Contacts of the helix formed by residues 227 - 232 (chain E) in PDB entry 1I3O
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 CYS 227 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316D MET* 3.9 9.3 + - - -
1E ZN 2.4 36.1 - - - -
202E ALA* 4.0 4.0 - - - -
203E CYS* 3.8 14.1 - - + -
224E PHE* 3.0 18.1 + - + +
225E PRO 3.4 0.6 - - - -
226E ASN* 1.3 77.8 - - - +
228E PHE* 1.3 56.5 + - - +
229E PHE* 3.3 19.7 - - - -
230E VAL* 3.4 15.1 - - + +
231E LEU* 2.7 37.6 + - - +
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Residues in contact with PHE 228 (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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379B GLU 5.7 0.4 - - - -
381B GLU 5.4 2.7 - - - -
316D MET* 4.4 15.2 - - + -
150E SER* 3.6 29.6 - - - -
151E ASP* 5.8 1.8 - - - -
154E TYR* 3.8 31.4 - + + -
202E ALA* 4.9 3.3 - - + +
203E CYS* 5.3 0.6 - - - +
226E ASN 4.2 6.3 - - - -
227E CYS* 1.3 72.3 - - - +
229E PHE* 1.3 58.6 + - - +
231E LEU* 4.3 3.4 - - + -
232E GLY* 2.6 33.1 + - - -
233E ARG* 3.1 71.2 + - + +
234E ASN 3.9 12.8 - - - -
235E LEU* 4.0 19.5 - - + -
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Residues in contact with PHE 229 (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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166E ARG* 4.8 7.2 - - - -
186E SER 4.0 13.9 - - - -
187E ALA* 3.5 33.9 - - - -
188E GLY* 3.7 7.9 - - - -
200E CYS* 4.8 0.9 - - - -
201E PHE* 3.5 27.6 - + + -
202E ALA* 3.7 14.5 - - + +
217E TRP* 6.1 4.7 - + - -
220E HIS* 4.3 7.2 - + - -
227E CYS* 3.3 13.3 - - - -
228E PHE* 1.3 80.6 - - - +
230E VAL* 1.3 63.1 + - - +
232E GLY* 3.7 7.6 + - - -
235E LEU* 4.1 12.6 - - + +
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Residues in contact with VAL 230 (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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217E TRP* 5.4 12.4 + - + +
220E HIS* 3.9 27.6 - - + +
221E ARG* 3.2 36.1 - - + -
224E PHE 3.6 11.4 - - - +
225E PRO* 4.4 10.5 - - + +
227E CYS* 3.1 30.9 + - + +
228E PHE 3.1 0.6 - - - -
229E PHE* 1.3 80.4 - - - +
231E LEU* 1.3 61.5 + - + +
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Residues in contact with LEU 231 (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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379B GLU* 3.6 79.8 + - + +
319D HIS* 4.4 4.5 - - + -
225E PRO 3.4 19.5 - - - +
226E ASN* 3.5 32.1 - - - +
227E CYS 2.7 18.2 + - - +
228E PHE* 3.8 7.6 - - + +
230E VAL* 1.3 76.7 - - + +
232E GLY* 1.3 58.1 + - - +
233E ARG* 3.4 4.7 - - + +
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Residues in contact with GLY 232 (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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376B LYS* 4.7 4.2 + - - -
379B GLU* 4.3 8.8 - - - -
228E PHE 2.6 13.9 + - - -
229E PHE* 3.7 5.9 + - - -
230E VAL 3.5 2.2 - - - -
231E LEU* 1.3 75.7 - - - +
233E ARG* 1.3 62.1 + - - -
234E ASN* 3.6 10.2 + - - -
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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