Contacts of the helix formed by residues 222 - 231 (chain O) 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 GLN 222 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166O MET 6.0 0.4 - - - -
167O GLY 3.3 13.3 + - - +
168O GLY 2.8 35.7 + - - +
169O LYS* 4.6 4.0 - - + -
172O PHE* 3.0 41.6 - - + +
187O SER 3.6 15.4 + - - -
188O ILE* 3.5 20.4 - - + +
219O ASP* 2.7 34.4 + - - +
220O CYS 3.1 0.2 - - - -
221O ALA* 1.3 88.1 - - + +
223O ALA* 1.3 67.3 + - - +
224O ASN 3.2 1.2 + - - -
225O THR 3.2 2.6 + - - -
226O ALA 2.9 19.4 + - - -
253O ARG* 4.4 2.6 + - - +
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Residues in contact with ALA 223 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172O PHE* 4.7 0.2 - - - -
188O ILE* 4.9 0.4 - - - +
219O ASP* 3.0 24.0 + - + +
222O GLN* 1.3 76.0 - - - +
224O ASN* 1.3 62.6 + - - +
226O ALA* 3.3 9.5 + - - +
227O MET* 3.1 21.0 + - - +
243O ALA 5.3 1.6 - - - +
246O ALA* 4.3 14.8 - - - +
247O ARG* 3.6 29.4 + - - +
250O SER* 3.9 15.9 - - - +
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Residues in contact with ASN 224 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219O ASP 3.6 0.8 + - - -
220O CYS* 3.1 45.8 + - - +
222O GLN 3.3 1.0 - - - -
223O ALA* 1.3 71.3 - - - +
225O THR* 1.3 56.8 + - - +
227O MET* 3.0 12.9 + - + +
228O PHE* 2.7 37.0 + - - +
247O ARG* 3.0 31.2 + - - -
269O CYS* 3.0 32.0 + - - +
271O TYR* 3.7 8.5 - - - -
295O HIS* 6.2 0.6 + - - -
500P B13 5.6 5.8 - - + -
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Residues in contact with THR 225 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172O PHE* 3.8 18.6 - - + -
173O ASP* 4.4 4.3 - - - +
176O VAL* 4.9 0.2 - - + -
220O CYS 3.4 4.8 + - - -
221O ALA* 3.6 16.3 + - - -
222O GLN 3.2 8.5 + - - -
224O ASN* 1.3 74.3 - - - +
226O ALA* 1.3 63.5 + - - +
228O PHE* 3.2 3.3 + - - +
229O ILE* 3.0 31.3 + - + +
138P ILE* 3.5 32.3 - - + -
500P B13 3.5 35.4 - - + +
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Residues in contact with ALA 226 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172O PHE* 4.0 13.6 - - + -
176O VAL* 4.2 5.6 - - + -
222O GLN 2.9 13.4 + - - +
223O ALA 3.4 9.9 - - - +
224O ASN 3.2 0.2 - - - -
225O THR* 1.3 76.0 - - - +
227O MET* 1.3 57.8 + - - +
229O ILE* 3.4 1.0 + - - -
230O GLY* 2.9 24.9 + - - -
238O LEU* 3.3 29.1 - - + +
242O ILE* 6.5 0.2 - - + -
243O ALA* 4.3 7.6 - - - +
246O ALA* 4.0 20.2 - - + -
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Residues in contact with MET 227 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223O ALA 3.1 12.4 + - - +
224O ASN* 3.0 16.7 + - + +
226O ALA* 1.3 76.4 - - - +
228O PHE* 1.3 65.4 + - + +
230O GLY* 3.2 3.3 + - - -
231O GLY* 3.0 19.6 + - - +
243O ALA* 4.5 3.7 - - - +
247O ARG* 3.5 20.2 - - - +
271O TYR* 3.7 32.3 - - + +
295O HIS* 4.2 12.3 - - + +
296O SER 4.7 3.1 - - - +
297O ASP* 4.2 12.8 - - + -
298O VAL* 5.6 1.3 - - + -
299O MET* 3.9 25.1 - - - +
366O GLN* 3.2 29.4 + - - +
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Residues in contact with PHE 228 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224O ASN 2.7 19.3 + - - +
225O THR* 3.8 4.0 - - - +
227O MET* 1.3 74.5 - - + +
229O ILE* 1.3 61.6 + - + +
231O GLY* 2.8 23.2 + - - +
235O ASN* 5.0 0.9 + - - -
295O HIS* 4.1 23.6 - + + -
296O SER 5.5 2.9 - - - -
500P B13 3.5 98.6 - - + +
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Residues in contact with ILE 229 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176O VAL* 4.4 11.4 - - + +
177O LEU* 4.3 13.0 - - + -
225O THR* 3.0 24.4 + - + +
226O ALA* 3.8 4.3 - - - +
228O PHE* 1.3 78.1 - - + +
230O GLY* 1.3 63.2 + - - +
231O GLY* 3.2 1.6 + - - -
235O ASN* 4.3 2.9 + - - -
237O ASN* 3.3 52.4 + - + +
238O LEU* 3.9 7.2 - - + -
95P LEU* 4.9 7.4 - - + -
138P ILE* 3.5 45.8 - - + -
500P B13 4.8 14.4 - - + +
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Residues in contact with GLY 230 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226O ALA 2.9 16.2 + - - -
227O MET* 3.4 6.5 - - - -
228O PHE 3.0 0.2 - - - -
229O ILE* 1.3 78.3 - - - +
231O GLY* 1.3 60.3 + - - +
235O ASN* 3.4 14.8 - - - +
238O LEU* 3.6 24.7 + - - +
240O HIS* 2.7 27.0 + - - -
243O ALA* 5.4 2.0 - - - -
366O GLN* 5.8 0.2 - - - -
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Residues in contact with GLY 231 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227O MET* 3.0 8.7 + - - +
228O PHE* 2.8 19.8 + - - -
229O ILE 3.1 0.2 - - - -
230O GLY* 1.3 81.0 - - - +
232O GLY* 1.3 58.8 + - - -
235O ASN* 3.5 13.2 - - - -
240O HIS* 3.2 13.2 + - - -
298O VAL* 5.9 2.1 - - - +
366O GLN* 5.1 1.7 + - - -
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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