Contacts of the helix formed by residues 227 - 242 (chain B) in PDB entry 4UFT
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 LEU 227 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ASP* 5.5 2.0 - - - +
225B GLU 3.8 2.3 + - - +
226B ASP* 1.3 76.6 + - - +
228B SER* 1.3 68.9 + - - +
229B LEU 3.2 1.6 - - - -
230B ARG* 3.2 37.2 + - - +
231B ARG* 3.3 42.5 + - - +
315B ILE 4.4 5.8 - - - +
316B LEU* 3.8 22.4 - - + +
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Residues in contact with SER 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ASP* 3.5 15.0 + - - +
96B ASP* 3.9 18.2 - - - -
97B VAL* 3.7 23.9 - - - +
226B ASP* 3.5 10.9 + - - -
227B LEU* 1.3 82.3 - - - +
229B LEU* 1.3 66.0 + - - +
231B ARG* 3.1 18.4 + - - +
232B PHE* 3.2 13.5 + - - +
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Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B THR* 4.1 31.9 - - + +
73B LEU* 3.8 39.5 - - + -
74B ILE* 5.5 7.4 - - + -
222B ARG* 4.5 12.8 - - + -
223B ILE* 3.8 28.0 - - + -
226B ASP* 3.2 26.2 + - + +
227B LEU 3.2 0.2 - - - -
228B SER* 1.3 76.9 - - - +
230B ARG* 1.3 61.7 + - - +
232B PHE* 3.7 6.9 + - - +
233B MET* 3.5 41.6 + - + +
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Residues in contact with ARG 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B VAL* 6.3 2.5 - - + -
182B VAL* 3.6 30.3 - - - +
223B ILE* 2.7 60.0 + - + +
224B ALA* 3.0 23.2 + - - +
225B GLU 4.4 0.6 + - - -
226B ASP 2.9 13.7 + - - +
227B LEU* 3.2 34.1 + - - +
228B SER 3.2 0.6 - - - -
229B LEU* 1.3 76.3 - - - +
231B ARG* 1.3 60.8 + - - +
233B MET* 3.2 12.8 + - + +
234B VAL* 3.0 34.5 + - + +
315B ILE* 3.6 29.8 + - + +
316B LEU* 4.7 2.0 - - + -
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Residues in contact with ARG 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B THR 5.2 5.4 - - - +
93B ASP 5.5 4.3 - - - +
94B ASP* 3.2 37.3 + - + +
95B PRO* 5.9 0.8 - - - +
96B ASP* 4.3 12.9 + - - +
227B LEU* 3.3 31.6 + - - +
228B SER* 3.1 13.7 + - - +
230B ARG* 1.3 80.2 - - - +
232B PHE* 1.3 61.0 + - - +
234B VAL* 3.6 1.8 + - - +
235B ALA* 3.1 26.4 + - + +
316B LEU* 3.7 32.0 - - + +
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Residues in contact with PHE 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 3.9 45.3 - - + -
77B LEU* 4.7 19.7 - - + -
78B SER* 4.8 8.5 - - - -
87B LEU* 5.3 2.5 - - + -
88B ILE* 4.4 26.5 - - + -
91B ILE* 3.9 28.2 - - + +
92B THR* 4.7 18.8 - - - -
94B ASP* 5.2 0.6 + - - +
99B ILE* 5.9 4.0 - - + -
228B SER 3.2 9.0 + - - +
229B LEU* 3.9 9.6 - - - +
230B ARG 3.2 0.2 - - - -
231B ARG* 1.3 78.8 - - - +
233B MET* 1.3 68.8 + - + +
235B ALA* 4.0 4.1 - - + +
236B LEU* 3.1 30.4 + - + +
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Residues in contact with MET 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 4.6 9.4 - - + -
77B LEU* 5.2 7.4 - - + -
174B ILE* 4.6 16.2 - - - -
175B TRP* 3.2 42.1 - - + -
178B VAL* 3.7 35.2 - - + -
223B ILE* 3.9 17.0 - - + -
229B LEU* 3.5 39.2 + - + +
230B ARG* 3.2 15.8 + - + +
232B PHE* 1.3 81.7 - - + +
234B VAL* 1.3 65.0 + - + +
236B LEU* 3.3 8.4 + - - -
237B ILE* 3.4 7.6 - - - +
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Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B VAL* 5.9 4.5 - - + -
230B ARG* 3.0 20.7 + - + +
231B ARG 4.0 3.4 - - - +
233B MET* 1.3 78.3 - - + +
235B ALA* 1.3 62.4 + - - +
237B ILE* 3.1 20.6 + - + +
238B LEU* 3.3 22.3 - - + +
309B THR* 5.0 4.5 - - - +
312B TYR* 3.8 42.6 - - + -
315B ILE* 4.2 14.1 - - + -
316B LEU* 3.8 23.8 - - + -
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ILE* 4.0 25.5 - - + +
92B THR 5.0 4.5 - - - +
93B ASP* 5.5 4.0 - - + +
231B ARG* 3.1 21.3 + - + +
232B PHE* 4.0 5.6 - - + +
234B VAL* 1.3 77.9 - - - +
236B LEU* 1.3 62.1 + - - +
237B ILE 3.4 0.2 + - - -
238B LEU* 3.5 9.8 + - - +
239B ASP* 3.5 20.1 + - - +
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Residues in contact with LEU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 4.2 19.7 - - + -
78B SER* 6.3 2.0 - - - -
80B PHE* 4.9 15.9 - - + -
87B LEU* 4.9 12.3 - - + -
91B ILE* 3.7 24.7 - - + +
175B TRP* 3.6 24.7 - - + -
232B PHE* 3.1 25.0 + - + +
233B MET* 3.4 7.9 - - - +
234B VAL 3.1 0.2 - - - -
235B ALA* 1.3 77.4 - - - +
237B ILE* 1.3 60.8 + - - +
239B ASP* 3.5 1.9 + - - +
240B ILE* 3.3 38.7 + - + +
254B ILE* 4.5 12.3 - - + -
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Residues in contact with ILE 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B TRP* 3.6 17.7 - - + -
178B VAL* 5.9 4.9 - - + -
233B MET 3.4 16.8 - - - +
234B VAL* 3.1 10.2 + - + +
236B LEU* 1.3 76.9 - - + +
238B LEU* 1.3 60.1 + - + +
240B ILE* 3.4 8.6 + - + +
241B LYS* 2.9 42.8 + - + +
255B CYS* 5.8 1.1 - - - -
258B ASP* 3.3 44.2 - - + +
261B ILE* 5.5 1.6 - - + -
312B TYR* 3.3 42.8 - - + +
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B VAL* 3.3 26.8 + - + +
235B ALA* 3.9 11.0 - - - +
236B LEU 3.4 0.2 - - - -
237B ILE* 1.3 80.1 - - + +
239B ASP* 1.3 59.2 + - - +
241B LYS* 4.2 14.3 - - - +
242B ARG* 2.8 44.4 + - - +
308B GLU* 3.8 40.6 - - + +
309B THR* 4.5 12.1 - - - +
312B TYR* 4.1 28.3 - - + -
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Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LEU* 4.4 10.7 - - - +
91B ILE* 3.5 37.5 - - + +
235B ALA 3.5 4.6 + - - +
236B LEU* 3.9 2.4 - - - +
237B ILE 3.1 0.8 - - - -
238B LEU* 1.3 77.9 - - - +
240B ILE* 1.3 68.0 + - + +
242B ARG* 3.3 24.0 - - - +
243B THR* 3.0 17.4 + - - -
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Residues in contact with ILE 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B PHE* 5.3 10.5 - - + -
236B LEU* 3.3 37.0 + - + +
237B ILE* 3.4 15.3 - - + +
239B ASP* 1.3 79.3 - - + +
241B LYS* 1.3 68.0 + - + +
242B ARG 3.4 0.2 - - - -
243B THR* 3.5 20.1 - - - +
247B LYS* 4.1 14.1 + - - +
251B ALA* 3.9 34.2 - - + +
254B ILE* 4.1 12.3 - - + -
255B CYS* 4.0 24.0 - - + +
258B ASP* 4.3 2.9 - - - +
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Residues in contact with LYS 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ILE* 2.9 26.3 + - + +
238B LEU* 4.2 14.4 - - - +
240B ILE* 1.3 84.3 - - + +
242B ARG* 1.3 61.6 + - - +
243B THR 3.2 5.9 + - - +
247B LYS* 4.6 11.9 + - - +
255B CYS* 4.8 15.5 - - - -
308B GLU* 4.6 13.1 + - - +
311B PRO* 5.6 5.3 - - - +
312B TYR* 5.0 13.7 + - - -
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Residues in contact with ARG 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B LEU* 2.8 41.1 + - - +
239B ASP* 3.3 19.3 - - - +
241B LYS* 1.3 78.2 - - - +
243B THR* 1.3 64.1 + - - +
244B PRO* 3.2 10.7 - - - +
308B GLU* 2.9 36.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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