5.4 - - - +
2070B ALA* 3.0 18.1 + - + +
2078B ALA* 4.0 18.6 - - + +
2081B LEU* 4.1 20.1 - - + +
2082B LEU* 3.4 37.2 - - + -
2086B ALA* 4.4 14.8 - - + +
2087B ASN 4.3 2.2 - - - +
2088B ARG* 3.7 33.7 - - + +
2098B PRO* 4.3 8.3 - - + -
2114B LEU* 3.8 12.1 - - + -
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Residues in contact with PHE2067 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2063B GLU* 3.4 39.5 - - + -
2064B THR* 2.7 37.7 + - + +
2066B LEU* 1.3 69.5 - - - +
2068B LEU* 1.3 58.9 + - + -
2070B ALA* 2.7 26.9 + - - +
2071B ARG* 2.8 18.8 + - + -
2091B THR 5.1 0.4 - - - -
2092B ASP* 3.3 27.4 - - + -
2096B ARG* 3.6 17.7 - - + -
2097B LEU 3.4 15.3 - - - -
2098B PRO* 3.3 26.9 - - + -
2101B ILE* 3.4 36.8 - - + -
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Residues in contact with LEU2068 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A GLU* 4.7 8.1 - - + +
2030B LYS* 4.0 28.9 - - + -
2034B HIS* 4.2 23.8 - - + +
2035B TRP* 5.4 0.2 - - - -
2037B ALA 4.2 2.0 - - - -
2038B ALA* 4.2 28.7 - - + +
2059B ASN* 4.8 0.4 - - - +
2063B GLU* 3.7 31.2 - - + +
2064B THR 3.5 14.6 - - - +
2065B PRO 3.3 4.0 + - - +
2067B PHE* 1.3 76.5 - - + +
2069B ALA* 1.3 67.9 + - - +
2071B ARG* 3.6 20.8 - - - +
2072B GLU* 3.0 25.2 + - + +
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Residues in contact with ALA2069 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2037B ALA* 3.4 24.6 + - + +
2065B PRO 3.1 11.2 + - - +
2066B LEU* 3.3 13.0 - - - +
2067B PHE 2.9 1.0 + - - -
2068B LEU* 1.3 78.7 - - - +
2070B ALA* 1.3 52.5 + - - +
2072B GLU 3.0 0.3 + - - -
2073B GLY* 2.5 34.3 + - - -
2074B SER* 3.3 21.4 + - - +
2078B ALA* 4.1 17.5 - - + +
2081B LEU* 4.9 0.9 - - + -
2110B ILE* 4.0 4.5 - - - -
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Residues in contact with ALA2070 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2066B LEU* 3.0 9.3 + - + +
2067B PHE 2.7 12.8 + - - +
2069B ALA* 1.3 74.5 - - - +
2071B ARG* 1.3 60.2 + - - +
2073B GLY 3.6 0.9 - - - -
2078B ALA* 5.2 1.1 - - + +
2098B PRO* 3.9 25.8 - - + +
2101B ILE* 4.1 2.7 - - + -
2102B ALA* 3.7 14.2 - - - +
2107B HIS* 3.4 12.8 + - - -
2110B ILE* 3.5 30.2 - - + +
2114B LEU* 4.0 10.1 - - + -
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Residues in contact with ARG2071 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A GLY* 4.2 4.8 - - - -
385A GLU* 2.2 43.2 + - - -
2063B GLU* 4.7 12.9 + - - -
2067B PHE* 2.8 20.8 + - + +
2068B LEU* 3.6 25.6 - - - +
2069B ALA 2.9 2.4 + - - -
2070B ALA* 1.3 67.2 - - - +
2072B GLU* 1.3 77.6 + - - +
2073B GLY 2.8 3.1 - - - -
2101B ILE* 3.8 34.4 - - + +
2105B ARG* 3.8 37.2 - - - +
2107B HIS* 2.5 34.8 - - - -
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Residues in contact with GLU2072 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A TYR* 2.9 21.3 + - - -
382A ARG 5.1 0.2 - - - +
383A CYS* 3.1 14.0 - - - +
384A GLY* 2.3 37.3 + - - -
385A GLU* 4.0 2.1 - - - +
2038B ALA* 3.5 27.4 - - + +
2068B LEU 3.0 15.7 + - - +
2069B ALA 3.7 1.8 - - - +
2071B ARG* 1.3 94.5 + - - +
2073B GLY* 1.3 60.8 + - - +
2074B SER* 3.1 6.7 + - - +
2107B HIS* 3.5 3.2 + - - -
37C CYS* 5.6 2.4 - - - -
40C ARG* 3.3 23.4 + - - -
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Residues in contact with GLY2073 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2069B ALA 2.5 11.3 + - - -
2071B ARG 2.8 3.6 + - - -
2072B GLU* 1.3 75.5 - - - +
2074B SER* 1.3 57.0 + - - -
2075B TYR* 2.9 13.2 + - - +
2107B HIS* 3.1 26.4 - - - +
2110B ILE* 3.2 22.5 - - - +
40C ARG* 3.5 17.7 + - - -
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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