Contacts of the helix formed by residues 230 - 245 (chain A) in PDB entry 5UFL
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 ASN 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A GLU* 3.0 26.2 + - - +
224A LYS* 3.2 29.6 + - - +
225A LEU 3.8 2.3 - - - +
227A HIS* 3.1 24.9 + - - +
229A ARG* 1.3 74.6 - - - +
231A ILE* 1.3 63.7 + - - +
232A HIS 3.1 2.9 - - - -
233A GLN* 3.2 27.7 + - + +
234A THR* 3.6 9.5 + - - -
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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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225A LEU 3.5 17.9 - - - +
226A PHE* 3.8 28.3 - - + -
227A HIS 3.0 20.0 + - - +
228A ALA* 4.3 10.5 - - - -
229A ARG* 4.3 2.5 - - - +
230A ASN* 1.3 73.8 + - - +
232A HIS* 1.3 68.4 + - + +
234A THR* 3.0 9.9 + - + -
235A PHE* 2.9 63.4 + - + -
261A LEU* 5.6 0.9 - - + -
267A ILE* 4.5 10.8 - - + -
270A TYR* 4.1 20.0 - - + +
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Residues in contact with HIS 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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229A ARG 4.3 10.0 + - - +
231A ILE* 1.3 83.0 - - + +
233A GLN* 1.3 75.1 + - + +
236A GLN* 3.1 46.8 + - - +
274A TYR* 3.4 27.8 - + - -
275A GLU* 3.5 34.0 - - - +
276A HIS* 4.0 21.1 + + - -
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Residues in contact with GLN 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 ARG 4.3 2.4 - - - +
230A ASN* 3.2 21.2 + - + +
232A HIS* 1.3 93.4 + - + +
234A THR* 1.3 60.0 + - - +
236A GLN* 3.4 11.4 + - + +
237A LEU* 2.9 30.7 + - - +
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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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209A LEU* 4.4 9.0 - - + -
225A LEU* 2.8 47.1 + - + +
226A PHE* 4.1 24.0 - - + -
230A ASN 3.6 4.6 + - - -
231A ILE* 3.0 13.6 + - + -
233A GLN* 1.3 79.0 - - - +
235A PHE* 1.3 56.0 + - + +
237A LEU* 3.5 6.7 + - - +
238A ILE* 3.0 51.5 + - + +
261A LEU* 5.1 0.4 - - + -
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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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231A ILE* 2.9 49.4 + - + +
234A THR* 1.3 73.3 - - - +
236A GLN* 1.3 60.9 + - - +
238A ILE* 3.9 7.1 - - + +
239A PHE* 2.9 40.9 + + + +
258A LEU* 4.8 15.9 - - + -
261A LEU* 5.0 3.6 - - + -
267A ILE* 3.6 37.0 - - + -
270A TYR* 3.9 7.6 - - + -
271A LEU* 3.7 41.3 - - + -
274A TYR* 3.7 42.4 - + + -
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Residues in contact with GLN 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 HIS* 3.1 38.3 + - - +
233A GLN* 3.6 11.6 - - - +
234A THR 3.4 0.2 - - - -
235A PHE* 1.3 76.4 - - - +
237A LEU* 1.3 57.7 + - - +
239A PHE* 4.1 3.1 - - - +
240A ASN* 3.1 30.0 + - + +
274A TYR* 3.3 17.4 + - - +
276A HIS* 5.2 5.4 + - + -
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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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197A LEU* 4.1 30.7 - - + +
202A LEU* 5.3 3.4 - - + -
205A VAL* 3.9 28.9 - - + -
209A LEU* 4.1 18.2 - - + -
225A LEU* 5.9 1.1 - - + -
233A GLN 2.9 17.3 + - - +
234A THR* 3.7 6.5 - - - +
236A GLN* 1.3 75.4 - - - +
238A ILE* 1.3 64.8 + - - +
240A ASN* 3.4 14.2 + - - +
241A ILE* 3.0 39.6 + - + +
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Residues in contact with ILE 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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209A LEU* 3.5 22.0 - - + -
234A THR* 3.0 35.2 + - + +
235A PHE* 3.4 9.2 + - + +
237A LEU* 1.3 76.4 - - - +
239A PHE* 1.3 57.9 + - + +
241A ILE* 3.4 9.1 + - - +
242A LEU* 3.0 24.2 + - + +
254A SER* 3.4 19.8 + - - +
257A LEU* 4.0 12.3 - - + -
258A LEU* 4.1 37.7 - - + -
261A LEU* 3.7 29.4 - - + -
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Residues in contact with PHE 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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235A PHE* 2.9 32.3 + + + +
236A GLN* 4.4 2.2 - - - +
238A ILE* 1.3 74.6 - - + +
240A ASN* 1.3 64.1 + - - +
242A LEU* 4.3 7.0 - - + -
243A ILE* 3.1 33.5 + - + +
258A LEU* 3.9 29.4 - - + -
271A LEU* 3.7 30.1 - - + -
274A TYR* 4.1 7.0 - + - -
277A PHE* 4.1 13.5 - + - -
280A CYS* 3.7 44.2 - - + -
281A LEU* 5.3 0.4 - - - -
284A VAL* 4.3 21.8 - - + -
306A PHE* 4.1 14.8 - + - -
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Residues in contact with ASN 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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202A LEU* 4.1 23.6 - - - +
236A GLN* 3.1 21.2 + - + +
237A LEU* 3.5 13.7 + - - +
238A ILE 3.3 0.2 - - - -
239A PHE* 1.3 74.1 - - - +
241A ILE* 1.3 58.4 + - - +
243A ILE* 5.4 0.4 - - - -
244A ASN* 2.8 64.5 + - - +
245A GLY 3.6 0.3 + - - -
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Residues in contact with ILE 241 (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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202A LEU* 4.1 33.7 - - + +
205A VAL* 3.8 24.7 - - + -
206A VAL* 3.9 39.9 - - + -
209A LEU* 4.7 6.1 - - + -
237A LEU* 3.0 28.7 + - + +
238A ILE* 3.6 10.3 - - + +
240A ASN* 1.3 75.4 - - - +
242A LEU* 1.3 59.4 + - - +
245A GLY* 2.9 25.1 + - - -
250A THR* 4.0 20.3 + - - -
254A SER* 4.0 9.6 - - - +
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Residues in contact with LEU 242 (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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238A ILE* 3.0 12.2 + - + +
239A PHE* 3.9 14.6 - - + +
240A ASN 3.2 0.2 - - - -
241A ILE* 1.3 80.3 - - - +
243A ILE* 1.3 59.1 + - + +
245A GLY 4.7 0.7 + - - -
246A ASP 5.3 0.9 - - - +
251A ARG* 3.0 40.9 + - - +
254A SER* 3.3 28.9 + - - +
255A VAL* 4.1 16.4 - - + +
258A LEU* 4.4 12.1 - - + -
284A VAL* 4.6 12.6 - - + -
287A LEU* 3.5 23.1 - - + +
299A VAL* 4.9 3.6 - - + -
302A LEU* 3.4 32.1 - - + -
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Residues in contact with ILE 243 (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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239A PHE* 3.1 28.9 + - + +
240A ASN* 5.4 0.4 - - - -
242A LEU* 1.3 79.7 - - + +
244A ASN* 1.3 75.3 + - - +
245A GLY 3.6 2.1 - - - +
251A ARG* 4.4 10.2 + - - -
280A CYS* 4.1 13.0 - - - +
283A GLN* 3.5 51.1 - - + +
284A VAL* 4.3 17.3 - - + -
287A LEU* 4.2 22.6 - - + +
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Residues in contact with ASN 244 (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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202A LEU* 4.2 8.0 - - + +
240A ASN* 2.8 41.7 + - - +
243A ILE* 1.3 89.7 - - - +
245A GLY* 1.3 67.6 + - - +
283A GLN* 5.0 4.4 + - - +
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Residues in contact with GLY 245 (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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202A LEU* 3.6 21.5 - - - +
240A ASN 3.6 1.2 + - - -
241A ILE 2.9 21.3 + - - -
242A LEU 4.6 0.9 - - - -
243A ILE 3.6 3.6 - - - +
244A ASN* 1.3 82.3 - - - +
246A ASP* 1.3 68.4 + - - +
247A GLY* 3.7 1.4 + - - -
250A THR* 4.0 1.8 - - - -
251A ARG* 5.9 0.5 + - - -
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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
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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