Contacts of the helix formed by residues 222 - 231 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166K MET 6.3 0.2 - - - -
167K GLY 3.2 20.7 + - - +
168K GLY 3.3 15.2 + - - -
169K LYS* 4.5 6.7 - - - -
172K PHE* 2.9 44.9 - - + +
187K SER 3.0 30.1 + - - -
188K ILE* 3.4 26.9 - - + +
219K ASP* 2.5 36.3 + - - +
220K CYS 3.1 0.2 + - - -
221K ALA* 1.3 85.7 - - + +
223K ALA* 1.3 66.2 + - - +
224K ASN 3.4 0.2 - - - -
225K THR 3.3 1.2 + - - -
226K ALA* 3.1 8.1 + - - +
253K ARG* 4.3 3.9 + - - +
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Residues in contact with ALA 223 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188K ILE* 4.9 0.4 - - - +
219K ASP* 2.8 27.2 + - + +
222K GLN* 1.3 74.3 - - - +
224K ASN* 1.3 58.1 + - - +
226K ALA* 3.3 9.6 - - - +
227K MET* 3.1 24.1 + - - +
243K ALA 5.4 1.4 - - - +
246K ALA* 4.2 14.1 - - - +
247K ARG* 3.3 30.1 + - - +
250K SER* 3.8 15.9 - - - +
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Residues in contact with ASN 224 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219K ASP 3.6 1.0 + - - -
220K CYS* 3.3 34.7 + - - +
223K ALA* 1.3 76.2 - - - +
225K THR* 1.3 59.0 + - - +
227K MET* 3.1 8.2 + - - +
228K PHE* 2.8 51.7 + - + -
247K ARG* 2.6 37.5 + - - -
269K CYS* 2.6 42.1 + - - +
271K TYR* 3.4 11.8 - - - -
287K GLU* 5.2 0.2 + - - -
295K HIS* 6.1 0.6 + - - -
500L B13 5.5 0.4 - - + -
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Residues in contact with THR 225 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172K PHE* 3.8 19.3 - - + -
173K ASP* 4.5 1.8 - - - +
220K CYS 3.4 7.2 + - - -
221K ALA 3.2 17.0 + - - -
222K GLN 3.3 8.5 + - - -
224K ASN* 1.3 74.7 - - - +
226K ALA* 1.3 57.4 + - - +
228K PHE* 3.3 4.0 + - - +
229K ILE* 2.9 41.9 + - + +
138L ILE* 3.5 32.1 - - + -
500L B13 3.3 33.9 - - + +
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Residues in contact with ALA 226 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172K PHE* 3.9 1.7 - - + -
176K VAL* 4.2 15.0 - - + -
222K GLN 3.1 12.7 + - - +
223K ALA 3.3 9.9 - - - +
225K THR* 1.3 75.6 - - - +
227K MET* 1.3 56.1 + - - +
229K ILE* 3.3 2.9 + - - +
230K GLY* 2.9 24.3 + - - -
238K LEU* 3.3 28.7 - - + +
243K ALA* 4.3 7.2 - - - +
246K ALA* 4.1 23.6 - - + -
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Residues in contact with MET 227 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223K ALA 3.1 12.8 + - - +
224K ASN* 3.1 13.2 + - - +
226K ALA* 1.3 74.2 - - - +
228K PHE* 1.3 83.7 + - + +
230K GLY* 3.0 5.0 + - - -
231K GLY* 2.8 26.1 + - - +
243K ALA* 4.5 3.0 - - - +
247K ARG* 3.8 15.9 - - - +
271K TYR* 3.6 31.9 - - + +
295K HIS* 4.3 0.2 - - + -
296K SER 4.9 1.6 - - - +
297K ASP* 4.3 13.0 - - + -
298K VAL* 5.5 0.9 - - + -
299K MET* 4.2 24.7 - - - +
366K GLN* 3.4 30.4 + - - +
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Residues in contact with PHE 228 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220K CYS* 5.6 2.2 - - - -
224K ASN* 2.8 51.2 + - + +
225K THR* 3.9 3.8 - - - +
227K MET* 1.3 79.3 - - + +
229K ILE* 1.3 68.2 + - - +
231K GLY* 3.0 16.3 + - - +
235K ASN* 5.0 1.0 + - - -
295K HIS* 3.2 59.7 - + + -
296K SER 4.2 7.6 - - - -
500L B13 3.2 61.0 - - + +
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Residues in contact with ILE 229 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176K VAL* 4.1 25.1 - - + +
177K LEU* 4.2 11.2 - - + -
225K THR* 2.9 41.4 + - + +
226K ALA 3.8 3.8 - - - +
228K PHE* 1.3 76.7 - - + +
230K GLY* 1.3 64.6 + - - +
231K GLY* 3.2 1.0 + - - -
235K ASN* 4.4 3.1 + - - -
237K ASN* 3.5 51.2 + - + +
238K LEU* 3.9 8.1 - - + -
95L LEU* 4.8 8.7 - - + -
138L ILE* 4.0 24.9 - - + -
142L ILE* 5.8 1.6 - - + -
500L B13 4.9 13.9 - - + +
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Residues in contact with GLY 230 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226K ALA 2.9 14.6 + - - -
227K MET* 3.0 6.2 + - - -
229K ILE* 1.3 76.5 - - - +
231K GLY* 1.3 60.4 + - - +
235K ASN* 3.3 15.6 - - - +
238K LEU* 3.6 25.6 + - - +
240K HIS* 2.7 26.5 + - - -
243K ALA* 5.4 2.5 - - - -
366K GLN* 5.5 0.7 - - - -
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Residues in contact with GLY 231 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227K MET* 2.8 15.9 + - - +
228K PHE* 3.0 16.2 + - - -
230K GLY* 1.3 78.3 - - - +
232K GLY* 1.3 61.6 + - - -
235K ASN* 3.6 11.2 - - - -
240K HIS* 3.2 10.4 - - - -
298K VAL* 5.8 3.3 - - - +
366K GLN* 5.1 2.1 + - - -
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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