Contacts of the helix formed by residues 228 - 246 (chain A) in PDB entry 1L1E
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 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A CYS* 3.9 17.4 - - - -
36A ALA 4.9 3.4 - - - +
37A TYR* 3.5 37.5 - - + -
52A LYS* 5.2 2.0 - - + -
55A LEU* 4.5 5.8 - - + -
167A HIS* 4.5 13.5 - - + -
226A GLN* 4.1 16.8 - - + +
227A SER* 1.3 79.8 - - - +
229A GLN* 1.3 67.1 + - - +
230A LEU 3.4 2.5 - - - -
231A HIS* 2.9 28.1 + - + -
232A TYR* 3.2 7.6 + - - +
280A VAL* 2.7 20.8 + - + +
282A GLN* 4.1 32.1 - - + +
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Residues in contact with GLN 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PRO* 5.3 2.0 - - - +
227A SER* 3.6 3.0 - - - +
228A LEU* 1.3 78.0 - - - +
230A LEU* 1.3 72.2 + - + +
232A TYR* 3.2 13.8 + - - +
233A ALA* 3.5 7.6 + - - +
273A PHE* 3.1 29.5 - - - +
274A ARG 5.7 0.2 - - - -
276A GLY* 3.3 25.9 + - - -
278A THR 3.0 25.7 + - - +
279A ASP* 3.4 31.8 + - - +
280A VAL 4.5 4.0 - - - +
221B ARG* 3.9 18.1 + - - +
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Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU 3.4 0.6 - - - -
229A GLN* 1.3 88.3 - - + +
231A HIS* 1.3 68.4 + - + +
233A ALA* 3.5 7.9 + - + +
234A ARG* 3.4 19.9 + - - +
273A PHE 4.4 13.2 - - - +
274A ARG* 4.5 21.8 + - + +
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Residues in contact with HIS 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A CYS* 3.7 2.5 - - - -
36A ALA 3.3 20.0 - - - +
37A TYR* 3.7 19.1 - + - -
38A PHE* 3.1 56.0 + - + +
227A SER 5.1 0.9 - - - -
228A LEU* 2.9 35.9 + - + +
230A LEU* 1.3 82.6 - - + +
232A TYR* 1.3 56.3 + - - +
234A ARG* 3.5 1.0 + - - +
235A THR* 2.7 34.0 + - - -
163B LYS* 5.3 6.0 + - - -
286B GLU* 5.3 8.1 + - - -
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Residues in contact with TYR 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER* 5.6 0.2 - - - -
35A CYS* 3.3 45.3 - - + -
169A ILE* 4.0 15.1 - - + +
200A PHE* 5.4 1.2 - - - -
228A LEU 3.2 5.2 + - - +
229A GLN 3.6 9.0 - - - +
230A LEU 3.2 0.2 - - - -
231A HIS* 1.3 77.3 - - - +
233A ALA* 1.3 65.2 + - - +
235A THR* 3.1 2.8 + - - -
236A LEU* 2.9 52.7 + - + +
239A TRP* 4.1 12.9 - + - -
265A TYR* 3.8 20.1 + - - -
269A CYS* 5.4 1.1 - - + -
273A PHE* 3.2 51.1 - + + -
280A VAL* 3.7 10.3 - - + -
903A CO3 3.6 16.0 + - - -
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Residues in contact with ALA 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 GLN 3.5 8.1 + - - +
230A LEU* 3.7 12.1 - - + +
232A TYR* 1.3 80.5 - - - +
234A ARG* 1.3 55.6 + - - +
236A LEU* 3.5 3.0 + - - +
237A ASP* 3.0 31.4 + - - +
270A ALA* 3.7 28.4 - - - +
273A PHE* 4.4 3.5 - - + +
274A ARG* 3.6 38.1 - - + +
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Residues in contact with ARG 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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38A PHE* 3.3 54.1 - - + +
41A ASP* 2.5 58.2 + - - +
43A MET 4.2 4.8 + - - -
230A LEU 3.4 12.8 + - - +
231A HIS 3.5 0.4 + - - +
232A TYR 3.2 0.4 - - - -
233A ALA* 1.3 77.7 - - - +
235A THR* 1.3 65.2 + - - +
237A ASP* 3.6 9.5 - - + +
238A MET* 3.0 43.7 + - + +
274A ARG* 3.9 8.0 - - - +
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Residues in contact with THR 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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34A SER 4.1 1.1 - - - +
35A CYS* 4.4 1.6 - - - -
36A ALA* 3.0 33.8 + - - +
38A PHE* 3.8 6.9 - - - -
45A LEU* 4.3 6.3 - - + -
49A GLN* 4.3 5.2 - - - +
231A HIS 2.7 20.8 + - - -
232A TYR* 3.1 12.3 + - + -
234A ARG* 1.3 75.1 - - - +
236A LEU* 1.3 59.3 + - - +
238A MET* 3.1 7.4 + - - +
239A TRP* 2.9 67.0 + - + +
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Residues in contact with LEU 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 TYR* 2.9 51.6 + - + +
233A ALA 3.7 3.6 - - - +
235A THR* 1.3 77.7 - - - +
237A ASP* 1.3 62.1 + - - +
239A TRP* 3.3 30.7 + - + +
240A ALA* 3.0 24.5 + - - +
265A TYR* 4.7 4.9 - - + +
266A LEU* 3.7 34.3 - - + +
269A CYS* 3.4 35.7 - - + +
270A ALA* 3.5 12.8 - - + +
273A PHE* 4.1 1.3 - - + -
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Residues in contact with ASP 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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233A ALA 3.0 14.9 + - - +
234A ARG* 3.6 10.5 - - + +
235A THR 3.2 0.2 - - - -
236A LEU* 1.3 74.7 - - - +
238A MET* 1.3 60.2 + - + +
240A ALA* 3.2 8.2 + - - +
241A THR* 2.9 33.8 + - - +
267A THR* 5.7 1.1 - - - +
270A ALA* 3.4 18.0 - - - +
274A ARG* 2.7 38.6 + - - -
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Residues in contact with MET 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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26A PHE 5.0 0.2 - - - +
38A PHE* 3.6 35.0 - - + -
43A MET 4.9 1.8 - - - +
44A THR* 4.5 5.2 - - - -
45A LEU* 3.7 44.0 - - + +
234A ARG* 3.0 29.6 + - + +
235A THR* 3.6 4.3 - - - +
237A ASP* 1.3 75.9 - - + +
239A TRP* 1.3 65.4 + - - +
241A THR* 3.4 6.9 + - - -
242A ALA* 3.1 23.7 + - - +
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Residues in contact with TRP 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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26A PHE* 3.3 49.0 + + + +
27A LEU* 3.7 13.5 - - + +
28A ASP 4.8 0.4 - - - +
32A THR 3.9 12.0 + - - -
33A TYR* 3.8 22.4 - + - -
34A SER* 3.5 38.1 - - - -
45A LEU* 3.7 21.4 - - + +
49A GLN* 3.9 2.5 - - - +
232A TYR* 4.1 9.9 - + - -
235A THR* 2.9 37.4 + - + +
236A LEU* 3.3 35.4 + - + +
238A MET* 1.3 76.2 - - - +
240A ALA* 1.3 57.8 + - - +
243A LEU* 3.0 26.5 + - - +
265A TYR* 4.7 2.0 - - - -
266A LEU* 3.8 17.3 - - + -
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Residues in contact with ALA 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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236A LEU 3.0 14.1 + - - +
237A ASP* 3.2 11.0 + - - +
239A TRP* 1.3 74.2 - - - +
241A THR* 1.3 60.0 + - - +
243A LEU* 3.2 2.6 + - - +
244A GLU* 2.8 32.2 + - - +
263A MET* 3.7 19.1 - - + +
266A LEU* 3.7 24.6 - - + +
267A THR* 4.2 11.2 - - - +
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Residues in contact with THR 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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237A ASP* 2.9 17.9 + - - +
238A MET* 3.8 7.1 - - - -
239A TRP 3.4 0.2 - - - -
240A ALA* 1.3 75.2 - - - +
242A ALA* 1.3 62.6 + - - +
244A GLU* 3.6 10.1 + - - +
245A ALA* 3.1 24.0 + - + +
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Residues in contact with ALA 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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25A LEU 3.8 4.5 - - - +
26A PHE* 3.8 23.3 - - - +
45A LEU* 6.3 0.2 - - + -
238A MET 3.1 17.5 + - - +
239A TRP 3.7 3.8 - - - +
240A ALA 3.2 0.2 - - - -
241A THR* 1.3 76.2 - - - +
243A LEU* 1.3 66.3 + - - +
245A ALA* 3.3 4.9 + - - +
246A ASN* 2.8 31.0 + - - +
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Residues in contact with LEU 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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22A PHE* 4.3 10.8 - - + -
25A LEU* 4.2 9.6 - - + -
26A PHE* 3.8 24.8 - - + +
239A TRP 3.0 18.5 + - - +
240A ALA* 3.6 3.8 - - - +
242A ALA* 1.3 74.5 - - - +
244A GLU* 1.3 64.5 + - - +
246A ASN* 3.0 14.2 + - - -
247A LYS 3.1 10.0 + - - -
250A ALA* 4.1 15.5 - - + -
259A TYR* 3.7 26.0 - - + -
262A TYR* 3.7 29.6 - - + -
263A MET* 3.7 20.6 - - + +
266A LEU* 4.0 10.3 - - + -
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Residues in contact with GLU 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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240A ALA 2.8 16.5 + - - +
241A THR* 3.7 9.5 - - - +
243A LEU* 1.3 77.1 - - - +
245A ALA* 1.3 63.1 + - - +
247A LYS* 3.0 21.7 + - + +
259A TYR* 3.3 20.0 - - - +
263A MET* 4.1 15.6 - - + +
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Residues in contact with ALA 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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241A THR* 3.1 16.0 + - + +
242A ALA* 3.3 7.8 + - - +
244A GLU* 1.3 80.7 - - - +
246A ASN* 1.3 64.3 + - - +
247A LYS 3.4 1.7 + - - -
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Residues in contact with ASN 246 (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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25A LEU* 3.5 42.2 - - + +
242A ALA* 2.8 23.8 + - - +
243A LEU 3.0 9.5 + - - +
245A ALA* 1.3 83.8 + - - +
247A LYS* 1.3 63.8 + - - +
248A ASP 3.5 2.0 - - - -
249A GLN* 3.4 10.3 + - + +
250A ALA* 3.0 20.8 + - - +
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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