Contacts of the helix formed by residues 2059 - 2063 (chain B) in PDB entry 1V9P
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 SER2059 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2014B ARG* 3.5 15.1 - - - +
2018B ARG* 4.4 0.2 - - - +
2044B LEU* 3.4 5.0 - - - +
2048B GLU* 2.8 26.2 + - - -
2056B SER* 3.2 16.7 + - - -
2057B PRO 4.3 0.5 - - - +
2058B ASP* 1.3 78.6 - - - +
2060B PRO* 1.3 70.1 - - - +
2061B THR* 2.7 32.7 + - - -
2062B GLU* 2.8 19.3 + - - +
2063B GLN* 4.2 4.4 + - - +
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Residues in contact with PRO2060 (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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2014B ARG* 4.0 11.0 - - + +
2017B ILE* 3.9 27.8 - - + -
2018B ARG* 4.1 14.1 - - + +
2037B TYR* 5.4 0.2 - - - +
2041B LEU* 3.7 24.8 - - + +
2044B LEU* 3.9 9.6 - - + -
2058B ASP 3.9 5.4 - - - +
2059B SER* 1.3 87.4 - - - +
2061B THR* 1.3 59.4 + - - +
2062B GLU 3.2 0.4 + - - -
2063B GLN* 3.6 6.5 + - + +
2064B VAL* 3.4 20.6 + - - +
2069B LEU* 4.2 30.1 - - + +
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Residues in contact with THR2061 (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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2041B LEU* 4.2 17.7 - - + +
2044B LEU* 4.6 1.6 - - + -
2045B LYS* 3.7 43.1 + - + +
2048B GLU* 2.6 29.1 + - - +
2059B SER* 2.7 18.3 + - - +
2060B PRO* 1.3 75.9 - - - +
2062B GLU* 1.3 67.8 + - - +
2063B GLN 3.2 0.7 + - - -
2064B VAL* 3.6 27.8 - - + +
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Residues in contact with GLU2062 (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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2045B LYS* 5.8 1.7 + - - -
2055B LYS* 6.5 0.2 - - - -
2056B SER 3.0 27.7 + - - +
2057B PRO* 3.1 40.7 - - + +
2059B SER* 2.8 11.3 + - - +
2061B THR* 1.3 86.8 + - - +
2063B GLN* 1.3 60.8 + - + +
2064B VAL* 4.9 1.8 - - - +
2072B THR* 5.7 1.3 - - + -
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Residues in contact with GLN2063 (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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2057B PRO 5.1 1.4 + - - -
2058B ASP 5.4 4.2 + - - -
2059B SER 4.6 6.2 + - - +
2060B PRO* 4.1 6.0 - - - +
2062B GLU* 1.3 77.7 - - + +
2064B VAL* 1.3 75.5 + - - +
2065B GLY* 4.2 0.5 - - - -
2067B ARG* 6.0 1.0 - - - +
2068B PRO 4.7 0.2 - - - +
2069B LEU* 3.7 28.6 - - + +
2070B GLU* 2.7 51.7 + - - +
2072B THR* 3.8 20.8 - - - +
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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