Contacts of the helix formed by residues 2021 - 2042 (chain A) in PDB entry 5NDD
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 ASN2021 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2020A ASP* 1.3 89.9 + - - +
2022A ALA* 1.3 64.6 + - - +
2023A ALA* 3.3 12.7 + - + +
2024A GLN* 3.2 47.9 - - - +
2025A VAL* 3.3 18.5 + - - +
2083A VAL* 4.2 0.7 - - - -
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Residues in contact with ALA2022 (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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2020A ASP 3.9 0.8 + - - -
2021A ASN* 1.3 71.3 - - - +
2023A ALA* 1.3 63.6 + - - +
2024A GLN 3.5 0.2 - - - -
2025A VAL* 3.7 5.3 + - - +
2026A LYS* 3.2 25.1 + - - +
2078A ALA* 5.4 9.5 - - - +
2081A GLY* 6.0 2.7 - - - -
2083A VAL* 3.7 33.9 - - + +
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Residues in contact with ALA2023 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2021A ASN* 3.1 15.4 - - + +
2022A ALA* 1.3 76.4 - - - +
2024A GLN* 1.3 62.3 + - + +
2026A LYS* 4.0 2.9 - - - +
2027A ASP* 3.0 31.0 + - - +
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Residues in contact with GLN2024 (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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2015A VAL* 4.5 11.4 - - + +
2018A LYS 4.8 0.9 - - - +
2019A ALA* 3.4 27.3 - - + +
2020A ASP* 4.3 3.9 - - - +
2021A ASN* 3.2 34.4 + - - +
2023A ALA* 1.3 80.2 - - + +
2025A VAL* 1.3 56.8 + - - +
2027A ASP* 3.8 6.1 - - - +
2028A ALA* 3.0 30.7 + - - +
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Residues in contact with VAL2025 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2016A ILE* 4.4 19.4 - - + +
2019A ALA* 4.2 11.4 - - + -
2021A ASN 3.3 16.6 - - - +
2022A ALA* 3.9 9.4 - - - +
2023A ALA 3.2 0.8 - - - -
2024A GLN* 1.3 75.9 - - - +
2026A LYS* 1.3 66.6 + - - +
2027A ASP 3.3 0.2 + - - -
2028A ALA* 3.3 4.6 + - - +
2029A LEU* 3.1 33.8 + - + +
2078A ALA* 4.5 4.0 - - + -
2083A VAL* 4.8 7.4 - - + +
2086A ALA* 4.1 27.6 - - + -
2087A GLN* 4.0 27.4 - - + +
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Residues in contact with LYS2026 (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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2022A ALA 3.2 15.1 + - - +
2023A ALA* 4.1 3.6 - - - +
2025A VAL* 1.3 79.2 - - - +
2027A ASP* 1.3 55.9 + - - +
2029A LEU* 3.5 5.3 + - - +
2030A THR* 2.7 38.1 + - - +
2075A LEU* 4.0 10.5 - - + +
2078A ALA* 4.1 21.7 - - + +
2079A ASN* 3.3 28.5 + - - +
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Residues in contact with ASP2027 (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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2012A ASN* 5.1 0.2 - - - +
2023A ALA 3.0 20.0 + - - +
2024A GLN* 3.8 7.5 - - - +
2026A LYS* 1.3 75.6 - - - +
2028A ALA* 1.3 66.6 + - - +
2030A THR* 3.3 6.2 + - - -
2031A LYS* 3.2 57.4 + - - +
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Residues in contact with ALA2028 (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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2012A ASN* 3.5 40.9 - - + +
2015A VAL* 4.2 11.9 - - + -
2016A ILE* 3.7 14.4 - - + -
2024A GLN 3.0 19.2 + - - +
2025A VAL 3.9 0.2 - - - +
2027A ASP* 1.3 77.0 + - - +
2029A LEU* 1.3 60.8 + - - +
2031A LYS 3.4 0.2 + - - -
2032A MET* 2.8 32.4 + - - +
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Residues in contact with LEU2029 (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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2016A ILE* 3.7 12.6 - - + -
2025A VAL* 3.1 28.0 + - + +
2026A LYS 3.8 0.7 - - - +
2027A ASP 3.3 0.2 - - - -
2028A ALA* 1.3 76.6 - - - +
2030A THR* 1.3 57.0 + - - +
2032A MET* 3.4 24.6 + - + +
2033A ARG* 2.9 29.6 + - - +
2071A ILE* 3.5 18.1 - - + +
2074A ALA* 3.6 49.8 - - + +
2075A LEU* 3.6 23.8 - - + +
2078A ALA* 4.1 8.5 - - + -
2086A ALA* 4.9 2.2 - - + +
2093A LEU* 4.2 5.6 - - + -
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Residues in contact with THR2030 (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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2026A LYS* 2.7 29.6 + - - +
2027A ASP* 3.7 6.1 - - - -
2028A ALA 3.3 0.2 - - - -
2029A LEU* 1.3 77.4 - - - +
2031A LYS* 1.3 63.4 + - + +
2033A ARG* 3.4 11.4 + - + +
2034A ALA* 3.3 21.5 + - - +
2075A LEU* 4.0 14.2 - - + +
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Residues in contact with LYS2031 (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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2008A THR* 4.0 7.6 - - + +
2012A ASN* 3.4 26.9 - - - +
2027A ASP* 3.2 44.4 + - - +
2030A THR* 1.3 75.2 - - + +
2032A MET* 1.3 64.3 + - - +
2034A ALA* 3.6 4.9 + - - +
2035A ALA* 3.1 23.4 + - - +
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Residues in contact with MET2032 (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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2008A THR 4.9 1.3 - - - -
2009A LEU* 3.6 25.6 - - + +
2012A ASN* 4.1 10.9 - - + +
2013A LEU* 3.7 34.8 - - + -
2016A ILE* 3.6 17.9 - - + -
2028A ALA 2.8 14.6 + - - +
2029A LEU* 3.6 34.1 - - + +
2031A LYS* 1.3 74.7 - - - +
2033A ARG* 1.3 64.9 + - - +
2035A ALA* 3.4 6.6 + - - +
2036A ALA* 3.1 22.3 + - - +
2067A LEU* 6.1 2.5 - - - -
2071A ILE* 4.3 12.1 - - + -
2093A LEU* 3.7 16.2 - - + -
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Residues in contact with ARG2033 (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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2029A LEU 2.9 17.9 + - - +
2030A THR* 3.5 12.3 - - - +
2031A LYS 3.2 0.2 - - - -
2032A MET* 1.3 77.7 - - - +
2034A ALA* 1.3 62.9 + - - +
2036A ALA* 3.3 4.5 + - - +
2037A LEU* 3.1 48.1 + - + +
2068A VAL* 3.2 28.3 + - + +
2071A ILE* 4.0 19.5 - - + +
2072A ASP* 2.5 45.9 + - - -
2075A LEU* 4.4 11.7 - - - -
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Residues in contact with ALA2034 (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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2030A THR 3.3 12.6 + - - +
2031A LYS* 4.1 5.8 - - - +
2033A ARG* 1.3 80.7 - - - +
2035A ALA* 1.3 59.9 + - - +
2037A LEU* 3.2 12.7 + - + +
2038A ASP* 2.8 36.9 + - - +
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Residues in contact with ALA2035 (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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2005A ASN* 3.7 25.1 - - - +
2008A THR* 3.7 29.2 - - + -
2009A LEU* 4.1 8.3 - - - +
2031A LYS 3.1 19.3 + - - +
2032A MET* 3.6 6.5 - - - +
2033A ARG 3.2 0.4 - - - -
2034A ALA* 1.3 79.9 - - - +
2036A ALA* 1.3 60.0 + - - +
2038A ASP* 3.7 2.2 + - - -
2039A ALA* 3.3 22.3 + - - +
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Residues in contact with ALA2036 (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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2009A LEU* 4.1 13.7 - - + +
2032A MET 3.1 16.6 + - - +
2033A ARG 3.3 4.9 + - - +
2034A ALA 3.2 0.2 - - - -
2035A ALA* 1.3 75.2 - - - +
2037A LEU* 1.3 61.1 + - - +
2038A ASP 3.3 0.4 - - - -
2039A ALA* 3.9 0.7 - - - -
2040A GLN* 3.1 24.3 + - - +
2064A PHE* 3.3 36.2 - - + +
2067A LEU* 4.4 7.0 - - + -
2068A VAL* 4.3 13.2 - - + -
2071A ILE* 4.7 2.9 - - + -
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Residues in contact with LEU2037 (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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2033A ARG* 3.1 47.9 + - + +
2034A ALA* 3.2 12.5 + - + +
2036A ALA* 1.3 79.6 - - - +
2038A ASP* 1.3 60.5 + - - +
2040A GLN* 3.7 23.3 - - - +
2041A LYS* 3.4 31.9 - - - +
2065A ASP* 6.1 0.7 - - - +
2068A VAL* 3.8 27.1 - - + -
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Residues in contact with ASP2038 (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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2005A ASN* 3.7 26.5 + - - +
2034A ALA* 2.8 30.4 + - - +
2035A ALA* 4.0 1.1 - - - +
2037A LEU* 1.3 76.0 - - - +
2039A ALA* 1.3 64.4 + - - +
2040A GLN 3.1 1.8 - - - -
2041A LYS* 3.2 27.1 + - - +
2042A ALA* 3.3 12.1 + - - +
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Residues in contact with ALA2039 (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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2002A LEU* 4.4 3.6 - - + +
2005A ASN* 3.6 22.1 - - + +
2035A ALA 3.3 15.8 + - - +
2036A ALA 3.6 0.2 + - - -
2038A ASP* 1.3 79.0 - - - +
2040A GLN* 1.3 61.2 + - - +
2042A ALA* 3.3 22.1 + - - +
2060A PHE* 3.5 12.3 - - - -
2064A PHE* 3.8 24.5 - - + -
2105A LEU* 4.3 14.4 - - + -
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Residues in contact with GLN2040 (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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2036A ALA 3.1 18.5 + - - +
2037A LEU* 3.7 27.5 - - - +
2039A ALA* 1.3 80.4 - - - +
2041A LYS* 1.3 62.9 + - - +
2042A ALA 3.5 0.9 + - - +
2057A MET* 4.9 1.7 - - - +
2060A PHE* 3.8 7.4 - - - -
2061A ARG* 3.3 52.7 + - + +
2064A PHE* 4.0 25.2 - - + +
2065A ASP* 2.9 30.5 + - - -
2068A VAL* 6.1 0.4 - - - -
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Residues in contact with LYS2041 (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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2037A LEU* 3.4 26.1 - - - +
2038A ASP* 3.2 19.2 + - - +
2040A GLN* 1.3 83.6 - - + +
2042A ALA* 1.3 61.9 + - - +
2043A THR* 4.1 1.7 + - - -
2057A MET* 5.8 1.5 - - - +
2061A ARG* 5.6 1.3 - - - +
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Residues in contact with ALA2042 (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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2002A LEU* 3.9 29.2 - - + +
2005A ASN* 4.9 3.1 - - - +
2038A ASP 3.3 12.0 + - - +
2039A ALA* 3.5 11.1 - - - +
2040A GLN 3.2 1.5 - - - +
2041A LYS* 1.3 81.9 - - - +
2043A THR* 1.3 64.5 + - - +
2044A PRO* 3.4 8.7 - - - +
2057A MET* 4.4 3.9 - - - +
2060A PHE* 3.5 14.6 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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