Contacts of the helix formed by residues 2002 - 2007 (chain H) in PDB entry 2VKZ
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 LYS2002 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLN* 5.1 11.0 - - - +
1497H GLU* 2.7 43.6 + - + +
1498H THR 5.2 2.6 + - - -
1819H ALA 5.5 3.0 + - - +
1999H GLU 4.7 5.4 - - - +
2000H ASN 3.4 11.0 + - - +
2001H VAL* 1.3 73.1 - - - +
2003H VAL* 1.3 67.9 + - - +
2004H ALA* 3.3 2.9 - - + +
2005H ARG* 3.2 35.7 + - + +
2006H LEU* 4.0 7.0 + - - +
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Residues in contact with VAL2003 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B PRO 5.1 0.9 - - - +
6B GLU* 4.0 31.6 - - + +
7B GLN* 3.9 37.5 - - + +
10B ALA* 3.4 28.0 - - + -
2001H VAL* 3.6 4.0 + - - +
2002H LYS* 1.3 72.3 - - - +
2004H ALA* 1.3 58.4 + - - +
2006H LEU* 3.1 8.7 + - - +
2007H ALA* 2.9 33.0 + - + +
2019H PHE* 4.9 3.8 - - + -
2021H VAL* 4.2 7.4 - - + -
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Residues in contact with ALA2004 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2002H LYS* 3.2 1.7 + - + -
2003H VAL* 1.3 78.2 - - - +
2005H ARG* 1.3 62.0 + - + +
2006H LEU 3.3 0.5 + - - -
2007H ALA* 4.0 14.2 + - - +
2009H LYS* 3.3 22.0 + - - -
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Residues in contact with ARG2005 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1496H LYS 6.3 0.2 - - - -
1497H GLU* 5.9 6.5 - - - +
1793H LYS* 4.4 9.2 - - - +
1804H PHE* 3.5 23.0 - - - -
1817H SER 5.0 0.2 + - - -
1818H LEU 2.7 35.4 + - - +
1819H ALA* 2.8 45.4 - - + +
1820H ASP* 3.1 27.1 + - - +
2002H LYS* 3.2 29.3 + - + +
2003H VAL 3.1 0.4 - - - -
2004H ALA* 1.3 78.2 - - + +
2006H LEU* 1.3 58.4 + - - +
2009H LYS* 4.0 16.9 + - - +
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Residues in contact with LEU2006 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 3.9 20.2 - - + -
1804H PHE* 3.9 7.9 - - + -
1815H LEU* 3.4 31.6 - - + -
1819H ALA* 3.5 22.4 - - + -
1821H VAL* 4.7 2.2 - - + -
2001H VAL* 3.8 29.4 - - + -
2002H LYS 4.3 7.0 - - - +
2003H VAL* 3.1 5.1 + - - +
2005H ARG* 1.3 79.8 - - - +
2007H ALA* 1.3 66.4 + - - +
2008H GLY 3.1 1.4 + - - -
2009H LYS* 2.9 2.2 + - - -
2010H TYR* 2.9 32.3 + - + +
2019H PHE* 3.6 28.8 - - + +
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Residues in contact with ALA2007 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2003H VAL* 2.9 25.6 + - + +
2004H ALA* 4.0 10.0 + - - +
2005H ARG 4.0 0.2 - - - -
2006H LEU* 1.3 74.0 - - - +
2008H GLY* 1.3 59.2 + - - +
2009H LYS* 3.2 13.7 + - - +
2019H PHE* 3.2 17.2 - - + +
2020H GLN* 4.2 14.1 - - - +
2021H VAL* 5.7 2.5 - - + +
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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