Contacts of the strand formed by residues 227 - 234 (chain C) in PDB entry 3ORH
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 GLN 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185C ILE* 3.4 19.9 + - + +
211C VAL* 3.7 21.6 - - + +
212C MET 3.3 13.2 - - - +
213C ALA* 4.7 5.3 - - + +
214C LEU 4.3 0.9 - - - -
223C TYR* 2.7 29.3 + - - -
225C PHE* 3.2 30.5 + - + -
226C PRO* 1.3 86.8 - - + +
228C MET* 1.3 60.3 + - - +
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Residues in contact with MET 228 (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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45C TRP* 4.4 9.9 - - + -
49C TYR* 3.4 36.6 - - + -
171C LEU* 3.6 37.5 - - + -
185C ILE* 3.9 2.7 - - - -
210C GLU 3.8 0.5 - - - +
211C VAL* 3.4 6.4 - - - +
212C MET* 3.0 37.8 + - + +
214C LEU* 3.7 40.8 - - + +
223C TYR* 3.5 26.7 - - + +
227C GLN* 1.3 83.8 - - - +
229C ILE* 1.3 60.4 + - - +
230C THR 4.3 0.2 - - - -
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Residues in contact with ILE 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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49C TYR* 2.7 28.2 + - - -
174C TRP* 3.6 29.4 - - + -
185C ILE* 3.7 45.0 - - + +
186C THR* 4.0 16.4 - - + -
188C MET* 4.2 7.6 - - + -
189C PHE* 3.9 19.5 - - + -
209C THR* 3.8 35.9 - - + +
210C GLU 3.4 4.7 - - - +
211C VAL* 4.1 5.8 - - + -
223C TYR* 4.9 0.2 + - - -
228C MET* 1.3 74.9 - - - +
230C THR* 1.3 61.6 + - - +
231C PRO* 3.7 1.6 - - - +
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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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49C TYR* 3.3 20.4 - - - -
52C ALA* 3.5 33.4 - - - +
53C LEU* 3.9 8.5 - - + +
56C ALA* 4.2 7.6 - - + -
167C THR* 3.7 17.3 - - - +
209C THR* 3.4 3.2 - - - -
210C GLU* 2.7 55.3 + - - +
212C MET* 5.2 3.3 - - - +
229C ILE* 1.3 70.9 - - - +
231C PRO* 1.3 67.0 - - - +
232C LEU* 3.6 4.7 - - + +
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Residues in contact with PRO 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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53C LEU* 4.3 1.3 - - + -
166C LEU 4.2 0.4 - - - -
167C THR* 2.7 36.1 + - - +
168C TYR* 3.2 51.8 - - + +
174C TRP* 4.3 3.1 - - + -
189C PHE* 3.6 33.4 - - + -
208C ARG 3.6 6.3 - - - +
209C THR* 4.3 3.6 - - + -
229C ILE 3.7 8.0 - - - +
230C THR* 1.3 84.6 - - + +
232C LEU* 1.3 62.2 + - - +
233C VAL* 4.0 8.3 - - + -
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Residues in contact with LEU 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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56C ALA* 3.8 27.8 - - + +
59C SER* 5.2 4.5 - - - +
165C VAL* 4.5 15.3 - - + -
166C LEU 3.8 2.9 - - - -
206C ASN 3.4 6.4 - - - +
207C ILE* 3.6 0.3 - - - -
208C ARG* 2.8 51.9 + - + +
209C THR 4.6 0.2 - - - -
210C GLU* 3.7 38.4 - - + +
230C THR* 3.6 19.5 - - + +
231C PRO* 1.3 74.1 - - - +
233C VAL* 1.3 59.7 + - - +
234C THR* 3.9 5.0 + - - +
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Residues in contact with VAL 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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160C LEU* 4.5 0.2 - - - +
164C GLY 3.9 0.5 - - - +
165C VAL* 3.6 1.6 - - - +
166C LEU* 2.7 58.5 + - + +
168C TYR* 4.8 1.8 - - + -
197C LEU* 4.0 30.3 - - + -
202C PHE* 3.4 47.8 - - + -
206C ASN 3.7 2.9 - - - -
207C ILE* 4.1 15.3 - - + +
231C PRO* 4.3 15.3 - - + -
232C LEU* 1.3 74.6 - - - +
234C THR* 1.3 59.5 + - - +
235C LYS 4.1 0.3 + - - -
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Residues in contact with THR 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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163C GLY* 3.7 23.1 - - - +
164C GLY 3.3 3.6 - - - +
165C VAL* 3.6 17.6 - - + +
202C PHE* 3.5 12.9 - - - +
206C ASN* 3.0 42.6 + - + +
208C ARG* 4.4 10.5 + - - +
232C LEU* 4.7 4.0 + - - +
233C VAL* 1.3 72.6 - - - +
235C LYS* 1.3 76.2 + - - +
236C GLY 3.7 0.9 + - - -
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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