Contacts of the helix formed by residues 2031 - 2039 (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 SER2031 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2001B ILE* 3.5 2.0 - - - -
2022B VAL 4.6 6.5 - - - -
2023B ASN 4.4 1.8 - - - -
2024B ALA 3.8 15.7 - - - -
2025B VAL* 3.9 1.4 - - - +
2030B LYS* 1.3 75.2 - - - +
2032B ALA* 1.3 59.8 + - - +
2033B LEU* 3.4 12.3 + - - +
2034B HIS* 2.7 47.1 + - - +
2035B TRP* 3.0 5.9 + - - -
2054B ASN 5.0 0.2 + - - -
2057B MET* 3.7 34.1 - - - +
2065B PRO* 5.0 0.3 - - - +
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Residues in contact with ALA2032 (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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2000B LEU* 3.4 46.0 - - + +
2001B ILE* 3.0 19.9 - - + +
2004B ALA* 3.7 11.8 - - + +
2022B VAL 4.8 3.0 + - - +
2024B ALA 4.4 1.6 + - - -
2031B SER* 1.3 74.0 - - - +
2033B LEU* 1.3 56.2 + - - +
2035B TRP* 4.4 2.2 - - - -
2036B ALA* 2.8 32.1 + - - +
2048B LEU* 4.0 9.0 - - + -
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Residues in contact with LEU2033 (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* 3.0 11.5 + - - +
2032B ALA* 1.3 74.1 - - - +
2034B HIS* 1.3 69.7 + - - +
2036B ALA* 3.5 2.2 + - - +
2037B ALA* 3.0 18.0 + - - +
2045B ALA* 3.9 39.3 - - + +
2048B LEU* 3.6 22.3 - - + +
2049B LEU* 4.3 11.0 - - + -
2053B ALA* 4.9 7.0 - - + -
2054B ASN 3.8 22.0 - - - +
2055B LYS* 3.8 15.9 - - - -
2057B MET* 6.0 0.2 - - + -
2065B PRO* 3.9 15.0 - - + -
2081B LEU* 3.9 16.8 - - + -
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Residues in contact with HIS2034 (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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2029B GLY 4.1 0.2 - - - -
2030B LYS* 3.3 18.8 - - + -
2031B SER* 2.7 36.0 + - - +
2033B LEU* 1.3 76.0 - - - +
2035B TRP* 1.3 52.7 + - - +
2037B ALA* 2.7 28.2 + - - +
2038B ALA* 3.0 9.4 + - - +
2057B MET* 3.4 31.2 + - + -
2058B GLN 3.7 12.1 - - - -
2059B ASN* 3.9 6.3 - - + -
2063B GLU 2.5 27.9 + - - -
2064B THR 3.7 0.9 - - - -
2065B PRO* 3.1 44.1 - - + +
2068B LEU* 4.2 16.4 - - + +
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Residues in contact with TRP2035 (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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360A THR* 5.1 3.4 - - + -
383A CYS* 4.3 15.7 - - - -
385A GLU* 4.5 17.5 - - + -
386A SER* 3.9 19.5 - - - -
1997B THR* 4.9 0.7 - - + -
2001B ILE* 3.4 25.9 - - + +
2004B ALA* 4.8 3.1 - - + -
2005B ARG* 3.2 59.0 - - + -
2026B ASP* 3.0 28.6 + - - -
2030B LYS* 3.7 35.3 - - + +
2031B SER 3.0 14.5 + - - -
2032B ALA* 3.8 7.6 - - - +
2034B HIS* 1.3 77.7 - - - +
2036B ALA* 1.3 55.5 + - - +
2038B ALA* 2.7 28.9 + - + +
2039B VAL* 2.8 18.3 + - - +
2068B LEU* 5.0 0.9 - - - +
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Residues in contact with ALA2036 (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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2004B ALA* 4.3 6.5 - - + +
2032B ALA 2.8 22.2 + - - +
2033B LEU* 3.6 7.9 - - - +
2035B TRP* 1.3 73.8 - - - +
2037B ALA* 1.3 59.3 + - - +
2039B VAL* 3.9 3.1 - - - -
2040B ASN 3.4 1.4 + - - -
2041B ASN* 2.7 41.0 + - + +
2044B ALA* 3.8 29.8 - - + -
2045B ALA* 4.3 8.7 - - + +
2048B LEU* 5.0 1.3 - - + -
2077B THR* 3.7 4.0 + - - -
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Residues in contact with ALA2037 (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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2033B LEU* 3.0 10.3 + - + +
2034B HIS 2.7 18.5 + - - +
2036B ALA* 1.3 71.9 - - - +
2038B ALA* 1.3 58.3 + - - -
2040B ASN 3.6 0.2 + - - -
2065B PRO* 3.6 29.8 - - + +
2069B ALA* 3.4 13.5 - - + +
2074B SER* 2.7 27.2 + - - -
2077B THR* 3.5 24.2 - - + +
2081B LEU* 4.8 4.0 - - + -
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Residues in contact with ALA2038 (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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382A ARG 4.4 0.7 - - - +
383A CYS* 3.6 27.6 - - + +
385A GLU* 4.9 2.9 - - - +
2034B HIS 3.0 6.9 + - - +
2035B TRP* 2.7 26.7 + - + +
2037B ALA* 1.3 73.8 - - - +
2039B VAL* 1.3 56.8 + - - +
2040B ASN 3.2 3.6 + - - -
2068B LEU* 4.2 22.6 - - + +
2072B GLU* 3.5 31.6 - - + +
2074B SER* 4.3 1.2 + - - -
33C HIS* 5.2 1.2 + - - -
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Residues in contact with VAL2039 (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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382A ARG* 3.8 55.0 + - + +
383A CYS* 3.8 20.9 - - - -
386A SER* 4.4 0.2 - - - +
2004B ALA 3.9 11.2 - - - +
2005B ARG* 4.0 17.9 - - + +
2035B TRP* 2.8 19.5 + - + +
2036B ALA* 4.0 1.1 - - - -
2037B ALA 3.3 0.2 - - - -
2038B ALA* 1.3 76.4 - - - +
2040B ASN* 1.3 68.6 + - - +
2041B ASN* 3.1 23.8 + - + -
33C HIS* 3.7 13.3 + - - -
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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