Contacts of the helix formed by residues 238 - 250 (chain A) in PDB entry 5E8W
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 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A PHE* 3.9 37.7 - - + +
217A GLY* 3.8 11.5 + - - -
234A PHE* 3.4 19.9 - - + +
235A SER* 2.9 41.5 + - - +
237A ARG* 1.4 84.0 + - + +
239A GLU* 1.3 63.3 + - - +
240A ARG* 3.3 3.1 - - - -
241A SER* 3.2 9.3 + - - +
242A TRP* 3.1 21.1 + - - +
276A LEU* 4.5 0.9 - - - -
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Residues in contact with GLU 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 SER 3.8 0.6 + - - -
236A SER* 3.2 17.1 + - - +
237A ARG 3.4 2.4 + - - -
238A GLU* 1.3 75.9 - - - +
240A ARG* 1.3 59.3 + - + +
242A TRP* 3.3 14.5 + - + +
243A PHE* 2.8 35.7 + - + +
276A LEU* 3.6 26.1 - - + +
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Residues in contact with ARG 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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237A ARG 4.7 13.3 + - - -
238A GLU 3.3 1.0 - - - -
239A GLU* 1.3 79.4 - - + +
241A SER* 1.4 57.3 - - - +
243A PHE* 4.0 5.1 - - - +
244A ARG* 3.0 30.5 + - - +
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Residues in contact with SER 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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216A PHE* 3.3 34.6 - - - -
234A PHE* 4.0 16.3 - - - -
238A GLU* 3.2 11.7 + - - +
240A ARG* 1.4 73.4 - - - +
242A TRP* 1.3 66.6 + - - +
244A ARG* 3.4 5.8 + - - +
245A GLU* 3.1 24.9 + - - +
353A GLY* 5.6 1.0 - - - +
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Residues in contact with TRP 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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234A PHE* 3.6 38.9 - + + -
238A GLU 3.1 9.8 + - - +
239A GLU* 3.7 22.0 - - + +
241A SER* 1.3 75.0 - - - +
243A PHE* 1.3 88.5 + + + +
245A GLU* 3.4 3.5 + - - +
246A ALA* 2.9 29.4 + - + +
265A ALA* 4.1 19.1 - - + -
266A ASP* 3.8 7.9 - - - -
267A ASN* 3.8 24.0 - - - -
276A LEU* 3.6 30.1 - - + -
277A TRP 3.0 24.1 + - - +
278A LEU* 3.6 23.9 - - + +
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Residues in contact with PHE 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 GLU* 2.8 24.3 + - + +
240A ARG* 4.0 5.4 - - - +
242A TRP* 1.3 96.4 - + + +
244A ARG* 1.3 61.1 + - - +
246A ALA* 3.2 9.0 + - + +
247A GLU* 2.8 57.2 + - + +
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Residues in contact with ARG 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 ARG 3.0 20.2 + - - +
241A SER* 3.8 6.1 - - - +
242A TRP 3.4 0.2 - - - -
243A PHE* 1.3 77.9 - - + +
245A GLU* 1.3 56.7 + - - +
247A GLU* 2.9 33.6 + - - +
248A ILE* 2.9 49.5 + - + +
353A GLY 3.6 19.7 - - - +
355A ALA 2.9 28.3 + - - -
356A VAL* 3.9 0.4 - - - +
366A ASP* 2.8 43.9 + - - -
367A ILE* 3.7 35.4 - - + +
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Residues in contact with GLU 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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215A ARG* 4.7 1.4 + - - -
232A LYS* 2.8 37.0 + - - +
234A PHE* 3.4 12.1 - - - -
241A SER 3.1 15.1 + - - +
244A ARG* 1.3 77.5 - - - +
246A ALA* 1.4 56.2 + - - +
248A ILE* 3.3 3.9 + - - +
249A TYR* 2.9 59.8 + - + -
278A LEU* 3.5 24.8 - - + +
351A ASP* 4.8 0.7 - - - -
352A LEU 4.5 0.7 + - - -
353A GLY* 3.8 31.1 - - - +
601A STU 3.9 10.2 - - - -
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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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242A TRP* 2.9 20.7 + - + +
243A PHE* 3.5 13.5 - - + +
245A GLU* 1.4 74.4 - - - +
247A GLU* 1.3 57.0 + - - +
249A TYR* 3.4 4.5 + - - +
250A GLN* 3.0 44.4 + - - +
262A PHE* 4.9 1.3 - - - -
265A ALA* 3.8 17.9 - - + -
278A LEU* 3.8 21.7 - - + +
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Residues in contact with GLU 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 PHE* 2.8 42.5 + - + +
244A ARG* 2.9 39.9 + - - +
246A ALA* 1.3 72.9 - - - +
248A ILE* 1.4 67.4 + - - +
250A GLN* 3.3 13.5 + - - +
251A THR* 3.4 10.2 + - - -
357A ARG* 3.5 28.7 + - - +
366A ASP* 5.0 0.2 - - - -
367A ILE* 5.5 0.2 - - - +
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Residues in contact with ILE 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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244A ARG* 2.9 59.7 + - + +
245A GLU* 3.8 4.3 - - - +
247A GLU* 1.4 74.4 - - - +
249A TYR* 1.4 63.9 + - - +
251A THR* 2.6 25.8 + - - +
254A LEU* 3.4 6.2 - - + +
329A ILE* 4.9 9.0 - - + -
352A LEU* 3.6 50.3 - - + +
355A ALA* 4.1 14.6 - - + +
357A ARG* 3.7 26.9 - - + +
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Residues in contact with TYR 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 GLU* 2.9 50.7 + - + +
246A ALA 3.9 2.2 - - - +
248A ILE* 1.4 76.7 - - - +
250A GLN* 1.3 59.0 + - - +
251A THR 3.3 2.9 + - - +
254A LEU* 3.7 16.2 - - + +
259A ILE* 4.9 0.4 - - + -
260A LEU* 3.5 50.6 - - + +
262A PHE* 3.5 54.9 - + + +
278A LEU* 5.4 3.1 - - + -
280A SER* 6.0 0.7 - - - -
350A ALA 3.9 0.3 - - - -
351A ASP 3.6 13.0 + - - -
352A LEU* 3.4 46.2 - - + +
601A STU 4.8 1.0 - + - -
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Residues in contact with GLN 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 ALA* 3.0 35.5 + - - +
247A GLU* 3.3 7.2 + - - +
248A ILE 3.2 0.8 - - - -
249A TYR* 1.3 74.8 - - - +
251A THR* 1.4 66.6 + - - +
252A VAL* 3.3 5.2 + - - +
262A PHE* 3.5 34.9 - - + -
265A ALA* 3.9 8.9 - - - +
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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