Contacts of the helix formed by residues 225 - 234 (chain A) in PDB entry 1ORB
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 PRO 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A LYS 4.0 4.7 - - - +
224A SER* 1.3 85.5 - - - +
226A GLU* 1.3 64.4 + - - +
228A LEU* 3.8 11.9 - - + -
229A ARG* 2.8 49.7 + - - +
262A LEU* 3.9 33.7 - - + +
263A CYS* 3.8 5.3 - - - -
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Residues in contact with GLU 226 (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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224A SER* 2.7 36.4 + - - +
225A PRO* 1.3 86.2 - - - +
227A GLU* 1.3 63.3 + - + +
229A ARG* 3.7 9.8 - - - +
230A ALA* 3.2 22.5 + - - +
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Residues in contact with GLU 227 (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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217A THR* 4.7 7.2 - - - +
223A LYS* 3.6 31.9 + - + +
224A SER* 2.4 54.0 + - - +
226A GLU* 1.3 72.6 - - + +
228A LEU* 1.4 61.6 + - - +
230A ALA* 3.3 7.4 + - - +
231A MET* 3.1 25.9 + - - +
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Residues in contact with LEU 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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215A PHE* 3.8 28.3 - - + +
222A GLU* 3.9 18.6 - - - +
223A LYS* 3.6 36.1 - - + +
224A SER 2.9 9.2 + - - +
225A PRO* 3.8 11.9 - - + +
227A GLU* 1.4 70.4 - - - +
229A ARG* 1.3 62.1 + - - +
231A MET* 2.9 24.1 + - - +
232A PHE* 3.0 27.0 + - + -
259A ALA* 4.0 19.1 - - + +
262A LEU* 4.4 12.8 - - + -
263A CYS* 3.7 13.5 - - - -
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Residues in contact with ARG 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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225A PRO* 2.8 44.7 + - - +
226A GLU* 3.7 8.5 - - - +
228A LEU* 1.3 75.4 - - - +
230A ALA* 1.3 63.4 + - - +
232A PHE* 3.6 6.4 + - - +
233A GLU* 3.1 31.1 + - - +
239A LEU* 4.8 13.3 - - + +
262A LEU 5.3 0.4 + - - -
263A CYS* 3.2 40.7 + - - +
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Residues in contact with ALA 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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226A GLU 3.2 15.3 + - - +
227A GLU* 3.6 6.7 - - - +
228A LEU 3.2 0.2 - - - -
229A ARG* 1.3 81.9 - - - +
231A MET* 1.3 53.6 + - - +
233A GLU* 3.3 8.4 + - - +
234A ALA* 2.7 35.7 + - - +
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Residues in contact with MET 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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210A MET* 3.8 13.9 - - + -
214A ASN* 3.5 37.2 - - + +
215A PHE* 3.4 37.7 - - + -
223A LYS* 3.9 22.7 - - - +
227A GLU* 3.1 14.7 + - - +
228A LEU* 2.9 13.0 + - - +
230A ALA* 1.3 74.0 - - + +
232A PHE* 1.3 69.8 + - - +
233A GLU 2.9 2.1 + - - -
234A ALA* 3.0 15.1 + - - +
235A LYS* 3.2 14.6 + - - +
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Residues in contact with PHE 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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179A VAL* 5.6 0.2 - - + -
210A MET* 3.7 27.3 - - + +
215A PHE* 4.3 9.4 - + - -
228A LEU* 3.0 31.7 + - + +
229A ARG 4.0 4.0 - - - +
231A MET* 1.3 77.0 - - - +
233A GLU* 1.3 60.2 + - - +
235A LYS* 3.3 3.9 + - - +
236A LYS 3.1 3.6 + - - -
237A VAL* 2.8 60.1 + - + +
239A LEU* 3.9 31.6 - - + -
243A LEU* 4.8 3.1 - - + -
256A ILE* 4.0 35.0 - - + -
259A ALA* 4.1 15.7 - - + -
260A ALA* 4.0 20.6 - - + -
263A CYS* 4.7 2.0 - - - -
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Residues in contact with GLU 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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229A ARG* 3.1 23.4 + - - +
230A ALA* 3.4 9.0 - - - +
231A MET 2.9 1.0 + - - -
232A PHE* 1.3 77.1 - - - +
234A ALA* 1.3 63.0 + - - +
235A LYS 2.9 1.8 - - - -
236A LYS* 2.7 58.3 + - - +
237A VAL 4.4 4.2 - - - +
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Residues in contact with ALA 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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230A ALA 2.7 20.6 + - - +
231A MET* 3.0 6.5 + - - +
233A GLU* 1.3 74.3 - - - +
235A LYS* 1.3 62.3 + - + +
236A LYS* 3.6 3.3 + - - +
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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