Contacts of the helix formed by residues 231 - 249 (chain A) in PDB entry 2I5B
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 GLU 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LEU* 4.4 0.2 - - - -
229A GLY 3.8 2.1 + - - +
230A ALA* 1.3 77.4 - - - +
232A VAL* 1.3 60.2 + - - +
233A LYS* 4.5 2.5 - - + +
234A GLU* 3.2 26.3 + - + +
235A ALA* 2.8 27.9 + - - +
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Residues in contact with VAL 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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103A ASN* 5.1 2.7 - - - +
136A THR* 4.0 14.4 - - + -
137A VAL* 3.6 22.9 - - + -
174A TYR* 3.5 55.4 - - + +
226A LEU* 3.9 19.1 - - + -
230A ALA 3.9 0.4 + - - +
231A GLU* 1.3 71.7 - - - +
233A LYS* 1.3 64.6 + - - +
235A ALA* 3.1 5.4 + - - +
236A ILE* 2.9 28.9 + - + +
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Residues in contact with LYS 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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174A TYR* 4.3 19.3 - - + -
192A LEU* 4.0 26.0 - - + -
194A ASP* 2.7 32.1 + - - -
197A THR* 5.2 4.0 + - - -
199A GLU* 4.5 8.7 + - - -
231A GLU* 3.4 2.5 - - + +
232A VAL* 1.3 77.5 - - - +
234A GLU* 1.3 63.7 + - - +
236A ILE* 3.1 10.4 + - - +
237A TYR* 2.9 48.3 + - + +
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Residues in contact with GLU 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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225A GLU* 5.2 3.4 - - + +
230A ALA* 3.7 20.6 - - + +
231A GLU* 3.2 39.6 + - + +
233A LYS* 1.3 79.5 - - - +
235A ALA* 1.3 61.5 + - - +
237A TYR* 3.3 13.5 + - - +
238A ALA* 3.0 22.6 + - + +
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Residues in contact with ALA 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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222A VAL* 4.1 9.6 - - + +
225A GLU* 3.6 33.7 - - + +
226A LEU* 4.0 21.5 - - + +
230A ALA* 4.2 2.4 - - + +
231A GLU 2.8 16.4 + - - +
232A VAL 3.1 8.9 + - - +
234A GLU* 1.3 71.9 - - - +
236A ILE* 1.3 65.1 + - - +
238A ALA* 3.1 3.5 + - - +
239A ALA* 2.8 24.8 + - - +
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Residues in contact with ILE 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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137A VAL* 4.1 9.9 - - + -
174A TYR* 4.8 0.7 - - + -
176A VAL* 3.7 28.3 - - + -
192A LEU* 3.7 33.0 - - + -
201A LEU* 3.8 22.7 - - + -
218A PHE* 4.1 9.0 - - + -
222A VAL* 4.3 23.8 - - + -
232A VAL* 2.9 35.9 + - + +
233A LYS* 3.6 6.3 - - - +
235A ALA* 1.3 75.8 - - - +
237A TYR* 1.3 57.6 + - + +
239A ALA* 3.2 2.6 + - - +
240A LYS* 2.8 27.4 + - - +
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Residues in contact with TYR 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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192A LEU* 4.0 8.0 - - + +
199A GLU* 2.7 41.1 + - - -
201A LEU* 3.5 24.0 - - + -
233A LYS* 2.9 47.7 + - + +
234A GLU* 3.7 10.1 - - - +
236A ILE* 1.3 76.6 - - - +
238A ALA* 1.3 63.7 + - - +
240A LYS* 3.1 9.6 + - + +
241A GLU* 3.0 21.7 + - - +
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Residues in contact with ALA 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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30A LYS* 4.7 7.7 + - - +
225A GLU* 3.8 30.3 - - + +
234A GLU 3.0 13.8 + - - +
235A ALA 3.1 7.6 + - - +
237A TYR* 1.3 75.5 - - - +
239A ALA* 1.3 56.0 + - - +
241A GLU* 3.2 15.1 + - - +
242A PHE* 3.0 26.2 + - - +
265A LEU* 5.2 1.4 - - - +
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Residues in contact with ALA 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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30A LYS* 5.4 0.7 - - - +
218A PHE* 3.7 9.2 - - + +
221A ALA* 3.6 28.2 + - + +
222A VAL* 3.5 28.0 - - + +
235A ALA 2.8 17.0 + - - +
236A ILE 3.5 4.7 - - - +
238A ALA* 1.3 72.5 - - - +
240A LYS* 1.3 66.8 + - - +
242A PHE* 3.2 10.7 + - - +
243A ILE* 3.2 19.9 + - - +
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Residues in contact with LYS 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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188A ALA* 2.9 27.1 + - - +
190A ASP* 2.9 31.0 + - - +
201A LEU* 4.3 24.0 - - + -
202A GLU 4.1 5.6 - - - +
203A SER* 3.3 33.7 - - - +
218A PHE* 3.7 6.0 - - + -
236A ILE 2.8 13.8 + - - +
237A TYR* 3.1 13.9 + - + +
239A ALA* 1.3 76.6 - - - +
241A GLU* 1.3 56.3 + - - +
243A ILE* 3.3 14.4 - - + +
244A THR* 2.6 29.4 + - - -
301A ADP 3.1 20.8 + - - +
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Residues in contact with GLU 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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203A SER* 5.6 0.9 - - - -
237A TYR 3.0 12.9 + - - +
238A ALA* 3.3 15.2 - - - +
240A LYS* 1.3 76.9 - - - +
242A PHE* 1.3 60.4 + - - +
244A THR* 3.6 5.2 - - - -
245A ALA* 3.2 23.7 + - - +
265A LEU* 3.9 15.5 - - + +
269A GLN* 2.6 33.6 + - - +
270A GLN 5.2 1.7 - - - +
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Residues in contact with PHE 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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26A THR* 3.8 16.2 - - + -
29A GLU* 4.0 23.8 - - + -
30A LYS* 3.6 28.0 - - + -
217A THR* 3.7 28.9 - - + -
221A ALA* 4.1 10.3 - - + -
238A ALA 3.0 12.9 + - - +
239A ALA* 3.2 12.5 + - - +
241A GLU* 1.3 74.0 - - - +
243A ILE* 1.3 62.0 + - + +
245A ALA* 3.3 5.5 + - - +
246A ALA* 2.9 27.3 + - + +
262A HIS* 3.3 36.6 - + + -
265A LEU* 3.8 29.9 + - + +
266A ARG 6.0 0.2 - - - -
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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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214A ALA* 3.7 31.0 - - + +
217A THR* 3.8 21.8 - - + -
218A PHE* 3.7 20.0 - - + +
239A ALA 3.3 12.6 - - - +
240A LYS* 3.3 30.3 - - + +
242A PHE* 1.3 75.3 - - + +
244A THR* 1.3 65.0 + - - +
246A ALA* 4.0 6.7 - - + -
247A ILE* 2.7 50.1 + - + +
260A THR* 4.8 1.6 - - + -
301A ADP 3.4 30.5 - - - +
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Residues in contact with THR 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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203A SER* 3.1 35.1 + - - +
204A GLU* 4.5 8.3 - - + +
206A ILE* 4.0 18.6 - - + +
240A LYS* 2.6 26.6 + - - -
241A GLU* 3.6 7.0 - - - -
242A PHE 3.3 0.8 - - - -
243A ILE* 1.3 80.7 - - - +
245A ALA* 1.3 58.1 + - - +
247A ILE* 3.8 5.8 - - - +
248A LYS* 2.9 33.6 + - + +
269A GLN* 6.2 0.2 - - - +
301A ADP 5.2 4.9 + - + -
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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 GLU 3.2 11.3 + - - +
242A PHE 3.6 8.3 - - - +
243A ILE 3.2 0.4 - - - -
244A THR* 1.3 79.9 - - - +
246A ALA* 1.3 60.1 + - - +
248A LYS* 3.3 12.8 + - - +
249A GLU* 3.2 20.3 + - - +
264A ALA* 3.3 11.6 - - + +
265A LEU* 3.9 28.5 - - + +
268A ASN* 5.9 0.9 - - + +
269A GLN* 4.0 20.8 + - + +
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Residues in contact with ALA 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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217A THR* 5.1 0.2 - - + -
242A PHE* 2.9 24.2 + - + +
243A ILE* 3.1 10.3 + - + +
245A ALA* 1.3 75.5 - - - +
247A ILE* 1.3 61.3 + - - +
249A GLU 3.7 0.7 + - - -
250A SER 3.4 8.0 + - - -
260A THR* 3.4 19.4 - - - +
261A LYS* 2.8 50.8 + - - +
262A HIS* 4.3 5.8 - - - +
264A ALA* 3.8 0.9 - - + +
265A LEU 6.0 0.2 - - - +
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Residues in contact with ILE 247 (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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206A ILE* 3.9 18.6 - - + +
208A THR* 3.7 23.1 - - + -
210A TYR 4.8 0.2 - - - +
211A THR* 4.0 12.6 - - + -
214A ALA* 4.2 4.7 - - + -
243A ILE* 2.7 32.2 + - + +
244A THR* 3.9 3.1 - - - +
246A ALA* 1.3 70.1 - - - +
248A LYS* 1.3 65.6 + - - +
249A GLU 3.1 1.8 - - - -
250A SER* 3.0 26.9 + - - +
260A THR* 3.9 19.1 - - + -
301A ADP 3.3 57.4 - - + +
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Residues in contact with LYS 248 (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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204A GLU* 2.7 33.1 + - - +
206A ILE* 3.7 26.3 - - + +
244A THR* 2.9 22.1 + - + +
245A ALA* 3.3 12.5 + - - +
247A ILE* 1.3 76.9 - - - +
249A GLU* 1.3 73.4 + - + +
250A SER 3.7 1.6 + - - +
268A ASN 5.9 3.4 - - - +
269A GLN* 6.1 0.9 - - - +
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Residues in contact with GLU 249 (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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245A ALA 3.2 15.9 + - - +
246A ALA 3.7 3.3 + - - -
247A ILE 3.1 0.8 - - - -
248A LYS* 1.3 93.3 - - + +
250A SER* 1.3 65.4 + - - +
251A PHE* 3.7 7.1 - - - +
261A LYS* 3.4 32.8 + - + +
264A ALA* 3.7 5.4 - - + -
268A ASN* 2.9 49.1 + - + +
2B SER* 4.7 4.5 + - - -
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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