Contacts of the strand formed by residues 2209 - 2213 (chain L) in PDB entry 2BT4
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 ILE2209 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2204L LEU* 4.4 17.0 - - + -
2208L PRO* 1.3 72.7 - - - +
2210L MET* 1.3 73.0 + - - +
2211L ILE* 3.6 6.1 + - + -
2244L ALA* 4.7 4.5 - - + -
2250L THR 2.8 17.9 + - - +
2251L VAL* 3.2 7.3 - - + +
2252L ASP 2.9 23.5 + - - -
2273L HIS* 4.2 0.4 - - - -
2274L CYS* 3.7 18.4 - - - -
2275L GLY 3.7 14.8 - - - +
2277L VAL* 4.0 20.6 - - + -
2342L VAL* 3.8 31.9 - - + +
2345L ILE* 4.0 20.6 - - + -
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Residues in contact with MET2210 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2208L PRO 3.8 2.8 + - - -
2209L ILE* 1.3 71.6 - - - +
2211L ILE* 1.3 60.3 + - - +
2212L LEU* 3.3 34.5 - - + -
2252L ASP* 3.5 18.2 - - - +
2254L ARG* 3.5 36.3 - - - +
2265L TRP 3.6 22.2 - - - +
2268L GLU* 4.4 1.8 - - - -
2269L ALA* 3.9 14.1 - - + +
2273L HIS* 3.3 41.9 - - + +
2275L GLY 3.0 14.9 + - - +
2276L ILE* 3.3 5.2 - - + +
2277L VAL 2.8 26.2 + - - +
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Residues in contact with ILE2211 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2209L ILE* 3.8 10.8 - - + +
2210L MET* 1.3 73.9 - - - +
2212L LEU* 1.3 63.9 + - - +
2213L ASN* 3.9 2.2 + - - +
2240L CYS* 3.8 20.4 - - + -
2251L VAL* 3.9 25.4 - - + -
2252L ASP 2.9 10.2 + - - +
2253L PHE* 3.7 28.9 - - + -
2254L ARG 2.9 27.2 + - - +
2277L VAL* 3.2 22.0 - - + +
2338L TYR* 4.1 22.7 - - + -
2342L VAL* 4.1 13.7 - - + -
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Residues in contact with LEU2212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2210L MET* 3.3 39.7 - - + -
2211L ILE* 1.3 77.5 - - - +
2213L ASN* 1.3 63.3 + - - +
2254L ARG* 3.8 5.2 - - + -
2262L LEU* 4.6 10.8 - - + +
2265L TRP* 4.1 27.8 - - + -
2266L ILE* 3.7 40.8 - - + +
2276L ILE* 4.3 13.7 - - + -
2277L VAL 2.8 10.3 + - - +
2278L ILE* 3.3 17.9 - - + -
2279L ASN 2.9 27.1 + - - +
2338L TYR* 5.3 0.2 - - - -
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Residues in contact with ASN2213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2211L ILE* 3.9 5.9 + - - +
2212L LEU* 1.3 80.1 - - - +
2214L GLY* 1.3 59.5 + - - +
2217L LEU* 3.9 10.1 - - + +
2233L LEU* 4.2 6.6 - - + +
2253L PHE* 3.2 35.1 - - - -
2254L ARG 3.0 24.7 + - - +
2255L GLN* 3.1 15.7 - - + -
2256L SER 3.0 25.8 + - - +
2262L LEU* 3.8 7.5 - - - +
2278L ILE* 6.1 0.2 - - - -
2279L ASN* 3.4 3.2 - - - +
2338L TYR* 2.7 35.0 + - - -
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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