Contacts of the strand formed by residues 224 - 228 (chain C) in PDB entry 1EJI
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 TYR 224 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131C LEU* 4.1 40.8 - - + +
196C LYS* 3.2 19.8 + - + +
197C LEU* 3.3 13.9 - - + -
198C ILE* 2.8 28.4 + - - +
218C ALA* 4.5 0.7 - - - -
223C ALA* 1.3 76.4 - - - +
225C LEU* 1.3 61.6 + - - +
226C MSE 3.9 1.1 + - + -
249C HIS* 3.6 29.6 - + + -
250C VAL* 5.6 1.6 - - + -
286C TYR* 5.2 7.6 - + - -
287C GLU* 4.9 12.3 + - - +
288C LEU* 3.6 31.8 - - + +
291C LEU* 5.4 1.2 - - - +
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Residues in contact with LEU 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C ILE* 3.6 29.4 - - + +
200C ALA* 4.1 12.6 - - + -
211C TYR* 4.0 9.2 - - + +
214C LEU* 4.0 21.8 - - + +
215C ARG* 3.6 38.6 - - + +
218C ALA* 4.1 11.4 - - + -
223C ALA 3.9 0.2 + - - -
224C TYR* 1.3 73.0 - - - +
226C MSE 1.3 59.4 + - - +
247C HIS 4.0 1.8 - - - +
248C CYS* 3.6 29.1 - - - +
249C HIS* 3.0 42.9 + - + +
250C VAL* 3.4 4.4 + - - -
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Residues in contact with MSE 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ASN* 3.4 23.8 - - - +
127C VAL* 4.0 20.4 - - - -
128C TYR* 3.6 36.1 - - + +
197C LEU* 4.3 15.9 - - + -
198C ILE 2.9 12.0 + - - +
199C ILE* 3.3 29.8 - - + +
200C ALA* 2.8 25.6 + - - -
224C TYR* 3.9 1.3 + - + -
225C LEU* 1.3 74.3 - - - +
227C ALA* 1.3 66.7 + - - +
228C ASP* 4.3 7.2 - - + +
248C CYS* 4.7 1.6 - - - -
250C VAL* 3.2 24.9 - - + +
252C THR* 4.0 16.2 - - + +
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Residues in contact with ALA 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C ALA 3.2 12.3 - - - +
211C TYR* 4.4 3.4 - - + +
226C MSE 1.3 75.3 - - - +
228C ASP* 1.3 60.4 + - - +
229C MSE 3.6 3.1 - - + +
244C PRO* 3.8 22.0 - - + -
248C CYS* 3.5 25.7 - - - -
250C VAL 2.8 7.5 + - - -
251C VAL* 3.2 11.6 - - + +
252C THR* 2.8 28.6 + - - +
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Residues in contact with ASP 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ASN* 2.8 19.9 + - - +
151C HIS* 2.9 24.8 + - + +
199C ILE* 4.4 0.9 - - + -
200C ALA 3.2 8.6 + - - -
201C GLY* 3.6 15.8 - - - -
202C THR 4.2 3.1 + - - +
226C MSE 4.0 7.1 + - + -
227C ALA* 1.3 73.4 - - - +
229C MSE 1.3 55.9 + - - +
230C ALA* 3.0 15.9 + - - +
231C HIS 4.9 0.3 + - - -
252C THR* 3.6 20.3 + - - +
253C THR* 4.6 1.2 - - - -
502C PLG 2.8 41.5 + - - +
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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