Contacts of the helix formed by residues 223 - 234 (chain A) in PDB entry 1UFK
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 ARG 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A ALA* 3.5 24.5 - - + +
195A GLU* 3.5 31.9 + - - +
220A LEU* 2.9 34.7 + - + +
222A ASP* 1.3 127.1 + - - +
224A ALA* 1.3 67.2 + - - +
225A PRO* 3.3 3.1 - - - -
226A LEU* 3.1 31.9 + - + +
227A VAL 3.8 0.9 + - - -
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Residues in contact with ALA 224 (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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219A ILE* 3.8 16.8 - - + -
220A LEU 3.2 5.5 + - - +
221A LYS* 3.1 14.7 + - - +
223A ARG* 1.3 78.1 - - - +
225A PRO* 1.3 70.5 - - + +
227A VAL* 2.9 16.5 + - - +
228A ARG* 3.0 37.5 + - - +
248A VAL* 4.6 10.5 - - + -
250A LEU* 4.3 4.4 - - + +
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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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221A LYS 3.8 7.0 - - - +
222A ASP* 4.3 4.9 - - - +
223A ARG* 3.4 6.3 - - - +
224A ALA* 1.3 95.8 - - + +
226A LEU* 1.3 67.0 + - + +
228A ARG* 3.3 18.3 + - + +
229A GLU* 2.9 27.6 + - - +
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Residues in contact with LEU 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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194A ALA* 4.7 3.4 - - + +
195A GLU* 4.1 33.4 - - + +
198A ALA* 4.2 13.5 - - + +
222A ASP 4.5 4.5 - - - +
223A ARG* 3.4 34.3 - - + +
224A ALA 3.1 0.4 + - - -
225A PRO* 1.3 82.3 - - + +
227A VAL* 1.3 61.0 + - + +
229A GLU* 3.6 11.8 + - - +
230A ALA* 3.0 28.9 + - - +
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Residues in contact with VAL 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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194A ALA* 3.7 40.4 - - + +
197A HIS* 4.3 9.0 - - + -
198A ALA* 5.1 2.7 - - - +
216A LEU* 4.1 16.2 - - + -
219A ILE* 3.9 18.6 - - + -
223A ARG 4.1 1.6 - - - +
224A ALA 2.9 9.4 + - - +
226A LEU* 1.3 74.1 - - - +
228A ARG* 1.3 66.6 + - - +
229A GLU 3.1 1.1 - - - -
230A ALA* 4.4 3.6 - - - +
231A MET* 2.9 40.6 + - + +
250A LEU* 3.8 20.0 - - + -
252A TYR* 3.9 1.8 - - - +
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Residues in contact with ARG 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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224A ALA* 3.0 38.0 + - - +
225A PRO* 3.8 22.8 - - + +
227A VAL* 1.3 75.3 - - - +
229A GLU* 1.3 56.6 + - - +
231A MET* 4.0 1.0 - - - +
232A ALA* 3.0 31.4 + - - +
238A PRO* 6.6 0.2 - - - -
241A GLU* 2.7 43.9 + - - +
248A VAL* 6.0 0.2 - - - +
250A LEU* 4.5 6.7 - - + +
252A TYR* 3.5 21.0 - - + +
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Residues in contact with GLU 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 2.9 17.3 + - - +
226A LEU* 3.7 9.9 - - - +
228A ARG* 1.3 75.7 - - - +
230A ALA* 1.3 60.0 + - - +
232A ALA* 3.6 4.4 + - - +
233A GLY* 3.0 25.5 + - - -
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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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198A ALA* 3.5 43.3 - - + +
201A ALA* 3.5 8.6 - - + +
202A PRO* 5.9 0.3 - - - +
226A LEU 3.0 14.4 + - - +
227A VAL* 4.1 2.5 - - + +
229A GLU* 1.3 77.4 - - - +
231A MET* 1.3 58.4 + - + +
233A GLY* 3.4 2.6 + - - -
234A ALA* 2.9 28.4 + - - +
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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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197A HIS 5.2 2.2 - - - +
201A ALA* 3.9 17.9 - - - -
204A TYR* 4.1 8.7 - - + -
214A ALA* 4.1 6.3 - - + -
216A LEU* 3.8 17.7 - - + -
227A VAL* 2.9 28.5 + - + +
230A ALA* 1.3 75.3 - - + +
232A ALA* 1.3 65.2 + - - +
234A ALA 3.1 7.6 + - - +
235A GLY 3.2 0.2 + - - -
236A PHE* 3.0 75.3 + - + +
252A TYR* 3.7 49.6 - - + -
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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 ARG 3.0 20.3 + - - +
229A GLU* 3.9 4.9 - - - +
231A MET* 1.3 74.7 - - - +
233A GLY* 1.3 58.7 + - - +
235A GLY* 2.8 22.3 + - - -
236A PHE 4.0 11.8 - - - +
238A PRO* 6.4 2.5 - - + -
252A TYR* 5.3 1.4 - - - -
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Residues in contact with GLY 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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229A GLU 3.0 15.9 + - - -
230A ALA* 3.6 4.9 - - - -
232A ALA* 1.3 79.2 - - - +
234A ALA* 1.3 56.8 + - - +
235A GLY 3.4 0.7 + - - -
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Residues in contact with ALA 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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201A ALA* 3.8 32.3 - - + +
202A PRO* 4.1 11.4 - - + -
205A ARG* 2.9 29.1 + - + +
230A ALA 2.9 16.5 + - - +
231A MET 3.1 5.1 + - - +
232A ALA 3.1 0.8 - - - -
233A GLY* 1.3 77.6 - - - +
235A GLY* 1.3 59.3 + - - +
236A PHE* 3.6 9.7 - - + -
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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