Contacts of the strand formed by residues 1712 - 1715 (chain C) in PDB entry 3COJ
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 TRP1712 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1856B PRO* 5.7 8.1 - - + +
1685C THR* 3.0 22.8 + - - +
1686C HIS* 3.4 27.6 - + + +
1687C VAL 2.8 26.7 + - - +
1710C GLY 5.4 1.1 - - - -
1711C LYS* 1.3 72.1 - - - +
1713C VAL* 1.3 62.8 + - - +
1714C VAL* 3.4 22.2 + - + +
1731C GLU* 4.2 7.2 - - + -
1732C HIS* 3.3 66.2 - + - -
1735C GLU* 3.9 19.5 - - + -
1753C ARG* 3.5 46.8 - - - +
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Residues in contact with VAL1713 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1687C VAL* 3.1 16.8 - - + +
1689C MET* 3.8 26.7 - - + -
1703C TYR* 4.0 9.4 - - + +
1706C GLY* 3.7 37.2 - - - -
1707C ILE* 3.9 11.0 - - + +
1711C LYS 3.4 6.6 + - - +
1712C TRP* 1.3 71.8 - - - +
1714C VAL* 1.3 59.5 + - - +
1735C GLU* 3.6 13.1 + - - +
1736C VAL* 2.9 46.4 + - + +
1749C PRO* 4.1 10.6 + - + +
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Residues in contact with VAL1714 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1686C HIS* 4.8 2.2 - - + -
1687C VAL 2.8 8.1 + - - +
1688C VAL* 3.0 15.1 - - + -
1689C MET 2.9 23.1 + - - -
1712C TRP* 3.8 28.7 - - + +
1713C VAL* 1.3 78.9 - - - +
1715C SER* 1.3 73.4 + - - +
1718C TRP* 3.8 15.3 - - + -
1731C GLU* 3.4 35.4 - - + +
1734C PHE* 3.4 25.8 - - + +
1735C GLU* 4.4 1.3 - - - -
1736C VAL* 4.7 2.9 - - - -
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Residues in contact with SER1715 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1688C VAL* 4.0 2.8 - - - +
1689C MET 3.4 7.2 - - - -
1691C THR* 2.4 36.3 + - - -
1695C PHE* 3.9 17.1 - - - -
1714C VAL* 1.3 74.1 - - - +
1716C TYR* 1.3 59.0 + - - +
1717C PHE* 3.0 19.4 + - - +
1718C TRP* 3.0 29.2 + - - +
1734C PHE* 2.7 20.5 + - - -
1736C VAL* 4.4 2.8 - - - +
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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