Contacts of the strand formed by residues 228 - 237 (chain C) in PDB entry 1EQR
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 GLU 228 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214C LYS* 2.8 37.1 + - + +
215C CYS 3.6 6.5 - - - +
216C PHE* 3.6 30.9 - - + -
226C GLN* 3.0 21.3 + - + +
227C PRO* 1.3 87.8 - - + +
229C PHE* 1.3 68.7 + - - +
552C ILE* 5.1 4.0 - - - +
556C LYS* 3.9 22.3 + - + +
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Residues in contact with PHE 229 (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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192C GLN 5.3 0.7 - - - -
214C LYS* 3.4 7.1 - - - +
215C CYS* 2.8 55.1 + - + +
216C PHE 3.4 21.5 - - - -
217C ARG* 3.1 53.4 - - + +
226C GLN* 5.4 1.1 - - + -
228C GLU* 1.3 83.9 - - - +
230C THR* 1.3 66.6 + - - +
231C GLN* 3.8 37.5 - - + -
536C ASP* 3.3 18.6 - - - +
548C ILE* 5.9 1.8 - - + -
552C ILE* 6.1 0.9 - - - -
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Residues in contact with THR 230 (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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141C ARG* 4.2 9.9 + - - -
212C ILE* 3.7 31.0 - - + +
213C VAL 3.5 14.4 - - - +
214C LYS* 3.7 20.2 - - + +
229C PHE* 1.3 77.9 - - - +
231C GLN* 1.3 71.3 + - - +
534C GLY* 4.0 1.7 - - - -
535C LEU* 3.1 40.7 + - + +
536C ASP* 3.4 12.4 + - - +
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Residues in contact with GLN 231 (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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193C SER* 5.1 3.6 - - - -
194C PRO* 4.9 6.9 - - - +
211C GLN 3.3 2.8 - - - +
212C ILE* 3.3 3.3 - - - -
213C VAL* 3.0 38.8 + - + +
215C CYS* 4.1 18.5 - - + +
229C PHE* 3.8 28.9 - - + -
230C THR* 1.3 82.4 - - - +
232C ILE* 1.3 68.3 + - - +
233C ASP* 3.3 4.1 + - + +
532C ALA* 4.0 23.7 + - + +
533C PHE 3.0 17.3 + - - +
534C GLY* 4.8 4.0 - - - -
535C LEU* 4.2 0.9 - - - +
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Residues in contact with ILE 232 (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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148C VAL* 3.8 45.5 - - + -
152C MET* 5.2 3.4 - - + -
210C TYR* 5.1 6.5 - - + -
211C GLN 3.5 5.8 - - - +
212C ILE* 4.4 14.6 - - + +
231C GLN* 1.3 72.0 - - - +
233C ASP* 1.3 58.3 + - - +
234C VAL* 3.7 17.9 + - + +
251C LEU* 5.6 2.0 - - + -
532C ALA* 3.3 3.5 - - - -
533C PHE* 2.8 51.0 + - + +
535C LEU* 4.0 23.6 - - + -
538C LEU* 4.0 25.6 - - + -
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Residues in contact with ASP 233 (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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194C PRO* 3.2 26.6 - - - +
198C LYS* 3.1 33.2 + - - +
209C TYR* 2.6 27.6 + - - +
210C TYR* 3.0 7.8 - - - +
211C GLN 2.7 41.4 + - - +
213C VAL* 4.0 13.7 - - + -
231C GLN* 3.3 4.3 + - + +
232C ILE* 1.3 72.1 - - - +
234C VAL* 1.3 61.1 + - - +
531C LEU 4.0 0.9 - - - -
532C ALA* 3.7 13.9 - - + +
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Residues in contact with VAL 234 (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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152C MET* 3.6 22.2 - - + -
157C PHE* 3.5 28.9 - - + -
198C LYS* 2.9 14.1 + - - -
209C TYR* 3.9 3.1 - - - +
232C ILE* 3.9 18.2 - - + +
233C ASP* 1.3 80.7 + - - +
235C GLU* 1.3 66.2 + - - +
236C THR* 4.5 3.1 - - + -
244C VAL* 5.8 2.0 - - + -
247C VAL* 6.2 0.2 - - + -
248C MET* 3.9 25.8 - - + -
530C GLY* 3.0 1.9 - - - -
531C LEU* 2.6 47.6 + - + +
533C PHE* 5.0 0.2 - - + -
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Residues in contact with GLU 235 (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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198C LYS* 3.1 27.2 - - + +
199C GLN* 3.5 12.6 - - - +
202C MET* 3.5 26.3 - - + +
209C TYR* 2.9 45.3 + - + +
234C VAL* 1.3 75.4 - - - +
236C THR* 1.3 70.2 + - - +
489C ARG* 2.9 56.5 + - - +
528C HIS* 3.6 3.6 - - - -
529C ALA* 3.9 3.1 - - - +
530C GLY* 3.0 16.6 - - - -
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Residues in contact with THR 236 (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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157C PHE* 3.3 26.2 - - + -
202C MET* 3.6 2.5 - - - +
207C ASP 3.7 6.3 - - - -
208C ARG* 4.3 1.6 - - + -
234C VAL* 4.5 4.5 - - + -
235C GLU* 1.3 81.5 - - - +
237C SER* 1.3 63.3 + - - +
239C MET* 3.0 45.1 - - + +
244C VAL* 3.9 11.9 - - + +
247C VAL* 5.7 1.3 - - + -
528C HIS* 3.1 8.8 - - - +
529C ALA 2.6 49.1 + - - +
530C GLY* 5.4 0.4 - - - -
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Residues in contact with SER 237 (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 MET* 3.0 38.1 + - - +
206C PHE 3.9 2.8 + - - -
207C ASP* 3.1 23.5 + - - +
236C THR* 1.3 73.7 - - - +
238C PHE* 1.3 92.2 + - - +
239C MET* 3.3 13.2 + - - +
526C PRO* 4.3 7.4 - - - -
527C PRO 3.2 9.2 - - - -
528C HIS* 4.2 0.2 - - - +
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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