Contacts of the strand formed by residues 208 - 216 (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 ARG 208 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C HIS* 3.0 35.6 + - - +
156C GLY* 3.4 17.5 + - - +
157C PHE* 3.7 24.5 - - + -
158C LEU* 3.0 30.8 + - - +
202C MET* 4.5 0.8 - - - +
206C PHE* 4.9 0.9 - - - +
207C ASP* 1.3 98.1 + - + +
209C TYR* 1.3 61.6 + - - +
235C GLU 3.7 4.5 - - - -
236C THR* 4.3 0.2 - - + -
239C MET* 2.8 45.0 - - + +
247C VAL* 5.5 4.1 - - - +
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Residues in contact with TYR 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C PHE* 3.0 18.4 - - - -
158C LEU 3.1 12.1 - - - +
160C ILE* 3.6 29.6 - - + -
162C THR* 4.2 3.8 - - + +
194C PRO* 3.9 5.0 - - - +
198C LYS* 3.7 14.4 - - + +
201C LEU* 3.6 28.9 - - + -
202C MET* 3.8 19.5 - - + -
206C PHE* 5.7 0.2 - - + -
208C ARG* 1.3 76.2 - - - +
210C TYR* 1.3 71.1 + - - +
211C GLN* 3.1 26.9 + - + +
233C ASP* 2.6 46.6 + - - -
234C VAL* 3.9 0.3 - - - +
235C GLU* 2.9 34.3 + - + +
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Residues in contact with TYR 210 (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* 5.2 0.7 - - + -
149C ARG* 3.3 43.3 + - + +
152C MET* 3.7 48.0 - - + -
153C ASP* 3.2 29.1 + - - -
157C PHE* 3.7 10.3 - - + -
158C LEU 2.8 17.3 + - - +
159C ASP* 3.3 44.1 + - + +
160C ILE 3.6 3.6 + - - -
209C TYR* 1.3 84.8 - - - +
211C GLN* 1.3 81.1 + - - +
212C ILE* 4.5 12.3 - - + -
232C ILE* 5.1 5.6 - - + -
233C ASP 3.0 15.3 - - - +
234C VAL* 4.7 0.4 - - + -
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Residues in contact with GLN 211 (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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159C ASP* 3.6 15.7 - - - +
160C ILE 3.0 20.9 - - - +
161C GLU* 3.4 25.4 - - - +
162C THR* 3.3 26.6 + - - +
164C MET* 5.4 0.6 - - - +
194C PRO* 4.4 0.5 - - - +
209C TYR* 3.1 22.3 + - - +
210C TYR* 1.3 79.3 - - - +
212C ILE* 1.3 65.1 + - - +
213C VAL* 3.5 27.5 - - + +
231C GLN 3.3 1.0 - - - +
232C ILE* 3.5 1.6 - - - +
233C ASP* 2.7 40.4 + - + +
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Residues in contact with ILE 212 (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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145C THR* 3.8 22.9 - - + +
148C VAL* 4.6 9.2 - - + -
149C ARG* 2.9 60.4 + - + +
159C ASP* 5.0 0.8 + - - -
210C TYR* 4.5 9.3 - - + -
211C GLN* 1.3 76.3 + - - +
213C VAL* 1.3 58.8 + - - +
230C THR* 3.7 22.3 - - + +
231C GLN 3.3 5.2 - - - +
232C ILE* 4.4 17.3 - - + -
535C LEU* 4.3 10.3 - - + -
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Residues in contact with VAL 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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162C THR* 4.9 0.2 - - - +
164C MET* 3.6 25.1 - - + -
194C PRO* 3.4 31.9 - - + -
211C GLN* 3.9 25.8 - - - +
212C ILE* 1.3 74.7 - - - +
214C LYS* 1.3 78.2 + - - +
215C CYS* 3.6 1.1 + - + +
229C PHE 3.8 0.2 - - - +
230C THR* 3.5 5.7 - - - -
231C GLN* 3.0 33.1 + - + +
233C ASP* 4.0 19.1 - - + -
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Residues in contact with LYS 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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164C MET* 4.0 16.2 - - - +
191C PRO* 4.1 4.0 - - - +
194C PRO* 5.0 0.7 - - - +
213C VAL* 1.3 90.3 - - - +
215C CYS* 1.3 59.7 + - - +
216C PHE* 4.4 17.5 - - + -
228C GLU* 2.8 30.9 + - + +
229C PHE* 3.4 13.7 - - - +
230C THR* 3.7 21.5 - - + +
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Residues in contact with CYS 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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191C PRO* 3.7 4.3 - - - -
192C GLN 3.1 30.3 - - - -
193C SER* 3.1 26.2 - - - -
194C PRO* 4.2 4.9 - - + -
213C VAL 4.4 4.5 - - - +
214C LYS* 1.3 75.6 - - - +
216C PHE* 1.3 63.8 + - - +
228C GLU* 3.6 2.4 - - - +
229C PHE* 2.8 57.9 + - + +
231C GLN* 4.1 15.7 - - + +
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Residues in contact with PHE 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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164C MET* 4.3 12.3 - - + -
175C ASP* 6.5 0.2 - - + -
176C TYR* 3.7 18.6 - + + -
190C LEU* 3.7 40.8 - - + +
191C PRO* 2.8 40.7 + - + +
192C GLN* 3.5 19.7 + - + +
214C LYS* 4.4 11.9 - - + -
215C CYS* 1.3 76.7 - - - +
217C ARG* 1.3 70.4 + - - +
227C PRO* 3.6 8.3 - - + -
228C GLU* 3.6 39.7 - - + -
229C PHE* 3.4 9.4 - - - -
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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