Contacts of the helix formed by residues 2064 - 2073 (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 THR2064 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2056E ASP* 3.8 21.0 + - - -
2057E MET 3.4 7.9 - - - -
2058E GLN* 4.5 1.4 - - - +
2062E GLU 3.6 4.8 + - - -
2063E GLU* 1.3 73.6 - - - +
2065E PRO* 1.4 73.1 - - - +
2066E LEU* 3.7 13.7 + - + +
2067E PHE* 2.7 45.6 + - + +
2068E LEU* 3.4 4.0 + - - +
2087E ASN 4.1 5.6 + - - +
2090E ILE* 3.8 36.6 - - + +
2091E THR 4.9 1.3 - - - +
2098E PRO* 4.7 5.4 - - + -
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Residues in contact with PRO2065 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2031E SER* 4.9 0.9 - - - +
2033E LEU* 3.8 22.0 - - + +
2034E HIS* 3.0 48.9 - - + +
2037E ALA* 3.6 10.7 - - + +
2054E ASN 4.6 3.6 - - - +
2055E LYS 3.3 23.6 - - - +
2057E MET 3.5 7.9 - - - +
2064E THR* 1.4 84.5 - - - +
2066E LEU* 1.3 61.2 + - - +
2067E PHE 2.9 5.6 + - - -
2068E LEU* 3.3 3.8 + - + -
2069E ALA* 3.1 18.5 + - - +
2081E LEU* 4.2 9.6 - - + -
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Residues in contact with LEU2066 (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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2064E THR* 3.2 13.2 - - + +
2065E PRO* 1.3 79.7 - - - +
2067E PHE* 1.3 56.6 + - - +
2069E ALA* 3.5 0.6 - - - +
2070E ALA* 3.1 25.3 + - + +
2078E ALA* 3.9 20.4 - - + +
2081E LEU* 4.0 19.5 - - + +
2082E LEU* 3.3 37.9 - - + -
2086E ALA* 4.3 15.7 - - + -
2087E ASN 4.4 3.1 - - - +
2088E ARG* 3.7 34.1 - - + +
2098E PRO* 4.4 7.9 - - + -
2114E LEU* 3.7 11.4 - - + -
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Residues in contact with PHE2067 (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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2063E GLU* 3.3 41.1 - - + -
2064E THR* 2.7 39.2 + - + +
2066E LEU* 1.3 68.7 - - - +
2068E LEU* 1.3 53.5 + - + -
2069E ALA 3.1 0.4 - - - -
2070E ALA* 2.7 24.9 + - - +
2071E ARG* 2.7 24.1 + - + -
2091E THR 5.2 0.4 - - - -
2092E ASP* 3.3 26.9 - - + -
2096E ARG* 3.7 17.7 - - - -
2097E LEU 3.5 14.1 - - - -
2098E PRO* 3.3 29.2 - - + -
2101E ILE* 3.3 38.1 - - + -
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Residues in contact with LEU2068 (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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385D GLU* 4.7 9.0 - - + +
2030E LYS* 4.0 26.9 - - + -
2034E HIS* 4.0 26.7 - - + +
2035E TRP* 4.9 0.7 - - - +
2037E ALA 4.2 2.5 - - - -
2038E ALA* 4.2 28.3 - - + +
2059E ASN* 4.8 0.7 - - - +
2063E GLU* 3.7 31.0 - - + +
2064E THR 3.5 14.8 - - - +
2065E PRO 3.3 4.2 + - - +
2067E PHE* 1.3 78.8 - - + +
2069E ALA* 1.3 67.3 + - - +
2071E ARG* 3.1 20.3 + - - +
2072E GLU* 2.9 25.8 + - + +
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Residues in contact with ALA2069 (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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2037E ALA* 3.4 26.2 + - + +
2065E PRO 3.1 12.5 + - - +
2066E LEU* 3.5 12.1 - - - +
2067E PHE 3.1 0.2 - - - -
2068E LEU* 1.3 78.9 - - - +
2070E ALA* 1.3 53.7 + - - +
2072E GLU 3.5 0.2 - - - -
2073E GLY* 2.5 35.0 + - - -
2074E SER* 3.3 19.4 + - - +
2078E ALA* 4.1 17.7 - - + +
2081E LEU* 4.8 0.4 - - + -
2110E ILE* 4.0 3.8 - - - -
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Residues in contact with ALA2070 (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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2066E LEU* 3.1 11.6 + - + +
2067E PHE 2.7 11.4 + - - +
2069E ALA* 1.3 74.3 - - - +
2071E ARG* 1.3 62.7 + - - +
2073E GLY 3.8 0.9 - - - -
2078E ALA* 5.1 1.1 - - + +
2098E PRO* 3.9 24.2 - - + +
2101E ILE* 3.9 3.1 - - + +
2102E ALA* 3.6 14.9 - - - +
2107E HIS* 3.5 12.0 + - - -
2110E ILE* 3.5 31.0 - - + +
2114E LEU* 4.0 10.3 - - + -
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Residues in contact with ARG2071 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384D GLY* 4.3 4.6 - - - -
385D GLU* 2.3 40.6 + - - -
2063E GLU* 4.7 13.7 + - - -
2067E PHE* 2.7 21.6 + - + +
2068E LEU* 3.5 23.6 - - - +
2069E ALA 2.9 0.8 + - - -
2070E ALA* 1.3 68.7 - - - +
2072E GLU* 1.4 76.6 + - - +
2073E GLY 2.8 3.1 - - - -
2101E ILE* 3.8 33.8 - - + +
2105E ARG* 3.8 36.8 + - - +
2107E HIS* 2.5 36.6 + - - -
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Residues in contact with GLU2072 (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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381D TYR* 2.8 22.8 + - - -
382D ARG 5.1 0.2 - - - +
383D CYS* 3.1 13.8 - - - +
384D GLY* 2.5 35.2 + - - -
385D GLU* 3.7 3.1 - - - +
2038E ALA* 3.5 26.1 - - + +
2068E LEU* 2.9 19.6 + - - +
2069E ALA 3.9 1.3 - - - +
2071E ARG* 1.4 89.4 + - - +
2073E GLY* 1.3 60.1 + - - +
2074E SER* 3.2 8.4 + - - +
2107E HIS* 3.5 3.3 - - - -
37F CYS* 5.7 2.3 - - - -
40F ARG* 3.3 22.5 + - - -
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Residues in contact with GLY2073 (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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2069E ALA 2.5 16.1 + - - -
2070E ALA 4.0 0.2 - - - -
2071E ARG 2.8 2.8 + - - -
2072E GLU* 1.3 74.8 - - - +
2074E SER* 1.3 58.2 + - - -
2075E TYR* 2.8 13.3 + - - +
2107E HIS* 3.1 26.6 - - - +
2110E ILE* 3.2 17.7 - - - +
40F ARG* 3.5 18.5 + - - -
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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