Contacts of the helix formed by residues 224 - 233 (chain A) in PDB entry 1FIU
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 THR 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ASN* 4.8 3.4 - - - +
39A ARG* 4.8 1.8 - - + -
40A SER* 3.7 40.6 - - - +
43A ILE* 4.4 7.4 - - + -
222A GLU* 2.8 20.7 + - - +
223A PRO* 1.3 77.9 - - - +
225A PRO* 1.3 71.3 - - - +
226A SER* 3.6 11.5 + - - -
227A ARG* 3.3 23.9 + - - +
228A ILE* 3.0 24.0 + - - +
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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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43A ILE* 4.3 9.9 - - + -
223A PRO 3.6 8.1 - - - +
224A THR* 1.3 84.5 - - - +
226A SER* 1.3 56.8 + - - +
228A ILE* 3.3 5.6 + - + -
229A SER* 2.8 31.7 + - - -
249A LEU* 4.5 7.0 - - + -
253A LEU* 3.9 19.7 - - + -
261A ALA* 3.7 40.6 - - + +
264A LEU* 3.8 9.6 - - + -
265A PHE* 4.3 4.5 - - + +
268A MET* 3.4 22.7 - - + +
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Residues in contact with SER 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 THR* 3.6 12.1 + - - -
225A PRO* 1.3 80.2 - - - +
227A ARG* 1.3 68.0 + - - +
229A SER* 2.6 20.4 + - - -
230A SER* 3.5 5.7 + - - -
264A LEU* 3.7 16.2 - - - +
3E C 4.8 15.2 + - - -
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Residues in contact with ARG 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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34A ASP* 2.9 41.8 + - - +
37A ASN* 5.1 4.2 - - - +
40A SER* 4.7 6.3 + - - -
190A ILE* 3.3 37.5 + - + +
191A ARG* 3.6 18.3 - - - +
192A SER* 4.9 6.5 - - - +
222A GLU* 3.5 27.0 + - + -
224A THR* 3.2 15.6 + - - +
226A SER* 1.3 82.0 + - - +
228A ILE* 1.3 64.3 + - - +
230A SER* 2.7 27.7 + - - -
3E C 3.4 27.2 - - + +
4E G 2.8 30.7 + - - -
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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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190A ILE* 4.0 8.1 - - - -
220A THR* 4.5 7.9 - - + -
222A GLU* 3.5 31.4 - - + +
224A THR 3.0 26.3 + - - +
225A PRO* 3.6 11.4 - - + +
227A ARG* 1.3 75.5 - - - +
229A SER* 1.3 60.6 + - - +
231A ILE* 3.1 9.4 + - - +
232A ALA* 3.0 27.3 + - + -
241A VAL* 4.5 8.1 - - + -
243A HIS* 3.7 16.6 - - + -
249A LEU* 4.1 12.8 - - + -
268A MET* 3.8 16.2 - - - -
274A LEU* 4.0 26.7 - - + -
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Residues in contact with SER 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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199A ARG* 4.4 1.2 + - - -
225A PRO 2.8 15.2 + - - -
226A SER* 2.6 22.0 + - - -
228A ILE* 1.3 77.6 - - - +
230A SER* 1.3 60.9 + - - +
232A ALA 3.8 1.1 - - - +
233A LEU* 3.1 49.2 + - - +
264A LEU* 3.9 12.8 - - - +
268A MET* 3.6 17.9 - - - -
133B SER* 5.8 0.3 - - - -
134B ASP* 5.0 1.9 - - - +
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Residues in contact with SER 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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190A ILE* 3.6 15.2 - - - +
192A SER* 3.6 31.1 - - - -
195A ALA* 4.0 4.2 - - - +
196A GLN* 3.0 23.4 + - - +
199A ARG* 3.0 14.8 + - - -
226A SER 3.5 3.8 + - - -
227A ARG* 2.7 21.5 + - - -
229A SER* 1.3 80.4 + - - +
231A ILE* 1.3 58.4 + - - +
134B ASP* 3.4 15.1 - - - +
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Residues in contact with ILE 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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187A LYS* 5.5 2.0 - - + -
190A ILE* 4.1 22.0 - - + -
195A ALA* 3.6 21.1 - - + +
196A GLN* 4.8 0.2 - - - +
198A ALA* 3.5 32.8 - - + -
199A ARG* 3.5 42.6 + - + +
218A VAL* 4.3 20.4 - - + -
228A ILE 3.1 9.6 + - - +
230A SER* 1.3 79.9 + - - +
232A ALA* 1.3 64.3 + - - +
233A LEU 3.5 1.8 - - - +
234A GLY 5.4 0.2 - - - +
238A ILE* 4.0 16.2 - - + +
241A VAL* 4.2 16.9 - - + +
273A ARG* 5.6 0.3 + - - -
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Residues in contact with ALA 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 ILE* 3.0 21.2 + - + +
231A ILE* 1.3 78.3 - - - +
233A LEU* 1.3 64.9 + - - +
234A GLY 3.6 1.7 - - - +
238A ILE* 5.9 0.2 - - - -
241A VAL* 3.7 17.3 - - + -
268A MET* 3.8 21.5 - - + -
273A ARG* 3.2 50.4 + - + +
274A LEU* 5.0 0.4 - - + -
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Residues in contact with LEU 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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199A ARG* 3.0 29.7 + - - +
229A SER* 3.1 39.0 + - - +
231A ILE 3.9 0.2 - - - +
232A ALA* 1.3 79.4 - - - +
234A GLY* 1.3 58.9 + - - +
264A LEU* 4.5 10.1 - - + -
267A ILE* 4.3 8.5 - - + -
268A MET* 3.9 22.7 - - + -
273A ARG* 5.0 1.8 - - + -
128B ALA* 3.6 20.6 - - + +
129B ALA* 4.1 12.6 - - - -
132B GLY* 3.8 13.4 - - - +
133B SER* 3.5 30.1 - - - +
134B ASP* 6.0 1.1 - - - +
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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