Contacts of the strand formed by residues 227 - 238 (chain A) in PDB entry 1ORI
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 LEU 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A THR* 3.7 30.1 - - + +
184A ALA 3.7 2.2 - - - -
185A ILE* 3.6 21.1 - - + -
222A VAL* 5.0 0.7 - - + -
223A ASP 4.7 1.1 - - - +
224A PRO* 3.2 33.1 + - + +
226A GLN* 1.3 75.3 - - - +
228A VAL* 1.3 62.2 + - - +
229A THR 3.7 10.1 - - - +
258A LYS* 5.8 0.7 - - - +
259A ARG* 3.5 19.1 + - - -
287A PRO* 4.3 17.5 - - + -
288A GLU* 3.8 30.7 - - + +
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Residues in contact with VAL 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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184A ALA 3.1 9.0 + - - +
185A ILE 4.1 1.8 - - - -
186A GLU* 3.7 26.0 - - + +
226A GLN 3.7 3.4 - - - +
227A LEU* 1.3 74.4 - - - +
229A THR* 1.3 56.2 + - + +
257A VAL* 4.0 4.0 - - + -
258A LYS* 2.7 39.3 + - - +
259A ARG* 3.7 28.0 + - + +
261A ASP* 3.7 29.6 - - + +
263A VAL* 4.1 15.3 - - + -
307A VAL* 3.9 20.6 - - + -
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Residues in contact with THR 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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183A THR* 3.9 5.4 + - - -
184A ALA* 3.3 37.9 + - + +
227A LEU* 4.3 11.8 - - - +
228A VAL* 1.3 85.4 - - + +
230A ASN* 1.3 75.3 + - - +
255A LEU* 3.8 12.7 - - + +
256A GLN 3.3 20.4 - - - +
257A VAL* 4.0 12.1 - - + -
258A LYS* 4.1 8.3 - - - +
313A ILE* 4.1 17.3 - - + -
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Residues in contact with ASN 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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183A THR* 2.9 18.5 + - - -
229A THR* 1.3 84.3 + - - +
231A ALA* 1.3 69.0 + - - +
254A CYS 4.3 3.3 + - - +
255A LEU* 3.6 14.0 - - - +
256A GLN* 3.1 37.2 + - - +
258A LYS* 3.9 21.9 - - - +
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Residues in contact with ALA 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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181A TYR* 4.5 11.1 - - + -
182A VAL 3.4 9.6 - - - +
183A THR* 4.5 3.6 - - - -
230A ASN* 1.3 88.1 + - - +
232A CYS* 1.3 61.8 + - - +
255A LEU* 4.2 1.8 - - - -
269A TYR* 3.4 31.6 - - + +
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Residues in contact with CYS 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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181A TYR* 3.4 5.8 - - - -
182A VAL* 3.0 34.9 + - + +
231A ALA* 1.3 75.8 - - - +
233A LEU* 1.3 72.6 + - - +
234A ILE 3.5 0.9 + - - -
252A PRO 4.8 1.3 - - - -
253A PHE* 3.8 18.8 - - + -
254A CYS* 3.5 43.1 - - - +
255A LEU* 3.7 9.2 - - + +
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Residues in contact with LEU 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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177A ARG* 5.8 1.1 - - - +
179A THR* 3.8 18.4 - - + -
180A LEU 3.1 18.2 - - - +
181A TYR* 3.6 27.9 - - + +
232A CYS* 1.3 80.5 - - - +
234A ILE* 1.3 61.9 + - - +
235A LYS 3.4 23.6 - - - +
236A GLU* 4.1 22.7 - - + +
252A PRO 4.7 3.3 - - - +
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Residues in contact with ILE 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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180A LEU* 3.0 43.0 + - + +
181A TYR* 4.3 3.6 - - - +
182A VAL* 3.9 32.5 - - + -
232A CYS 3.9 0.7 - - - +
233A LEU* 1.3 78.4 - - - +
235A LYS* 1.3 64.5 + - + +
249A PHE* 3.7 7.5 - - + -
251A SER* 2.7 33.8 + - - -
252A PRO 4.3 5.4 - - - +
253A PHE* 4.0 16.6 - - + -
268A ALA* 5.6 2.0 - - + -
317A ILE* 3.8 37.7 - - + -
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Residues in contact with LYS 235 (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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150A LEU* 5.6 0.6 - - + +
151A PHE* 4.1 17.7 - - + -
178A ALA 4.8 0.2 - - - -
179A THR* 3.3 5.4 - - - -
180A LEU* 2.9 44.1 + - + -
233A LEU* 3.4 10.2 - - - +
234A ILE* 1.3 83.3 - - + +
236A GLU* 1.3 76.5 + - - +
237A VAL* 4.2 12.6 - - + -
246A ASP* 2.9 35.8 + - - +
247A LEU* 5.7 1.1 - - - -
249A PHE* 3.7 45.5 - - + +
251A SER* 5.3 0.2 - - - +
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Residues in contact with GLU 236 (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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177A ARG* 2.5 39.7 + - - +
178A ALA 3.7 2.2 - - - -
179A THR* 3.6 17.3 - - + -
233A LEU* 4.1 19.8 - - + +
235A LYS* 1.3 83.5 - - - +
237A VAL* 1.3 67.2 + - - +
238A ASP 4.2 0.8 + - - -
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Residues in contact with VAL 237 (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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145A TRP* 4.8 4.3 - - + -
150A LEU* 4.8 5.4 - - + -
151A PHE* 3.9 30.5 - - + -
156A LEU* 4.1 14.6 - - + -
177A ARG* 3.5 11.0 - - - +
178A ALA* 2.8 41.8 + - + +
235A LYS* 4.2 11.9 - - + -
236A GLU* 1.3 82.2 + - - +
238A ASP* 1.3 61.3 + - - +
239A ILE* 3.7 9.9 + - + +
242A VAL* 4.1 32.3 - - + -
247A LEU* 5.4 0.4 - - + -
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Residues in contact with ASP 238 (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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176A ASP 3.9 5.8 - - - +
177A ARG* 5.2 2.5 - - + +
236A GLU 4.2 0.8 + - - -
237A VAL* 1.3 71.5 - - - +
239A ILE* 1.3 59.7 + - - +
240A TYR* 2.8 35.9 + - - +
241A THR* 3.1 22.0 + - - +
242A VAL* 2.8 32.2 + - - +
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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