Contacts of the strand formed by residues 212 - 216 (chain C) in PDB entry 2P2N
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 ILE 212 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A TYR* 2.5 32.8 + - + -
220A GLY 5.2 3.2 + - - +
210C GLN* 3.4 8.0 + - + +
211C PRO* 1.3 79.3 - - - +
213C GLY* 1.3 63.2 + - - +
214C VAL* 5.2 0.2 - - + -
234C VAL* 4.7 2.7 - - - -
236C ALA* 3.4 23.3 - - + +
238C ILE* 4.2 12.1 - - + -
306C LEU* 3.7 23.8 - - + -
309C LEU* 3.8 23.1 - - + -
310C HIS* 3.5 35.4 - - + +
313C LEU* 4.1 18.8 - - + -
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Residues in contact with GLY 213 (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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218A TYR* 3.5 4.7 - - - -
212C ILE* 1.3 75.8 - - - +
214C VAL* 1.3 65.2 + - - +
215C VAL 4.1 0.2 - - - -
229C PHE* 3.7 25.8 - - - -
234C VAL* 4.3 4.2 - - - +
236C ALA 3.1 10.4 + - - -
237C LEU* 3.5 10.6 - - - -
238C ILE 2.9 24.9 + - - -
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Residues in contact with VAL 214 (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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214A VAL 4.8 4.5 - - - +
215A VAL* 5.6 0.5 - - - -
216A THR* 4.0 27.4 + - + +
218A TYR* 3.6 42.9 + - + -
212C ILE* 5.1 0.4 - - + +
213C GLY* 1.3 76.3 - - - +
215C VAL* 1.3 61.9 + - - +
216C THR 4.0 1.2 + - - -
229C PHE* 4.5 7.9 - - - -
238C ILE* 3.6 25.1 - - + +
240C ARG* 4.0 30.1 - - + -
302C VAL* 4.5 14.4 - - + -
306C LEU* 5.0 2.9 - - + -
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Residues in contact with VAL 215 (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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214A VAL 5.6 0.9 - - - -
214C VAL* 1.3 74.7 - - - +
216C THR* 1.3 58.3 + - - +
217C ILE* 3.9 4.8 + - + +
221C ILE* 3.7 28.7 - - + -
225C VAL* 4.4 12.3 - - + -
226C VAL* 5.3 4.7 - - + -
229C PHE* 3.7 27.1 - - + -
237C LEU* 3.9 26.2 - - + -
238C ILE 2.8 12.8 + - - +
239C LEU* 3.5 15.1 - - + -
240C ARG* 2.7 35.2 + - - +
253C PHE* 4.9 3.6 - - + -
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Residues in contact with THR 216 (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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214A VAL* 4.1 32.5 + - + +
216A THR* 3.5 15.9 + - - -
302A VAL* 5.5 0.7 - - + -
214C VAL 4.0 1.8 + - - -
215C VAL* 1.3 74.2 - - - +
217C ILE* 1.3 71.3 + - - +
218C TYR* 3.0 28.5 - - + -
221C ILE* 3.5 8.7 - - - +
240C ARG* 2.9 39.7 + - - +
272C GLN* 4.1 3.4 - - - +
9010C EDO 4.0 16.4 - - - +
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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