Contacts of the helix formed by residues 224 - 238 (chain A) in PDB entry 4UTX
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 ASP 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A ILE 5.6 1.2 + - - -
217A VAL* 5.8 1.6 - - - +
222A THR 3.9 0.4 + - - -
223A LEU* 1.3 73.3 - - - +
225A SER* 1.3 81.0 + - - +
226A ASP* 2.9 26.7 + - - +
227A ILE* 3.4 37.7 + - + +
228A LEU* 3.2 22.1 + - - +
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Residues in contact with SER 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 LEU 3.6 5.2 + - - -
224A ASP* 1.3 74.8 + - - +
226A ASP* 1.3 56.0 + - - -
228A LEU* 3.2 11.5 + - - +
229A THR* 2.7 39.7 + - - -
0C BEZ 5.2 6.1 + - - -
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Residues in contact with ASP 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 ASP* 2.9 20.6 + - - +
225A SER* 1.3 78.6 - - - +
227A ILE* 1.3 65.1 + - + +
229A THR* 3.3 8.4 + - - -
230A ALA* 3.2 18.7 + - - +
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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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151A TYR* 4.3 18.2 - - + -
152A GLU 4.0 20.9 - - - +
153A ILE* 4.4 21.3 - - + +
224A ASP* 3.4 34.9 + - + +
225A SER 3.2 0.6 - - - -
226A ASP* 1.3 76.1 - - + +
228A LEU* 1.3 64.3 + - + +
230A ALA* 2.9 19.1 + - - +
231A VAL* 3.0 27.8 + - + +
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Residues in contact with LEU 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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153A ILE* 5.7 6.7 - - + -
223A LEU* 3.8 36.8 - - + +
224A ASP 3.2 13.3 + - - +
225A SER* 3.2 10.1 + - - +
227A ILE* 1.3 80.3 - - + +
229A THR* 1.3 57.0 + - - +
231A VAL* 3.7 7.7 - - + +
232A GLU* 3.0 29.1 + - - +
255A MET* 4.5 5.8 - - - -
256A PHE* 4.0 30.3 - - + -
1C GLY* 6.1 0.7 - - - -
2C VAL* 3.7 29.6 - - + +
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Residues in contact with THR 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 SER* 2.7 28.1 + - - -
226A ASP* 3.5 9.3 + - - -
228A LEU* 1.3 74.3 - - - +
230A ALA* 1.3 60.1 + - - +
232A GLU* 3.5 18.4 - - - +
233A ARG* 3.1 24.4 + - - +
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Residues in contact with ALA 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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151A TYR* 3.7 31.0 - - + +
226A ASP 3.2 7.9 + - - +
227A ILE* 2.9 11.6 + - - +
229A THR* 1.3 79.1 - - - +
231A VAL* 1.3 67.1 + - - +
233A ARG* 3.0 9.7 + - - +
234A GLU* 2.9 26.9 + - - +
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Residues in contact with VAL 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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134A ILE* 3.9 26.2 - - + -
151A TYR* 4.3 22.0 - - + -
153A ILE* 4.7 4.7 - - + -
227A ILE* 3.0 29.1 + - + +
228A LEU* 3.7 10.5 - - + +
229A THR 3.3 0.2 - - - -
230A ALA* 1.3 76.0 - - - +
232A GLU* 1.3 57.2 + - - +
234A GLU* 3.1 8.5 + - - +
235A LEU* 2.8 48.7 + - + +
256A PHE* 3.9 19.1 - - + -
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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 LEU 3.0 18.2 + - - +
229A THR* 3.5 21.3 - - - +
231A VAL* 1.3 76.9 - - - +
233A ARG* 1.3 64.7 + - - +
235A LEU* 3.0 3.0 + - - -
236A GLU* 2.9 23.4 + - + +
256A PHE* 5.2 3.3 - - + -
259A GLN* 3.2 32.6 + - - +
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Residues in contact with ARG 233 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A THR 3.1 10.5 + - - +
230A ALA* 3.0 12.2 + - - +
232A GLU* 1.3 82.3 + - - +
234A GLU* 1.3 64.9 + - + +
236A GLU* 3.2 6.6 + - - +
237A LYS* 3.2 52.9 + - + +
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Residues in contact with GLU 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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48A HIS* 5.8 0.2 - - - +
50A ALA* 5.2 1.8 - - - +
130A SER* 5.3 2.6 + - - -
132A VAL* 3.9 31.8 - - + +
134A ILE* 5.6 2.2 - - + -
149A HIS* 5.9 0.9 - - - +
151A TYR* 3.2 38.3 + - + +
230A ALA 2.9 19.7 + - - +
231A VAL* 3.4 9.0 - - + +
232A GLU 3.1 0.2 - - - -
233A ARG* 1.3 78.4 - - + +
235A LEU* 1.3 63.5 + - + +
237A LYS* 3.3 10.8 + - - +
238A CYS* 3.2 22.6 + - - +
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Residues in contact with LEU 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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50A ALA* 3.9 26.0 - - + -
52A ILE* 4.9 10.1 - - + -
134A ILE* 4.0 11.2 - - + -
231A VAL* 2.8 29.7 + - + +
234A GLU* 1.3 75.0 - - - +
236A GLU* 1.3 55.8 + - - +
237A LYS 3.2 0.2 - - - -
238A CYS* 3.5 13.4 + - - -
241A CYS* 4.9 2.2 - - - -
256A PHE* 3.4 46.7 - - + -
259A GLN* 3.7 15.9 - - - +
260A VAL* 3.8 21.1 - - + +
263A ARG* 2.6 29.9 + - - -
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Residues in contact with GLU 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* 2.9 16.6 + - + +
233A ARG* 3.6 8.5 - - - +
235A LEU* 1.3 78.4 - - - +
237A LYS* 1.3 58.5 - - + +
259A GLN* 3.3 23.1 + - - +
263A ARG* 3.2 50.5 + - - +
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Residues in contact with LYS 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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48A HIS* 3.4 33.3 - - + +
233A ARG* 3.2 46.4 + - + +
234A GLU* 3.3 9.8 + - - +
235A LEU 3.2 0.6 - - - -
236A GLU* 1.3 79.3 - - + +
238A CYS* 1.3 62.4 + - - +
239A ASP* 3.7 2.1 + - - +
263A ARG* 4.3 0.7 - - - -
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Residues in contact with CYS 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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48A HIS* 3.2 21.5 - - + +
49A ILE 4.7 0.2 - - - -
50A ALA* 4.2 18.6 - - + -
132A VAL* 6.2 0.9 - - + -
234A GLU 3.2 12.7 + - - +
235A LEU* 3.7 15.9 - - - -
236A GLU 3.4 2.6 - - - -
237A LYS* 1.3 79.7 - - - +
239A ASP* 1.3 56.1 + - - +
240A LEU 3.6 23.1 - - - +
241A CYS* 4.4 5.2 - - - -
260A VAL* 4.4 14.4 - - - -
263A ARG* 2.5 31.0 + - - -
265A VAL* 3.7 4.9 - - - +
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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