Contacts of the helix formed by residues 221 - 227 (chain A) in PDB entry 2XIJ
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 ILE 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A ASN 3.8 24.7 - - - +
190A GLY* 4.2 3.6 - - - +
219A ASN 3.8 3.4 + - - -
220A ASP* 1.3 72.4 - - - +
222A LEU* 1.3 71.0 + - + +
223A LYS 3.2 0.7 - - - -
224A GLU* 2.9 25.5 + - + +
225A PHE* 3.1 34.0 + - + -
231A TYR* 3.9 25.8 - - - -
232A ILE 5.0 0.9 - - - +
238A SER* 3.9 25.4 - - - +
239A MET* 3.8 19.3 - - - -
242A ILE* 3.7 23.8 - - + +
287A TYR* 2.9 4.0 + - - +
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Residues in contact with LEU 222 (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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221A ILE* 1.3 78.6 - - - +
223A LYS* 1.3 62.5 + - - +
225A PHE* 3.3 14.2 + - + +
226A MET* 3.1 27.8 + - + +
235A PRO* 5.8 3.4 - - + -
239A MET* 4.1 17.5 - - + -
283A ASP* 3.4 38.1 - - - +
286A GLU* 4.1 20.9 - - + -
287A TYR* 2.9 30.9 + - + +
455A MET* 4.6 3.8 - - + -
456A ALA* 3.9 25.1 - - + +
459A VAL* 4.0 17.1 - - + +
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Residues in contact with LYS 223 (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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189A ASN* 2.8 24.4 + - - -
218A GLN* 2.9 20.5 + - - -
220A ASP* 2.9 34.3 + - - +
222A LEU* 1.3 74.5 - - - +
224A GLU* 1.3 86.9 + - - +
226A MET* 3.8 9.2 - - - -
227A VAL* 2.9 30.7 + - + +
228A ARG* 3.1 14.2 + - + +
262A SER* 4.2 9.2 - - - +
265A HIS* 3.3 33.9 - - + +
266A MET* 4.1 24.0 - - + -
283A ASP* 4.0 1.2 + - - +
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Residues in contact with GLU 224 (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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189A ASN* 3.1 15.6 + - + -
220A ASP 3.5 13.2 - - - +
221A ILE* 2.9 21.0 + - + +
223A LYS* 1.3 101.9 + - - +
225A PHE* 1.3 63.1 + - - +
227A VAL 3.7 0.3 + - - -
228A ARG* 3.0 36.7 + - - +
229A ASN* 2.8 27.5 + - - +
230A THR* 2.7 38.6 + - - +
231A TYR* 3.5 18.6 - - + +
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Residues in contact with PHE 225 (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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221A ILE* 3.1 43.5 + - + -
222A LEU* 3.7 9.2 - - + +
224A GLU* 1.3 76.6 - - - +
226A MET* 1.3 61.6 + - - +
229A ASN* 4.6 5.4 - - - +
231A TYR* 3.5 36.3 - + + -
233A PHE 3.3 24.5 - - - -
235A PRO* 3.6 34.3 - - + -
238A SER* 3.7 5.8 - - - -
239A MET* 6.3 0.2 - - - -
459A VAL* 3.6 24.0 - - + +
460A ALA* 6.3 0.4 - - - -
465A LYS* 4.0 12.5 - - - +
576A HIS* 3.6 29.6 - + - -
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Residues in contact with MET 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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222A LEU 3.1 20.9 + - - +
223A LYS* 4.1 4.5 - - + +
224A GLU 3.3 0.2 - - - -
225A PHE* 1.3 78.0 - - - +
227A VAL* 1.3 74.8 + - + +
266A MET* 3.6 20.4 - - + +
279A TYR* 4.1 10.8 - - - -
283A ASP* 3.1 38.1 - - - +
455A MET* 3.7 22.2 - - + -
459A VAL* 3.7 18.2 - - + -
464A PRO* 3.7 20.6 - - + -
465A LYS* 3.3 36.7 + - + +
468A ILE* 4.6 4.9 - - + -
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Residues in contact with VAL 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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223A LYS* 2.9 21.6 + - + +
224A GLU 4.1 0.4 - - - -
225A PHE 3.6 0.8 - - - -
226A MET* 1.3 82.6 - - + +
228A ARG* 1.3 62.2 + - - +
229A ASN* 3.6 11.3 + - - -
265A HIS* 3.7 35.2 - - + +
266A MET* 3.9 12.6 - - + +
269A ALA* 3.5 28.5 - - + -
465A LYS* 4.3 4.3 - - + +
468A ILE* 3.6 29.2 - - + -
626A GLY 4.4 0.5 - - - +
800A B12 2.8 30.7 + - + +
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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