Contacts of the helix formed by residues 224 - 234 (chain C) in PDB entry 2I6A
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 GLU 224 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223C ASN* 1.3 87.3 - - - +
225C THR* 1.3 81.6 + - - +
227C ALA* 3.2 1.4 + - - +
228C ALA* 2.8 31.4 + - - +
241C ILE* 4.1 16.5 - - + +
265C THR 2.9 4.8 + - - +
266C GLN* 3.5 50.3 - - + +
267C GLY* 4.6 1.2 + - - -
295C THR* 5.9 2.9 - - - +
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Residues in contact with THR 225 (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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200C PRO* 4.6 14.1 - - - +
223C ASN* 3.2 13.1 + - - +
224C GLU* 1.3 96.1 - - - +
226C GLU* 1.3 57.0 + - - +
228C ALA* 3.6 5.6 + - - +
229C THR* 2.7 37.0 + - - -
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Residues in contact with GLU 226 (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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38C GLN* 3.8 8.7 + - - -
196C ASN* 4.2 1.4 - - - +
197C LEU* 3.2 25.6 - - + +
198C SER 3.0 29.5 + - - +
199C ALA* 3.5 32.4 - - - +
200C PRO* 3.9 5.2 - - + +
203C SER* 4.6 2.6 + - - -
222C GLY* 3.5 7.4 - - - -
223C ASN* 2.7 54.7 + - - +
225C THR* 1.3 72.7 + - - +
227C ALA* 1.3 58.4 + - - +
229C THR* 3.9 4.8 - - - -
230C PHE* 2.9 23.2 + - - +
296C ASN* 5.3 0.7 + - - -
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Residues in contact with ALA 227 (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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197C LEU* 3.7 8.9 - - - +
223C ASN 2.8 17.3 + - - +
224C GLU 3.6 4.3 - - - +
226C GLU* 1.3 75.0 - - - +
228C ALA* 1.3 59.0 + - - +
230C PHE* 3.7 2.5 - - - +
231C ALA* 3.0 22.2 + - - +
241C ILE* 4.0 10.8 - - + -
244C ILE* 3.5 17.1 - - + +
264C PHE* 3.8 38.1 - - + -
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Residues in contact with ALA 228 (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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224C GLU 2.8 17.6 + - - +
225C THR* 4.0 5.6 - - - +
227C ALA* 1.3 74.3 - - - +
229C THR* 1.3 66.0 + - - +
231C ALA* 3.3 3.3 + - - +
232C ARG* 3.2 22.9 + - - +
238C THR 5.5 0.6 - - - +
239C LYS* 5.9 8.1 - - + +
244C ILE* 4.0 14.3 - - + +
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Residues in contact with THR 229 (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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200C PRO* 3.6 30.6 - - + +
203C SER* 4.2 4.9 - - - -
204C GLN* 3.6 34.3 - - + +
225C THR* 2.7 21.3 + - - -
226C GLU 3.9 3.8 - - - -
228C ALA* 1.3 76.7 - - - +
230C PHE* 1.3 64.5 + - - +
232C ARG* 3.3 7.8 + - + +
233C GLU* 3.0 32.2 + - + +
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Residues in contact with PHE 230 (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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197C LEU* 3.8 15.7 - - + -
203C SER* 3.4 25.5 - - - +
210C LEU* 3.5 24.5 - - + -
211C MET* 4.0 7.2 - - - -
214C MET* 3.5 22.0 - - + -
220C LEU* 5.4 0.2 - - + -
226C GLU 2.9 20.0 + - - +
227C ALA* 3.7 6.3 - - - +
229C THR* 1.3 78.3 - - - +
231C ALA* 1.3 58.1 + - - +
233C GLU* 3.5 1.6 + - + +
234C GLN* 2.9 60.9 + - + +
236C PHE* 4.2 7.2 - + - -
244C ILE* 5.1 1.8 - - + -
248C THR* 3.5 35.0 - - + -
251C LEU* 4.0 12.1 - - + -
264C PHE* 5.7 1.3 - + - -
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Residues in contact with ALA 231 (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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227C ALA 3.0 8.4 + - - +
228C ALA 3.3 3.6 + - - +
230C PHE* 1.3 76.1 - - - +
232C ARG* 1.3 56.1 + - - +
234C GLN 3.5 0.3 + - - -
235C GLY 3.0 5.9 + - - -
236C PHE* 2.7 56.6 + - + -
237C GLU 4.2 1.5 + - - -
238C THR 3.9 7.4 - - - +
244C ILE* 3.4 42.2 - - + -
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Residues in contact with ARG 232 (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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228C ALA 3.2 13.0 + - - +
229C THR* 3.7 10.1 - - - +
230C PHE 3.2 0.4 - - - -
231C ALA* 1.3 73.3 - - - +
233C GLU* 1.3 71.9 + - - +
234C GLN 3.0 0.9 - - - -
235C GLY* 2.7 26.4 + - - +
237C GLU 5.6 1.3 - - - +
239C LYS* 4.8 16.4 - - - +
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Residues in contact with GLU 233 (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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203C SER* 3.1 30.7 - - - +
204C GLN* 4.0 24.2 + - - +
207C LYS* 2.4 52.5 + - + +
229C THR* 3.0 23.6 + - + +
230C PHE* 4.0 3.6 - - + +
232C ARG* 1.3 90.2 - - - +
234C GLN* 1.3 65.0 + - + +
235C GLY 3.5 0.3 + - - -
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Residues in contact with GLN 234 (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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207C LYS* 4.4 13.7 - - - +
211C MET* 3.5 41.4 - - - +
230C PHE* 2.9 48.5 + - + +
233C GLU* 1.3 81.3 - - + +
235C GLY* 1.3 59.9 + - - +
236C PHE* 3.2 30.0 + - + -
251C LEU* 5.3 4.6 - - + +
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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