Contacts of the helix formed by residues 1998 - 2006 (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 THR1998 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1967B HIS* 3.7 2.2 - - - -
1989B LEU 5.3 0.2 - - - -
1990B ASP* 4.1 21.3 - - - +
1991B ALA 3.5 3.4 - - - +
1992B ARG* 4.5 9.6 - - + +
1996B GLY 3.6 6.9 + - - +
1997B THR* 1.3 75.8 - - - +
1999B PRO* 1.4 68.3 - - - +
2000B LEU* 3.6 11.6 + - - +
2001B ILE* 2.7 58.7 + - + +
2002B LEU* 3.3 7.8 + - - +
2024B ALA* 4.0 27.2 + - + +
2025B VAL 4.9 2.0 - - - +
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Residues in contact with PRO1999 (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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1964B THR* 5.5 0.9 - - + -
1966B LEU* 3.4 36.3 - - + -
1967B HIS* 3.3 29.8 - - + +
1970B VAL* 3.9 13.9 - - + +
1989B LEU 3.7 13.5 - - - +
1991B ALA 3.4 10.8 - - - +
1998B THR* 1.4 83.4 - - - +
2000B LEU* 1.3 54.4 + - - +
2002B LEU* 3.4 6.9 + - + +
2003B ALA* 2.8 35.9 + - - +
2015B LEU* 3.7 14.5 - - + +
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Residues in contact with LEU2000 (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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1989B LEU 5.1 1.9 + - - +
1990B ASP* 5.2 1.8 - - - +
1998B THR* 3.1 11.0 - - - +
1999B PRO* 1.3 81.3 - - - +
2001B ILE* 1.3 59.5 + - - +
2003B ALA* 4.0 0.7 - - + -
2004B ALA* 3.3 14.4 + - - +
2012B LEU* 3.6 36.7 - - + +
2015B LEU* 3.5 24.8 - - + +
2016B ILE* 4.3 10.8 - - + -
2020B ALA* 4.5 17.3 - - + -
2021B ASP 4.6 7.9 - - - +
2022B VAL* 4.4 19.7 - - - +
2032B ALA* 3.4 36.6 - - + +
2048B LEU* 4.3 12.1 - - + -
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Residues in contact with ILE2001 (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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1997B THR* 4.1 10.3 - - + -
1998B THR* 2.7 47.6 + - + +
2000B LEU* 1.3 73.1 - - - +
2002B LEU* 1.3 68.6 + - - +
2004B ALA* 2.8 14.7 + - - +
2005B ARG* 3.0 24.0 + - - +
2024B ALA 4.5 5.6 - - - +
2026B ASP* 5.1 4.5 - - + +
2030B LYS 3.7 12.8 - - - +
2031B SER* 3.5 7.2 - - - -
2032B ALA* 3.0 38.1 - - + +
2035B TRP* 3.4 33.4 - - + +
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Residues in contact with LEU2002 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A GLU* 4.8 3.4 - - - +
1963B ARG* 5.0 1.1 - - - +
1967B HIS* 3.6 33.9 - - + +
1970B VAL* 3.9 13.7 - - + -
1971B SER* 3.8 13.7 - - - +
1993B MET* 3.6 30.7 - - + -
1997B THR* 4.4 7.0 - - - -
1998B THR 3.3 9.6 + - - +
1999B PRO* 3.8 3.4 - - + +
2001B ILE* 1.3 73.7 - - - +
2003B ALA* 1.3 67.9 + - - +
2005B ARG* 2.8 51.7 + - - +
2006B LEU* 2.8 24.6 + - + +
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Residues in contact with ALA2003 (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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1970B VAL* 3.6 16.9 - - + +
1999B PRO 2.8 23.2 + - - +
2000B LEU* 3.7 9.2 - - - +
2002B LEU* 1.3 74.8 - - - +
2004B ALA* 1.3 61.0 + - - +
2007B ALA* 4.0 1.7 + - - -
2008B VAL* 3.7 28.2 + - - +
2011B MET* 4.6 3.4 - - + -
2012B LEU* 4.1 32.4 - - - +
2015B LEU* 4.4 5.4 - - + -
2041B ASN* 4.8 1.0 + - - -
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Residues in contact with ALA2004 (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 3.3 10.4 + - - +
2001B ILE 2.8 15.2 + - - +
2003B ALA* 1.3 75.2 - - - +
2005B ARG* 1.3 59.5 + - - +
2007B ALA 4.1 0.3 + - - -
2012B LEU* 4.0 12.5 - - + +
2032B ALA* 3.7 29.4 - - + +
2035B TRP* 4.8 1.3 - - + -
2036B ALA* 4.3 11.7 - - + +
2039B VAL* 3.9 5.6 - - - +
2041B ASN* 2.6 32.3 + - - +
2044B ALA* 4.8 2.0 - - + -
2048B LEU* 5.1 0.4 - - + -
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Residues in contact with ARG2005 (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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347A GLN* 4.9 6.7 - - - +
358A GLU* 2.9 40.8 + - - +
360A THR* 4.0 15.5 - - - +
382A ARG* 2.9 30.7 + - + -
386A SER* 4.9 2.2 - - - +
1963B ARG* 6.1 0.2 - - - +
1993B MET* 5.5 1.0 - - - +
1995B ASP* 4.9 2.6 + - - -
1997B THR* 3.6 21.8 + - - +
2001B ILE* 3.0 12.4 + - - +
2002B LEU* 2.8 39.9 + - - +
2004B ALA* 1.3 68.7 - - - +
2006B LEU* 1.3 63.3 + - + +
2007B ALA 2.6 18.4 + - - -
2035B TRP* 3.2 64.3 - - + -
2039B VAL* 4.0 17.9 - - + -
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Residues in contact with LEU2006 (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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349A ASN* 3.3 23.8 - - - +
358A GLU* 3.6 36.6 - - + +
382A ARG* 4.8 4.3 - - + +
388A LEU* 4.1 17.8 - - + +
1970B VAL* 4.6 2.2 - - + +
1971B SER* 3.5 35.9 - - - +
2002B LEU* 2.8 31.6 + - + +
2003B ALA* 5.3 0.2 - - - -
2005B ARG* 1.3 75.7 - - + +
2007B ALA* 1.3 70.0 + - - +
2008B VAL* 3.3 16.2 + - + +
26C ARG* 3.9 10.3 + - - +
30C CYS* 5.2 3.3 - - - -
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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