Contacts of the helix formed by residues 215 - 221 (chain L) 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 ASN 215 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48I ARG* 5.9 1.2 - - - +
64I ARG* 5.8 2.0 - - - +
213L ALA 4.9 3.1 - - - +
214L VAL* 1.3 76.7 - - - +
216L GLN* 1.3 64.6 + - - +
217L ASP* 3.2 41.7 + - - +
218L PHE* 3.0 24.2 + - - +
219L VAL* 3.2 14.7 + - - +
227L TYR* 3.8 17.7 - - + +
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Residues in contact with GLN 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64I ARG* 3.9 19.5 - - - +
215L ASN* 1.3 77.7 - - - +
217L ASP* 1.3 67.6 + - - +
219L VAL* 3.3 3.6 - - - +
220L SER* 3.1 29.3 + - - -
227L TYR* 3.5 28.9 - - + -
256L HIS* 3.1 44.7 - - + +
257L LYS* 3.3 14.0 + - - +
258L HIS* 3.2 34.6 - - + +
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Residues in contact with ASP 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I ARG* 4.0 19.8 + - - -
64I ARG* 4.2 16.6 + - - -
215L ASN* 3.2 18.0 + - - +
216L GLN* 1.3 82.1 + - - +
218L PHE* 1.3 61.5 + - - +
220L SER* 3.4 19.1 + - - -
221L GLN* 3.8 9.7 + - - +
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Residues in contact with PHE 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188L MET* 3.3 58.6 - - + -
189L TYR* 3.6 35.0 - + - -
191L PHE* 4.3 2.9 - + - -
213L ALA 5.5 1.1 - - - +
214L VAL* 3.9 24.0 - - + -
215L ASN* 3.0 25.2 + - - +
217L ASP* 1.3 79.4 - - - +
219L VAL* 1.3 60.2 + - + +
221L GLN* 3.1 42.0 - - - +
222L PHE* 3.3 29.3 - + - -
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Residues in contact with VAL 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191L PHE* 5.5 0.2 - - + -
209L CYS* 3.7 24.0 - - + -
214L VAL* 3.7 22.9 - - + -
215L ASN 3.4 11.9 - - - +
216L GLN 3.3 9.2 - - - +
218L PHE* 1.3 79.2 - - + +
220L SER* 1.3 67.0 + - - +
221L GLN 3.3 0.9 - - - -
222L PHE* 3.2 31.6 + - + +
225L GLY* 3.8 13.8 - - - +
226L VAL 4.1 1.3 - - - -
227L TYR* 3.2 37.7 - - + +
256L HIS* 3.9 10.1 - - + +
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Residues in contact with SER 220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216L GLN* 3.1 21.9 + - - -
217L ASP* 3.5 10.6 - - - -
218L PHE 3.4 0.4 - - - -
219L VAL* 1.3 78.6 - - - +
221L GLN* 1.3 60.4 + - - +
222L PHE 3.3 0.5 - - - +
252L ARG* 3.0 36.4 + - - +
256L HIS* 3.2 22.7 + - - -
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Residues in contact with GLN 221 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189L TYR* 4.4 11.7 + - - -
192L LYS* 5.5 5.1 - - - -
217L ASP 3.8 5.5 + - - +
218L PHE* 3.1 53.8 + - - +
220L SER* 1.3 79.4 - - - +
222L PHE* 1.3 71.9 + - + +
223L ALA 3.9 1.2 + - - -
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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