Contacts of the helix formed by residues 218 - 221 (chain C) in PDB entry 2I2X
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 THR 218 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163C VAL 4.0 0.2 + - - -
164C GLU* 4.3 11.0 - - - +
165C SER 4.5 0.5 + - - +
217C ASP* 1.3 87.7 + - - +
219C ASP* 1.3 62.9 + - - +
220C CYS* 2.9 19.8 + - + +
221C ALA 4.6 1.0 + - - -
253C ARG* 3.0 14.0 + - - +
254C SER* 4.1 0.7 - - - -
267C LYS* 2.8 31.2 - - - +
269C CYS* 3.2 26.8 - - - +
270C GLY* 3.1 30.1 - - - +
272C GLU* 3.9 6.3 - - - +
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Residues in contact with ASP 219 (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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188C ILE* 3.5 7.9 - - - +
218C THR* 1.3 70.7 - - - +
220C CYS* 1.3 63.4 + - - +
221C ALA* 3.2 3.5 - - - +
222C GLN* 2.5 36.0 + - - +
223C ALA* 2.9 43.6 + - + +
224C ASN* 3.6 2.5 + - - -
250C SER* 3.3 26.9 - - - -
253C ARG* 3.1 22.8 + - - +
254C SER* 3.9 4.7 - - - +
272C GLU* 2.9 21.7 + - - +
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Residues in contact with CYS 220 (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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164C GLU* 3.2 11.7 - - + +
218C THR* 2.9 14.2 + - + +
219C ASP* 1.3 76.6 - - - +
221C ALA* 1.3 61.2 + - - +
222C GLN 3.1 1.6 + - - -
224C ASN* 3.0 49.4 - - - +
225C THR* 3.4 9.2 + - - -
228C PHE* 5.2 5.4 - - - -
269C CYS* 4.3 0.7 - - - -
313C GLU* 5.2 1.3 - - - -
502C ZN 2.3 37.0 - - - -
500D B13 4.8 9.8 - - + +
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Residues in contact with ALA 221 (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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164C GLU* 5.2 5.6 - - + +
165C SER 3.9 21.1 - - - +
166C MET* 4.6 7.0 - - + -
169C LYS* 4.1 23.9 - - + +
172C PHE* 4.0 6.9 - - - -
173C ASP* 4.9 1.6 - - - +
218C THR 4.6 1.6 + - - -
219C ASP* 3.1 1.4 + - - +
220C CYS* 1.3 76.6 - - - +
222C GLN* 1.3 65.3 + - + +
225C THR* 3.2 13.0 + - - -
500D B13 3.7 26.2 - - + +
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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