Contacts of the strand formed by residues 217 - 223 (chain C) in PDB entry 2I3T
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 ARG 217 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191C GLY 4.9 4.5 - - - -
192C LEU* 3.7 16.6 - - + +
193C LYS* 3.8 24.8 - - - +
212C SER* 3.5 4.2 - - - -
213C SER* 3.2 32.3 + - - +
215C ASP* 2.9 38.9 + - - +
216C GLY* 1.3 75.6 - - - +
218C VAL* 1.3 72.7 + - - +
237C ALA* 4.3 16.8 - - + +
238C PHE 3.4 13.6 - - - +
239C ARG* 4.4 6.5 - - - +
240C CYS* 4.1 1.3 - - - -
242C ARG* 3.2 25.4 - - - +
254C VAL* 3.8 4.2 - - - +
356D GLU* 5.0 1.2 + - - -
8E GLN* 5.0 5.8 + - - -
48E ASP* 2.6 36.9 + - - +
49E LEU 5.2 2.3 + - - -
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Residues in contact with VAL 218 (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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210C ALA* 4.7 0.7 - - + -
211C CYS 3.4 12.8 - - - +
212C SER* 4.2 14.4 - - - -
217C ARG* 1.3 79.8 - - - +
219C ALA* 1.3 69.5 + - - +
220C VAL* 4.3 2.9 - - + -
237C ALA* 3.3 2.6 - - - -
238C PHE* 3.0 61.7 + - + -
240C CYS* 3.5 21.1 - - - -
254C VAL* 4.3 1.6 - - + -
257C ILE* 4.7 1.8 - - + -
266C LEU* 4.0 16.2 - - + -
268C THR* 4.0 20.9 - - + -
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Residues in contact with ALA 219 (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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190C SER 3.7 22.9 - - - +
191C GLY* 4.0 13.9 - - - +
192C LEU* 3.9 19.0 - - + +
209C TYR* 4.0 1.0 - - - +
210C ALA* 3.2 3.8 - - - +
211C CYS* 2.9 35.4 + - - -
218C VAL* 1.3 74.4 - - - +
220C VAL* 1.3 63.5 + - - +
235C ARG* 5.4 2.7 - - + +
236C PHE 3.5 6.7 - - - +
237C ALA* 4.1 5.4 - - + -
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Residues in contact with VAL 220 (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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202C LEU* 4.1 14.4 - - + -
209C TYR* 3.3 11.2 - - - +
210C ALA* 4.1 7.2 - - + -
218C VAL* 4.3 9.0 - - + -
219C ALA* 1.3 79.2 - - - +
221C GLU* 1.3 65.0 + - - +
222C PHE* 3.8 30.5 - - + -
235C ARG* 3.2 8.7 - - - +
236C PHE* 2.8 49.9 + - + +
238C PHE* 4.4 3.4 - - + -
280C LEU* 3.9 32.3 - - + -
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Residues in contact with GLU 221 (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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188C GLU* 2.7 33.4 - - - +
202C LEU* 3.7 3.5 - - - +
208C GLY* 3.1 6.4 - - - -
209C TYR* 2.8 56.7 + - + +
220C VAL* 1.3 76.6 - - - +
222C PHE* 1.3 63.5 + - - +
223C PHE* 3.1 28.8 - - + -
233C SER* 4.1 11.5 + - - -
234C LYS 3.2 16.8 - - - +
235C ARG* 3.1 27.2 + - + +
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Residues in contact with PHE 222 (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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202C LEU* 3.4 30.7 - - + -
206C GLN* 4.3 23.6 - - + +
207C GLU 3.9 2.5 - - - +
220C VAL* 3.8 14.1 - - + -
221C GLU* 1.3 72.0 - - - +
223C PHE* 1.3 67.7 + - - +
224C ASP* 4.5 6.9 - - - +
233C SER* 3.0 5.7 - - - -
234C LYS* 2.7 61.8 + - + +
236C PHE* 3.4 32.1 - + - -
280C LEU* 4.4 20.6 - - + -
281C GLN* 5.3 3.4 - - + -
283C ARG* 4.5 6.5 - - - -
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Residues in contact with PHE 223 (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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174C TRP* 4.6 25.8 - + - -
188C GLU* 3.8 14.6 - - - -
206C GLN 3.6 12.5 - - - +
207C GLU* 3.0 29.5 + - + +
208C GLY* 4.3 9.9 - - - -
209C TYR* 5.1 4.0 - + - -
221C GLU* 3.1 38.4 - - + -
222C PHE* 1.3 83.0 - - - +
224C ASP* 1.3 72.4 + - - +
225C ASP* 3.8 6.8 - - - +
232C SER 3.8 6.1 - - - +
233C SER* 4.3 11.0 - - - -
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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