Contacts of the helix formed by residues 231 - 244 (chain A) in PDB entry 1EJC
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 ASP 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ILE* 3.4 1.8 - - - +
19A SER* 2.9 21.1 + - - +
20A GLY 4.1 3.4 - - - +
21A ALA* 3.6 24.7 - - - +
22A LYS* 4.6 3.6 + - - +
230A PRO* 1.3 69.7 - - - +
232A ARG* 1.3 61.4 + - - +
233A ILE* 2.9 14.4 + - - +
234A GLU* 2.8 37.2 + - + +
235A THR* 2.8 26.2 + - - -
371A ARG* 5.0 6.7 + - - -
398A GLY 4.3 14.2 - - - +
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Residues in contact with ARG 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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21A ALA* 5.0 0.8 - - - +
188A GLU* 3.5 21.2 - - - +
189A PRO* 3.6 21.0 - - - +
190A GLU* 2.9 39.9 + - - +
229A LEU* 6.3 0.4 - - - -
230A PRO* 3.2 8.2 + - - +
231A ASP* 1.3 73.2 + - - +
233A ILE* 1.3 77.5 + - + +
235A THR* 3.5 7.0 - - - -
236A GLY* 3.0 21.3 + - - -
258A THR* 3.5 37.7 + - - +
259A LEU* 3.3 23.6 - - + +
299A HIS* 4.0 15.9 + - - +
303A PRO* 3.9 27.1 - - - +
305A ASP* 5.9 1.2 + - - -
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Residues in contact with ILE 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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23A ASN* 5.7 4.0 - - - +
190A GLU* 5.9 0.4 - - - +
231A ASP* 2.9 8.5 + - - +
232A ARG* 1.3 106.4 - - + +
234A GLU* 1.3 67.1 + - - +
237A THR* 2.8 11.2 + - - +
259A LEU* 5.8 0.9 - - + -
303A PRO* 4.3 7.4 - - + -
305A ASP* 3.4 35.7 - - + +
306A MET* 2.7 62.8 - - + +
309A GLN* 4.0 0.2 - - - +
371A ARG* 3.3 35.9 - - - +
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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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18A ILE* 3.5 9.7 - - - +
19A SER* 2.8 35.0 + - - +
231A ASP* 2.8 27.3 + - + +
233A ILE* 1.3 76.6 - - - +
235A THR* 1.3 63.8 + - - +
237A THR* 3.1 2.8 + - - -
238A PHE* 3.1 47.7 + - + -
371A ARG* 4.8 0.2 - - - +
399A TYR* 3.9 27.9 - - + +
400A GLU 4.2 10.9 + - - +
402A ILE* 6.0 0.3 - - - -
405A LYS* 2.6 34.1 + - - +
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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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18A ILE* 3.2 27.4 - - + +
230A PRO* 5.0 1.0 - - - +
231A ASP 2.8 19.6 + - - -
232A ARG* 3.5 9.8 - - - -
233A ILE 3.1 0.2 - - - -
234A GLU* 1.3 76.0 - - - +
236A GLY* 1.3 63.6 + - - +
238A PHE* 3.2 4.9 + - - +
239A LEU* 3.0 31.7 + - + +
251A CYS* 4.2 16.1 - - + -
254A ALA* 4.6 6.5 - - + +
255A GLN 5.6 0.3 + - - -
259A LEU* 3.5 24.3 - - + +
280A ILE* 3.9 17.5 - - + -
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Residues in contact with GLY 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 ARG 3.0 13.9 + - - -
233A ILE 3.3 0.2 + - - -
235A THR* 1.3 76.2 - - - +
237A THR* 1.3 56.3 + - - +
239A LEU* 3.3 13.4 + - - +
240A VAL* 2.9 34.7 + - - +
259A LEU* 4.6 1.5 - - - +
262A VAL* 4.6 11.8 - - - +
306A MET* 3.6 21.8 - - - -
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Residues in contact with THR 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 ILE 2.8 21.2 + - - -
234A GLU 3.1 9.2 + - - -
236A GLY* 1.3 77.7 - - - +
238A PHE* 1.3 62.0 + - + +
240A VAL* 3.4 7.6 + - - +
241A ALA* 3.0 24.0 + - - +
306A MET* 3.6 2.4 - - - +
309A GLN* 3.2 18.1 + - + -
374A ALA* 4.6 10.5 - - + -
378A LEU* 3.7 24.5 - - + +
399A TYR* 2.8 36.4 + - + +
402A ILE* 5.0 5.6 - - + -
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Residues in contact with PHE 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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16A VAL* 4.0 17.5 - - + -
18A ILE* 4.2 5.6 - - + -
234A GLU* 3.1 54.4 + - + -
235A THR 3.9 4.9 - - - +
237A THR* 1.3 78.8 - - + +
239A LEU* 1.3 67.0 + - - +
241A ALA* 3.2 7.0 + - + +
242A ALA* 3.2 16.8 + - - +
249A ILE* 3.8 23.4 - - + +
251A CYS* 4.4 2.7 - - - -
378A LEU* 5.9 0.2 - - + -
399A TYR* 5.1 1.8 - + - -
402A ILE* 4.0 20.0 - - + -
405A LYS* 3.6 36.1 - - + -
406A LEU* 3.8 26.5 - - + -
409A LEU* 3.6 21.5 - - + -
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Residues in contact with LEU 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 THR* 3.0 34.3 + - + +
236A GLY* 3.7 10.5 - - - +
238A PHE* 1.3 75.8 - - - +
240A VAL* 1.3 58.1 + - - +
242A ALA* 3.3 3.3 + - - +
243A ALA* 3.0 27.4 + - - +
249A ILE* 4.2 7.4 - - + -
251A CYS* 3.8 20.0 - - - -
259A LEU* 4.8 2.2 - - + -
262A VAL* 4.9 1.3 - - + -
263A LEU* 3.6 31.4 - - + -
266A LEU* 3.8 17.7 - - + -
280A ILE* 4.0 18.8 - - + +
282A LEU* 3.7 33.0 - - + +
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Residues in contact with VAL 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 GLY 2.9 21.7 + - - +
237A THR 3.6 4.5 - - - +
239A LEU* 1.3 74.8 - - - +
241A ALA* 1.3 64.8 + - - +
243A ALA* 3.0 7.2 + - - -
244A ILE* 2.9 41.0 + - + +
266A LEU* 4.4 7.4 - - + -
309A GLN* 3.7 33.0 - - + +
310A PHE* 3.8 36.8 - - + -
312A LEU* 5.3 0.7 - - + -
313A LEU* 4.8 4.0 - - + -
378A LEU* 4.3 11.9 - - + -
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Residues in contact with ALA 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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12A LEU* 3.7 21.7 - - + +
237A THR 3.0 14.6 + - - +
238A PHE* 3.2 22.2 + - + +
240A VAL* 1.3 76.7 - - - +
242A ALA* 1.3 59.3 + - - +
244A ILE* 3.5 15.4 - - - +
245A SER* 2.8 18.7 + - - -
249A ILE* 5.7 0.2 - - + -
378A LEU* 3.7 25.1 - - + -
406A LEU* 4.8 1.6 - - + -
409A LEU* 5.2 2.5 - - + -
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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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12A LEU 3.7 21.8 - - - +
238A PHE 3.2 3.0 + - - +
239A LEU 3.8 3.6 - - - +
240A VAL 3.2 0.4 - - - -
241A ALA* 1.3 77.5 - - - +
243A ALA* 1.3 65.8 + - - +
245A SER 3.1 10.7 + - - -
246A GLY 3.3 0.7 + - - -
247A GLY 3.1 31.9 + - - +
249A ILE* 3.5 36.1 - - + +
282A LEU* 4.0 4.5 - - + -
284A MET* 3.6 3.6 - - - +
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Residues in contact with ALA 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 LEU 3.0 17.4 + - - +
240A VAL* 3.0 10.3 + - - +
242A ALA* 1.3 77.8 - - - +
244A ILE* 1.3 60.3 + - - +
245A SER 3.7 0.2 + - - -
246A GLY 4.4 0.9 + - - -
266A LEU* 4.1 10.1 - - + -
269A ALA* 6.1 0.9 - - + -
271A ALA* 5.3 0.9 - - + -
282A LEU* 3.8 5.8 - - + +
284A MET* 3.5 42.3 - - + +
287A LYS 4.7 0.2 - - - +
289A PRO* 3.7 12.7 - - - +
313A LEU* 4.1 18.2 - - + -
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Residues in contact with ILE 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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12A LEU* 5.7 0.9 - - + -
240A VAL* 2.9 34.0 + - + +
241A ALA* 3.5 12.8 - - - +
243A ALA* 1.3 78.4 - - - +
245A SER* 1.3 57.1 + - - +
246A GLY 3.7 0.7 - - - -
289A PRO* 4.6 10.5 - - - +
312A LEU* 3.6 27.4 - - + -
313A LEU* 3.7 35.2 - - + +
316A VAL* 4.1 15.2 - - + +
378A LEU* 4.1 19.7 - - + +
382A ILE* 3.8 31.2 - - + +
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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