Contacts of the helix formed by residues 236 - 252 (chain A) in PDB entry 2CEA
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 GLY 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A PHE 3.3 1.0 + - - -
235A VAL* 1.3 73.8 - - - +
237A VAL* 1.3 64.6 + - - +
238A GLY 2.9 4.3 + - - -
239A ALA* 3.0 16.2 + - - +
240A ALA* 3.2 12.5 + - - +
243A ARG* 5.1 1.4 + - - -
279A GLU* 3.1 20.0 + - - -
282A GLN* 3.9 11.6 + - - -
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Residues in contact with VAL 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 LEU* 3.5 22.0 - - + -
234A PHE* 3.5 43.9 + - + +
235A VAL 3.2 1.5 + - - +
236A GLY* 1.3 76.4 - - - +
238A GLY* 1.3 62.9 + - - +
240A ALA* 3.3 7.9 + - - +
241A ARG* 3.1 43.9 + - + +
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Residues in contact with GLY 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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230A PHE* 4.1 5.2 - - - -
233A LEU* 3.5 24.5 - - - +
234A PHE 4.3 1.2 + - - -
236A GLY 2.9 2.0 + - - +
237A VAL* 1.3 75.6 - - - +
239A ALA* 1.3 66.3 + - - +
241A ARG* 3.1 5.5 + - - +
242A VAL* 3.1 22.0 + - - +
279A GLU* 4.7 1.8 + - - -
283A THR* 3.9 25.5 - - - +
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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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236A GLY* 3.0 9.6 + - - +
238A GLY* 1.3 73.1 - - - +
240A ALA* 1.3 60.0 + - - +
242A VAL* 2.9 6.7 + - - +
243A ARG* 2.9 34.7 + - - +
279A GLU* 4.7 1.4 + - - -
282A GLN* 4.5 21.5 - - + +
283A THR* 4.2 8.7 + - - +
286A GLN* 3.7 37.6 - - + +
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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 GLY 3.2 9.1 + - - +
237A VAL* 3.6 12.1 - - - +
239A ALA* 1.3 79.4 - - - +
241A ARG* 1.3 57.9 + - + +
243A ARG* 3.3 30.5 + - - +
244A ASP* 3.0 28.2 + - - +
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Residues in contact with ARG 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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150A TYR* 3.3 47.1 + - - +
229A ASP* 4.6 17.2 + - - +
230A PHE* 4.0 11.1 - - + -
233A LEU* 3.6 37.1 - - + +
237A VAL* 3.1 32.3 + - + +
238A GLY 3.1 6.9 + - - +
240A ALA* 1.3 73.2 - - + +
242A VAL* 1.3 60.7 + - - +
244A ASP* 3.4 3.3 + - - +
245A LEU* 2.9 24.8 + - - +
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Residues in contact with VAL 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PHE* 3.6 27.4 - - + -
238A GLY 3.1 6.4 + - - +
239A ALA 2.9 7.9 + - - +
241A ARG* 1.3 75.7 - - - +
243A ARG* 1.3 67.7 + - - +
245A LEU* 3.2 9.8 + - + +
246A PHE* 3.2 32.1 + - + -
265A VAL* 6.3 0.2 - - + -
283A THR* 4.4 15.3 - - + +
286A GLN* 3.9 11.9 - - + -
287A LEU* 3.9 20.2 - - + +
290A GLU* 3.8 22.2 - - + -
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Residues in contact with ARG 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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236A GLY 5.1 1.2 + - - -
239A ALA* 2.9 13.9 + - - +
240A ALA* 3.3 45.2 + - - +
242A VAL* 1.3 76.9 - - - +
244A ASP* 1.3 63.6 + - - +
246A PHE* 3.1 4.5 + - - +
247A ALA* 3.0 22.3 + - - +
286A GLN* 3.3 37.5 + - - +
290A GLU* 3.4 14.1 - - - +
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Residues in contact with ASP 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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150A TYR* 3.6 26.1 + - + +
240A ALA 3.0 17.5 + - - +
241A ARG* 3.8 6.1 - - - +
242A VAL 3.3 0.4 - - - -
243A ARG* 1.3 75.8 - - - +
245A LEU* 1.3 62.1 + - - +
247A ALA* 3.2 8.1 + - - +
248A GLN* 3.0 45.7 + - - +
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Residues in contact with LEU 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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150A TYR* 3.9 22.8 - - + -
223A PHE* 4.2 17.0 - - + -
225A ILE* 3.7 39.9 - - + -
230A PHE* 5.4 5.2 - - + -
241A ARG 2.9 15.5 + - - +
242A VAL* 3.2 14.6 + - + +
244A ASP* 1.3 77.0 - - - +
246A PHE* 1.3 73.6 + - + +
248A GLN* 3.4 3.1 + - - +
249A ALA* 3.0 22.5 + - - +
257A VAL* 3.9 28.0 - - + -
259A ILE* 5.2 7.6 - - + -
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Residues in contact with PHE 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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242A VAL* 3.2 34.7 + - + +
243A ARG 3.1 5.3 + - - +
245A LEU* 1.3 96.9 - - + +
247A ALA* 1.3 66.9 + - - +
249A ALA* 3.1 11.4 + - + +
250A LYS* 3.0 36.4 + - + +
257A VAL* 5.1 4.7 - - + -
259A ILE* 5.4 1.6 - - + -
287A LEU* 4.1 22.0 - - + -
290A GLU* 3.7 45.5 - - + +
291A MET* 4.4 2.9 - - - -
294A PHE* 4.3 20.4 - + + -
300A ILE* 5.6 2.2 - - + -
302A VAL* 3.9 32.3 - - + -
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Residues in contact with ALA 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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243A ARG 3.0 12.6 + - - +
244A ASP* 3.4 17.3 - - - +
246A PHE* 1.3 77.9 - - - +
248A GLN* 1.3 66.4 + - - +
250A LYS* 3.2 10.7 + - - +
251A ALA* 3.2 19.6 + - - +
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Residues in contact with GLN 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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150A TYR* 3.4 27.6 - - + +
151A LYS* 6.0 0.7 - - - +
223A PHE* 4.2 14.8 - - + -
244A ASP* 3.0 42.0 + - - +
245A LEU* 3.5 7.9 - - - +
247A ALA* 1.3 79.2 - - - +
249A ALA* 1.3 65.3 + - - +
251A ALA* 3.0 15.4 + - - +
252A HIS* 3.1 36.6 + - - +
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Residues in contact with ALA 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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223A PHE* 4.0 13.4 - - + -
245A LEU 3.0 14.0 + - - +
246A PHE* 3.1 16.8 + - + +
248A GLN* 1.3 77.9 - - - +
250A LYS* 1.3 58.7 + - + +
252A HIS 3.5 0.2 + - - -
253A ALA* 3.1 24.3 + - - +
255A CYS* 3.5 13.5 - - - -
257A VAL* 3.6 28.9 - - + -
300A ILE* 4.1 12.0 - - + +
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Residues in contact with LYS 250 (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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246A PHE* 3.0 26.1 + - + +
247A ALA* 3.6 9.6 - - - +
248A GLN 3.0 0.2 - - - -
249A ALA* 1.3 76.0 - - + +
251A ALA* 1.3 64.8 - - - +
252A HIS 3.1 2.5 + - - -
253A ALA* 3.5 11.7 + - - +
290A GLU* 4.8 9.6 + - - -
293A GLY* 4.6 11.1 + - - -
294A PHE* 3.9 25.2 - - - +
295A ASP 5.7 0.2 - - - +
298A GLU* 5.1 7.3 - - + +
300A ILE* 4.0 20.6 - - + -
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Residues in contact with ALA 251 (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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247A ALA 3.2 11.3 + - - +
248A GLN* 3.0 10.2 + - - +
250A LYS* 1.3 77.0 - - - +
252A HIS* 1.3 79.9 + - + +
253A ALA 3.9 1.6 + - - +
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Residues in contact with HIS 252 (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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152A PRO* 3.5 38.8 - - + +
221A PRO* 3.8 17.8 - - + +
223A PHE* 3.9 18.6 - + + -
248A GLN* 3.1 31.6 + - - +
249A ALA 3.7 1.8 - - - -
250A LYS 3.1 0.4 - - - -
251A ALA* 1.3 93.2 - - + +
253A ALA* 1.3 64.3 + - - +
254A PRO 3.1 12.4 - - - +
255A CYS* 3.8 1.4 - - - +
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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