Contacts of the strand formed by residues 227 - 234 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ILE* 3.4 20.1 + - + +
211A VAL* 3.7 21.6 - - + +
212A MET 3.3 13.5 - - - +
213A ALA* 4.7 5.3 - - + +
214A LEU 4.2 0.9 - - - -
223A TYR* 2.7 29.5 + - - -
225A PHE* 3.1 30.2 + - + -
226A PRO* 1.3 87.2 - - + +
228A MET* 1.3 62.5 + - - +
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Residues in contact with MET 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TRP* 4.4 9.0 - - + -
49A TYR* 3.4 37.2 - - + -
171A LEU* 3.6 36.8 - - + -
185A ILE* 3.9 2.2 - - - -
210A GLU 3.8 0.5 - - - +
211A VAL* 3.4 5.9 - - - +
212A MET* 3.0 37.9 + - + +
214A LEU* 3.7 41.5 - - + +
223A TYR* 3.5 26.9 - - + +
227A GLN* 1.3 84.7 - - - +
229A ILE* 1.3 61.8 + - - +
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Residues in contact with ILE 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A TYR* 2.7 28.4 + - - -
174A TRP* 3.6 30.9 - - + -
185A ILE* 3.7 45.7 - - + +
186A THR* 4.0 16.4 - - + -
188A MET* 5.8 1.6 - - - -
189A PHE* 3.9 22.9 - - + -
209A THR* 3.7 35.4 - - + +
210A GLU 3.4 5.2 - - - +
211A VAL* 4.1 4.7 - - + -
223A TYR* 4.9 0.4 + - - -
228A MET* 1.3 75.5 - - - +
230A THR* 1.3 60.7 - - - +
231A PRO* 3.7 1.6 - - - +
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Residues in contact with THR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A TYR* 3.4 19.4 - - - -
52A ALA* 3.5 35.0 - - - +
53A LEU* 3.9 6.2 - - + +
56A ALA* 4.1 8.1 - - + -
167A THR* 3.7 17.0 - - - +
209A THR* 3.4 2.8 - - - -
210A GLU* 2.7 56.0 + - - +
212A MET* 5.2 3.3 - - - +
229A ILE* 1.3 72.0 - - - +
231A PRO* 1.3 67.6 - - - +
232A LEU* 3.6 4.4 - - + +
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Residues in contact with PRO 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 4.3 1.1 - - + -
166A LEU 4.2 0.7 - - - -
167A THR* 2.7 36.5 + - - +
168A TYR* 3.2 50.9 - - + +
174A TRP* 4.2 3.1 - - + -
189A PHE* 3.6 32.5 - - + -
208A ARG 3.7 5.8 - - - +
209A THR* 4.3 3.6 - - + -
229A ILE 3.7 7.6 - - - +
230A THR* 1.3 84.6 - - + +
232A LEU* 1.3 61.6 + - - +
233A VAL* 4.0 8.7 - - + -
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ALA* 3.9 27.4 - - + +
59A SER* 5.1 4.9 - - - +
165A VAL* 4.3 12.8 - - + -
166A LEU 3.7 3.1 - - - -
206A ASN 3.5 1.4 - - - +
207A ILE* 3.6 0.5 - - - -
208A ARG* 2.9 79.6 + - + +
209A THR* 4.6 1.8 - - - -
210A GLU* 3.7 38.4 - - + +
230A THR* 3.6 19.5 - - + +
231A PRO* 1.3 74.6 - - - +
233A VAL* 1.3 60.4 + - - +
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LEU* 4.4 0.2 - - - +
164A GLY 3.8 0.7 - - - +
165A VAL* 3.6 1.8 - - - +
166A LEU* 2.7 58.1 + - + +
168A TYR* 4.7 2.0 - - + -
197A LEU* 4.1 29.2 - - + -
202A PHE* 3.4 46.8 - - + -
206A ASN 3.7 2.7 - - - -
207A ILE* 4.1 16.4 - - + -
231A PRO* 4.3 15.5 - - + -
232A LEU* 1.3 74.4 - - - +
234A THR* 1.3 58.8 + - - +
235A LYS 4.1 0.3 + - - -
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Residues in contact with THR 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A GLY* 3.7 22.7 - - - +
164A GLY 3.3 5.5 + - - +
165A VAL* 4.5 9.2 - - - +
202A PHE* 3.5 13.2 - - - +
203A ARG 5.2 0.2 + - - -
206A ASN* 3.0 42.1 + - + +
208A ARG* 3.2 21.3 + - - -
233A VAL* 1.3 72.5 - - - +
235A LYS* 1.3 74.6 + - - +
236A GLY 3.7 0.7 + - - -
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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