Contacts of the strand formed by residues 290 - 294 (chain E) in PDB entry 1RBO
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 290 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E HIS* 3.8 18.6 - - + -
158E GLU* 3.8 49.8 - - + +
161E LYS* 5.5 9.0 - - + +
162E LEU* 4.1 24.9 - - + -
263E PRO* 2.9 22.8 + - + +
264E ILE* 3.8 21.8 - - + -
265E VAL* 3.0 28.9 + - - +
288E GLY 5.4 1.8 - - - +
289E LEU* 1.3 75.0 - - - +
291E LEU* 1.3 59.6 + - - +
324E ASP* 3.2 17.7 - - + +
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Residues in contact with LEU 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E PRO* 4.2 7.9 - - + -
264E ILE* 4.9 1.6 - - - -
265E VAL* 3.5 16.2 - - + +
267E HIS* 4.1 5.4 - - + +
277E ASN* 4.6 3.6 - - - +
280E LEU* 3.9 25.4 - - + -
281E SER* 3.9 28.3 - - - +
284E CYS* 4.1 12.1 - - - -
290E LEU* 1.3 74.8 - - - +
292E HIS* 1.3 65.7 + - - +
293E ILE* 3.7 21.5 + - + -
322E GLY 3.7 21.3 - - - +
323E GLY* 3.7 2.8 - - - -
324E ASP* 2.7 45.7 + - - +
325E HIS 3.3 4.2 + - - -
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Residues in contact with HIS 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201E LYS* 3.7 5.1 - - - -
239E TYR* 3.1 39.6 - + + -
264E ILE* 4.1 6.4 - - + +
265E VAL 2.9 14.8 + - - +
266E MET* 3.1 15.6 - - + +
267E HIS 3.0 25.5 + - - -
290E LEU 4.1 0.4 - - - -
291E LEU* 1.3 72.9 - - - +
293E ILE* 1.3 63.0 + - - +
294E HIS* 3.9 13.4 - + - -
325E HIS* 3.1 34.2 + - + +
327E HIS* 3.0 40.8 + + - -
377E VAL* 3.9 9.9 - - + -
401E GLN* 3.7 8.7 - - - -
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Residues in contact with ILE 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267E HIS* 3.4 8.3 - - + +
269E TYR* 3.3 38.8 - - + -
277E ASN* 3.3 28.0 - - - +
291E LEU* 3.7 25.4 - - + +
292E HIS* 1.3 82.1 + - - +
294E HIS* 1.3 62.1 - - - +
318E LEU* 3.9 11.9 - - + -
322E GLY 4.1 1.6 - - - +
323E GLY* 3.7 20.2 - - - -
325E HIS 2.9 21.9 + - - +
326E ILE* 3.4 7.1 - - + -
327E HIS* 3.3 28.9 + - - -
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Residues in contact with HIS 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E LYS* 2.7 30.6 + - - -
203E ASP* 4.9 0.2 - - - -
204E GLU* 3.6 33.9 + - + +
266E MET* 3.3 32.5 - - + +
267E HIS 3.0 6.3 + - - -
268E ASP* 3.2 21.5 - - - +
269E TYR* 3.3 26.7 + - - -
270E LEU 4.7 0.3 + - - -
292E HIS* 3.9 7.9 - + - -
293E ILE* 1.3 75.6 - - - +
295E ARG* 1.3 59.7 + - - +
296E ALA* 3.3 8.5 + - - +
326E ILE* 5.4 0.2 - - - -
327E HIS* 3.4 34.0 + + - -
476E CAP 3.8 9.3 - - - -
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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