Contacts of the strand formed by residues 233 - 240 (chain I) in PDB entry 5BRR
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 233 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82I LEU* 6.1 0.9 - - + -
86I TRP* 3.9 27.1 - - + -
90I GLU* 5.2 2.9 - - - +
91I ILE* 4.4 9.2 - - + -
171I PHE* 3.8 29.2 - - + -
227I PRO* 3.7 0.2 - - - +
228I TYR* 2.7 53.7 + - + +
231I ASP 4.1 1.0 - - - -
232I THR* 1.3 86.4 - - - +
234I SER* 1.3 56.1 + - - +
362I VAL* 4.3 6.5 - - + -
363I ARG 3.2 14.4 - - - +
364I HIS* 3.8 21.8 - - + -
365I ASN* 3.5 2.4 + - - -
371I LEU* 3.9 21.8 - - + -
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Residues in contact with SER 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225I GLU* 2.7 29.4 + - - +
226I LEU 3.9 3.6 - - - -
227I PRO* 3.6 10.2 - - - +
228I TYR* 4.2 4.0 - - - -
231I ASP* 5.3 0.3 + - - -
233I LEU* 1.3 72.8 - - - +
235I MET* 1.3 60.9 + - - +
236I PHE* 3.6 19.1 - - - -
361I VAL 3.8 0.3 - - - +
362I VAL* 3.3 5.2 - - - +
363I ARG* 2.9 31.8 + - - +
365I ASN* 3.0 28.3 + - - +
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Residues in contact with MET 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171I PHE* 4.8 0.4 - - + -
175I TRP* 4.3 9.2 - - + -
224I LEU 3.9 0.5 - - - +
225I GLU* 3.4 2.1 - - - +
226I LEU* 2.7 45.7 + - - +
228I TYR* 3.3 31.8 - - + +
234I SER* 1.3 74.4 - - - +
236I PHE* 1.3 66.0 + - - +
237I ILE* 3.6 26.1 + - + -
278I PHE* 4.9 3.1 - - - -
326I ILE* 4.5 6.1 - - + -
328I VAL* 3.7 28.0 - - + -
360I PHE* 3.9 24.7 - - + -
361I VAL 3.3 10.1 - - - +
362I VAL* 3.7 20.6 - - + -
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Residues in contact with PHE 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223I ILE* 4.5 1.3 - - + -
224I LEU 3.3 6.3 - - - +
225I GLU* 3.1 43.3 - - + -
234I SER* 3.6 22.9 - - - -
235I MET* 1.3 75.9 - - - +
237I ILE* 1.3 63.7 + - - +
238I ALA* 5.2 0.9 - - - +
259I ILE* 3.9 16.2 - - + -
262I TRP* 4.4 23.0 - + + -
263I LYS* 4.2 8.5 - - + -
266I MET* 3.8 22.4 - - + -
359I LEU 4.0 0.2 - - - +
360I PHE* 3.1 5.7 - - - -
361I VAL* 2.7 46.8 + - + +
363I ARG* 3.5 38.4 - - + -
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Residues in contact with ILE 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222I ASP 3.6 1.4 - - - +
223I ILE* 3.6 3.5 - - - +
224I LEU* 3.0 43.5 + - + +
226I LEU* 3.7 30.3 - - + -
235I MET* 3.6 30.3 - - + -
236I PHE* 1.3 73.2 - - - +
238I ALA* 1.3 70.2 + - - +
239I ALA 4.7 0.2 - - - +
275I LEU* 4.4 14.8 - - + -
354I ILE* 4.0 26.7 - - + -
358I PHE* 3.9 32.8 - - + -
359I LEU 3.6 2.7 - - - -
360I PHE* 4.4 4.3 - - + -
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Residues in contact with ALA 238 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221I TYR* 4.2 5.8 - - - -
222I ASP 3.3 5.8 - - - -
223I ILE* 3.7 22.0 - - + -
236I PHE 5.2 1.3 - - - +
237I ILE* 1.3 78.8 - - - +
239I ALA* 1.3 60.2 + - - +
240I PRO* 4.5 0.3 - - - +
250I LEU* 4.0 18.6 - - + -
262I TRP* 4.8 8.5 - - + -
358I PHE* 3.5 1.9 - - - +
359I LEU* 2.9 44.1 + - + +
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Residues in contact with ALA 239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221I TYR* 3.5 5.5 - - - -
222I ASP* 2.8 38.3 + - + +
237I ILE* 4.3 0.6 - - + +
238I ALA* 1.3 75.0 - - - +
240I PRO* 1.3 73.4 - - + +
354I ILE* 4.2 24.7 - - + -
356I ARG* 5.2 6.3 - - + +
357I PRO 4.7 0.9 - - - +
358I PHE* 3.6 17.5 - - + -
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Residues in contact with PRO 240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220I TYR 3.4 10.1 - - - +
221I TYR* 3.3 20.1 - - + -
222I ASP* 5.6 0.8 - - - +
239I ALA* 1.3 91.1 - - + +
241I TYR* 1.3 67.6 + - - +
242I GLU 3.9 4.4 - - - +
243I LYS* 5.1 2.2 - - - +
245I VAL* 2.9 46.4 - - + +
247I LEU* 4.2 6.1 - - + -
356I ARG* 4.3 17.3 - - + +
357I PRO 3.7 18.8 - - - +
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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
------------------------------------------------------------
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