Contacts of the strand formed by residues 2141 - 2143 (chain F) in PDB entry 5G1N
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 VAL2141 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2063F ILE* 3.8 42.2 - - + -
2067F LEU* 3.4 28.3 - - + -
2073F MET* 5.3 1.3 - - + -
2074F THR 3.0 5.8 + - - +
2075F ILE* 4.0 24.6 - - + +
2076F THR 2.8 31.7 + - - -
2090F LEU* 6.5 0.2 - - + -
2139F THR* 3.3 3.3 - - - +
2140F ASP* 1.3 76.6 - - + +
2142F LEU* 1.3 57.0 + - - +
2143F TYR* 3.7 10.2 + - + +
2180F VAL* 3.5 7.9 - - + +
2182F MET* 4.2 14.6 - - - -
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Residues in contact with LEU2142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2076F THR* 3.7 30.3 - - + +
2078F VAL* 4.1 9.0 - - + -
2132F ILE* 5.1 6.5 - - + +
2135F ALA* 5.8 0.7 - - + -
2136F LEU* 4.0 29.2 - - + -
2139F THR* 3.6 6.1 - - + +
2140F ASP 4.2 0.2 - - - -
2141F VAL* 1.3 69.4 - - - +
2143F TYR* 1.3 58.8 + - - +
2144F MET* 3.5 18.5 + - + -
2167F LEU* 3.8 32.5 - - + -
2179F MET* 3.8 20.4 - - + -
2180F VAL 2.8 10.9 + - - +
2181F VAL* 3.4 5.6 - - + +
2182F MET 2.8 28.3 + - - +
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Residues in contact with TYR2143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2059F ASP* 2.9 38.6 + - - -
2063F ILE* 6.2 0.2 - - + -
2075F ILE* 4.8 7.6 - - + -
2076F THR 3.0 12.3 + - - +
2077F MET* 4.4 9.4 - - + -
2078F VAL 3.0 25.8 + - - +
2086F THR* 3.0 28.3 + - - -
2087F VAL* 3.5 31.4 - - + -
2090F LEU* 3.5 20.2 - - + -
2141F VAL* 3.7 6.9 + - + -
2142F LEU* 1.3 69.8 - - - +
2144F MET* 1.3 64.2 + - - +
2145F THR* 4.1 4.7 - - + -
2182F MET* 4.1 22.0 - - + -
2184F PRO* 3.5 25.2 - - + +
2206F GLN* 4.0 6.5 - - - -
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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