Contacts of the helix formed by residues 224 - 229 (chain A) in PDB entry 1I09
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 ALA 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A TYR 3.4 3.0 + - - -
223A ARG* 1.3 74.1 - - - +
225A PRO* 1.3 72.0 - - + +
226A GLU* 3.0 27.8 - - - +
227A LEU* 2.7 24.2 + - + +
228A ILE* 3.1 7.7 + - - +
238A ILE* 3.9 21.3 + - + +
241A TRP* 3.5 22.7 - - + -
328A ARG* 4.2 0.7 - - - +
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Residues in contact with PRO 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ARG 3.7 0.8 - - - +
224A ALA* 1.3 82.0 - - + +
226A GLU* 1.3 64.4 + - - +
228A ILE* 3.0 18.3 + - + +
229A PHE* 2.7 43.3 + - + -
241A TRP* 3.4 37.2 - - + -
266A LEU* 5.1 2.9 - - + -
269A ILE* 4.5 8.3 - - + -
284A MET* 3.3 34.3 - - + -
323A TYR* 4.6 3.8 - - + -
328A ARG* 3.7 9.0 - - - +
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Residues in contact with GLU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ALA* 2.9 21.1 + - - +
225A PRO* 1.3 71.9 - - - +
227A LEU* 1.3 67.8 + - + +
229A PHE* 3.0 10.6 + - - +
230A GLY 2.9 5.4 + - - -
231A ALA* 2.9 34.8 + - + -
234A TYR* 4.4 12.6 - - + +
235A THR 5.2 0.9 + - - +
237A SER* 4.9 0.5 + - - -
238A ILE* 3.3 23.4 - - - +
284A MET* 3.9 29.4 - - + +
325A PRO* 3.8 20.8 - - + +
328A ARG* 2.7 37.6 + - - -
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A SER* 3.6 11.6 + - - +
217A ILE* 4.1 11.2 - - + -
218A CYS* 3.3 34.8 - - + -
223A ARG* 3.3 32.1 + - - +
224A ALA 2.7 27.0 + - - +
226A GLU* 1.3 72.2 - - - +
228A ILE* 1.3 58.4 + - - +
230A GLY* 2.9 19.2 + - - -
234A TYR* 3.4 43.1 - - + -
238A ILE* 4.0 28.3 - - + -
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Residues in contact with ILE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ARG* 3.8 35.0 + - + +
224A ALA 3.6 7.0 - - - +
225A PRO* 3.0 17.2 + - + +
227A LEU* 1.3 72.4 - - - +
229A PHE* 1.3 54.7 + - - +
230A GLY* 3.0 8.0 + - - -
262A GLY* 4.1 9.2 - - - -
265A GLN* 3.7 25.4 - - + +
266A LEU* 3.2 38.1 - - + -
269A ILE* 4.1 11.9 - - + -
215B SER* 4.8 2.1 + - - -
216B TYR* 3.2 40.1 + - + +
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Residues in contact with PHE 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A PRO* 2.7 29.2 + - + +
226A GLU* 3.0 7.1 + - - +
228A ILE* 1.3 72.5 - - - +
230A GLY* 1.3 62.6 + - - +
231A ALA 3.3 1.9 + - - -
266A LEU* 3.6 32.5 - - + -
276A PRO* 5.8 7.4 - - + -
281A ILE* 5.3 13.2 - - + -
284A MET* 3.2 42.0 - - + -
285A ASN 4.4 22.7 - - - -
323A TYR* 6.1 0.2 - + - -
215B SER* 5.3 2.6 + - - -
216B TYR* 3.8 27.8 - + - -
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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