Contacts of the helix formed by residues 2041 - 2050 (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 ASN2041 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382D ARG* 5.1 2.9 - - - +
2003E ALA 4.8 1.2 + - - -
2004E ALA* 2.8 24.4 + - - +
2007E ALA* 4.4 18.4 - - - +
2036E ALA* 2.8 23.6 + - - +
2039E VAL* 3.6 15.8 - - + +
2040E ASN* 1.3 70.1 - - - +
2042E VAL* 1.3 62.7 + - - +
2043E ASP* 3.2 6.0 + - - +
2044E ALA* 2.8 33.5 + - - +
2045E ALA* 3.1 8.0 + - - +
2077E THR* 3.1 2.2 + - - -
29F LEU* 6.3 1.3 - - - +
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Residues in contact with VAL2042 (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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2040E ASN* 3.4 8.2 + - - +
2041E ASN* 1.3 71.0 - - - +
2043E ASP* 1.3 69.4 + - - +
2045E ALA* 3.0 6.9 + - - +
2046E VAL* 3.0 25.4 + - + +
2076E GLU* 3.4 18.8 - - + +
2077E THR* 3.2 36.6 - - - +
2080E VAL* 3.9 26.2 - - + -
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Residues in contact with ASP2043 (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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2041E ASN* 3.0 5.3 + - - +
2042E VAL* 1.3 79.0 - - - +
2044E ALA* 1.3 64.4 + - - +
2046E VAL* 3.0 17.1 + - - +
2047E VAL* 3.1 19.1 + - + +
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Residues in contact with ALA2044 (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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2004E ALA* 4.7 3.1 - - - +
2012E LEU* 3.6 27.4 - - + -
2036E ALA* 3.9 12.6 - - + -
2041E ASN* 2.8 39.7 + - - +
2043E ASP* 1.3 72.1 - - - +
2045E ALA* 1.3 53.0 + - - +
2047E VAL* 3.5 1.4 + - - +
2048E LEU* 2.8 44.2 + - + +
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Residues in contact with ALA2045 (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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2033E LEU* 3.9 22.2 - - + +
2036E ALA* 4.2 6.6 - - + +
2041E ASN 3.1 6.9 + - - +
2042E VAL 3.0 11.6 + - - +
2044E ALA* 1.3 77.5 - - - +
2046E VAL* 1.3 58.6 + - - +
2048E LEU* 3.3 1.7 + - - +
2049E LEU* 2.7 37.0 + - + +
2077E THR* 4.1 23.8 - - + -
2080E VAL* 4.3 12.3 - - + -
2081E LEU* 5.6 0.9 - - + -
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Residues in contact with VAL2046 (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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2042E VAL* 3.0 19.1 + - + +
2043E ASP* 3.6 6.7 - - - +
2045E ALA* 1.3 72.8 - - - +
2047E VAL* 1.3 69.3 + - + +
2049E LEU* 2.9 17.5 + - - +
2050E LYS* 3.0 44.0 + - + +
2080E VAL* 4.0 30.1 - - + -
2084E HIS* 4.9 7.0 - - + -
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Residues in contact with VAL2047 (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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2012E LEU* 4.1 9.2 - - + -
2013E GLU* 3.8 39.0 - - + +
2016E ILE* 3.5 25.8 - - + -
2043E ASP* 3.1 12.1 + - + +
2044E ALA 3.7 6.3 - - - +
2046E VAL* 1.3 79.1 - - + +
2048E LEU* 1.3 65.7 + - - +
2050E LYS* 3.3 9.0 + - - -
2051E ASN* 3.0 29.9 - - - +
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Residues in contact with LEU2048 (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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2000E LEU* 4.3 3.8 - - + -
2004E ALA* 5.1 0.2 - - + -
2012E LEU* 3.5 31.2 - - + -
2016E ILE* 4.1 15.5 - - + -
2022E VAL* 4.3 18.5 - - + +
2032E ALA* 4.1 19.1 - - + +
2033E LEU* 3.6 37.9 - - + +
2036E ALA* 4.9 0.2 - - + -
2044E ALA* 2.8 37.3 + - + +
2045E ALA* 3.6 5.2 - - - +
2047E VAL* 1.3 74.5 - - - +
2049E LEU* 1.3 63.4 + - - +
2051E ASN* 3.2 10.9 + - - +
2053E ALA* 2.8 27.9 - - + +
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Residues in contact with LEU2049 (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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2033E LEU* 4.2 17.7 - - + -
2045E ALA* 2.7 27.6 + - + +
2046E VAL 2.9 2.6 + - - +
2048E LEU* 1.3 72.9 - - - +
2050E LYS* 1.3 54.7 + - - +
2051E ASN 2.8 10.9 + - - -
2052E GLY 3.0 18.9 + - - +
2053E ALA* 4.2 6.3 - - - +
2055E LYS* 3.6 32.8 - - + -
2080E VAL* 3.6 27.1 - - + +
2081E LEU* 4.8 7.6 - - + -
2084E HIS* 3.1 43.7 - - + +
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Residues in contact with LYS2050 (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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2046E VAL* 3.0 35.8 + - + +
2047E VAL* 3.3 5.4 + - - +
2049E LEU* 1.3 72.3 - - - +
2051E ASN* 1.3 74.7 + - - +
2052E GLY 3.7 1.1 - - - -
2084E HIS* 4.5 20.2 - - + +
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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