Contacts of the helix formed by residues 226 - 240 (chain A) in PDB entry 4IXU
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 GLY 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A ILE* 2.8 19.9 + - - -
223A ASP 4.5 0.6 - - - -
224A ARG 3.5 1.4 - - - -
225A LEU* 1.3 83.6 - - - +
227A ILE* 1.3 65.8 + - - -
228A GLN 3.3 3.9 + - - -
229A LYS 3.4 0.3 + - - -
230A VAL* 3.1 21.6 + - - +
223B ASP 6.0 0.9 - - - -
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Residues in contact with ILE 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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196A ILE* 4.5 0.9 - - + -
222A ILE* 4.2 29.6 - - + +
226A GLY* 1.3 70.2 - - - -
228A GLN* 1.3 68.2 + - - +
230A VAL* 3.6 15.4 - - + +
231A MET* 3.0 25.4 + - + +
275A GLU* 4.0 39.6 + - + +
278A TYR* 3.6 32.5 - - + -
279A ILE* 3.8 27.4 - - + -
223B ASP* 4.7 18.2 + - + +
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Residues in contact with GLN 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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226A GLY 3.3 1.4 - - - -
227A ILE* 1.3 83.6 - - + +
229A LYS* 1.3 61.8 + - + +
231A MET* 3.2 2.9 + - - +
232A GLU* 2.9 53.7 + - + +
278A TYR* 3.4 27.9 + - + +
223B ASP 5.1 1.4 + - - +
224B ARG* 3.1 69.2 + - - +
225B LEU* 5.8 1.0 - - - +
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Residues in contact with LYS 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 LEU* 3.6 44.4 + - + +
226A GLY 3.4 2.6 + - - +
228A GLN* 1.3 81.5 - - + +
230A VAL* 1.3 61.4 + - - +
232A GLU* 3.6 18.1 - - - +
233A ARG* 2.9 50.8 + - + +
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Residues in contact with VAL 230 (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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196A ILE* 4.1 23.8 - - + -
217A PHE* 3.7 43.9 - - + -
222A ILE* 3.9 24.5 - - + -
225A LEU* 4.1 14.1 - - + -
226A GLY 3.1 16.0 + - - +
227A ILE* 3.6 14.8 - - + +
228A GLN 3.3 0.2 - - - -
229A LYS* 1.3 77.0 - - - +
231A MET* 1.3 57.8 + - - +
233A ARG* 3.8 1.6 - - - +
234A THR* 2.8 36.5 + - - +
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Residues in contact with MET 231 (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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140A VAL* 5.2 0.7 - - + -
196A ILE* 3.6 29.2 - - + -
227A ILE* 3.0 22.7 + - + +
228A GLN 3.8 3.6 - - - +
230A VAL* 1.3 77.7 - - - +
232A GLU* 1.3 66.3 + - + +
234A THR* 3.6 4.8 - - + -
235A PHE* 3.1 62.3 + - + -
278A TYR* 3.9 18.2 - - + -
279A ILE* 3.9 41.5 - - + +
282A GLU* 3.9 20.4 - - + +
283A ILE* 4.6 4.3 - - + -
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Residues in contact with GLU 232 (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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228A GLN* 2.9 47.2 + - + +
229A LYS* 3.6 21.7 - - - +
231A MET* 1.3 77.5 - - - +
233A ARG* 1.3 59.2 + - + +
235A PHE* 3.5 5.2 + - - +
236A ASP* 3.1 27.2 + - - +
278A TYR* 5.9 0.2 - - - +
282A GLU* 6.1 0.9 - - - +
224B ARG* 5.0 2.1 + - - +
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Residues in contact with ARG 233 (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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217A PHE* 3.6 22.6 - - + -
225A LEU* 3.7 43.9 - - - +
229A LYS* 2.9 34.2 + - + +
232A GLU* 1.3 75.9 - - + +
234A THR* 1.3 65.6 + - - +
236A ASP* 3.4 6.7 + - - +
237A LEU* 3.0 29.4 + - + +
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Residues in contact with THR 234 (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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140A VAL* 4.1 22.9 - - + -
194A VAL* 3.6 22.2 - - + +
196A ILE* 3.9 15.8 - - + +
217A PHE* 3.3 23.7 - - - -
230A VAL 2.8 24.4 + - - -
231A MET* 3.6 9.4 - - + -
232A GLU 3.3 0.2 - - - -
233A ARG* 1.3 76.9 - - - +
235A PHE* 1.3 66.1 + - + +
237A LEU* 3.3 9.1 + - - +
238A LEU* 3.0 29.0 + - + +
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Residues in contact with PHE 235 (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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140A VAL* 4.6 4.3 - - + -
231A MET* 3.1 42.4 + - + +
232A GLU* 4.1 4.3 - - - +
234A THR* 1.3 82.3 - - + +
236A ASP* 1.3 60.3 + - - +
238A LEU* 4.3 4.5 - - + +
239A ILE* 2.6 49.9 + - + +
240A GLY* 3.0 4.7 + - - -
246A ILE* 4.1 9.2 - - + -
282A GLU* 3.5 39.9 - - + -
283A ILE* 3.8 22.4 - - + -
286A THR* 3.6 28.5 - - + -
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Residues in contact with ASP 236 (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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232A GLU 3.1 17.0 + - - +
233A ARG* 3.7 8.1 - - - +
235A PHE* 1.3 75.8 - - - +
237A LEU* 1.3 65.8 + - - +
240A GLY* 3.2 31.0 + - - -
241A LYS* 4.7 1.0 + - - +
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Residues in contact with LEU 237 (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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191A ALA 4.4 7.9 - - - +
194A VAL* 4.2 16.8 - - + -
215A GLN* 3.8 42.6 - - + +
217A PHE* 4.3 17.7 - - + -
233A ARG* 3.0 21.0 + - + +
234A THR 3.5 5.8 - - - +
236A ASP* 1.3 82.9 - - + +
238A LEU* 1.3 62.9 + - + +
240A GLY 4.9 0.2 + - - -
244A ARG* 5.3 1.2 + - - -
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Residues in contact with LEU 238 (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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138A CYS* 3.9 25.1 - - + -
139A VAL 3.6 20.0 - - - +
140A VAL* 3.6 22.7 - - + -
191A ALA 3.7 11.9 - - - +
192A SER* 3.5 32.8 - - - +
194A VAL* 3.7 22.9 - - + -
234A THR* 3.0 18.9 + - + +
235A PHE* 4.3 5.2 - - + +
237A LEU* 1.3 80.3 - - + +
239A ILE* 1.3 64.6 + - + +
240A GLY 3.6 0.7 - - - -
241A LYS 5.3 0.7 + - - -
242A ARG* 4.4 0.7 + - - +
244A ARG* 3.2 31.5 + - - +
246A ILE* 6.0 0.2 - - + -
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Residues in contact with ILE 239 (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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138A CYS* 4.2 10.8 - - - -
235A PHE* 2.6 37.5 + - + +
238A LEU* 1.3 79.1 - - + +
240A GLY* 1.3 61.4 + - - +
241A LYS 3.2 3.3 + - - +
242A ARG 3.3 25.3 + - - +
243A GLN* 4.7 10.3 + - - +
244A ARG* 3.8 29.2 - - + +
246A ILE* 4.4 4.0 - - + -
286A THR* 4.1 23.1 - - + -
288A LEU* 3.7 21.8 - - + -
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Residues in contact with GLY 240 (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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235A PHE 3.0 6.7 + - - -
236A ASP* 3.2 33.5 + - - +
237A LEU 4.7 0.2 - - - -
238A LEU 3.6 1.0 - - - -
239A ILE* 1.3 78.6 - - - +
241A LYS* 1.3 62.4 + - - +
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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