Contacts of the helix formed by residues 229 - 245 (chain A) in PDB entry 5E9W
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 ALA 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ASP* 2.8 12.9 + - - +
228A ILE* 1.3 79.2 - - + +
230A ASP* 1.3 65.6 + - - +
231A VAL* 3.3 3.1 - - + +
232A SER* 3.1 20.8 + - - +
233A VAL* 3.1 22.3 + - - +
500A SAH 3.9 8.3 - - - +
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Residues in contact with ASP 230 (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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228A ILE 3.6 4.9 + - - -
229A ALA* 1.3 69.8 - - - +
231A VAL* 1.3 64.1 + - + +
233A VAL* 3.1 3.0 + - - +
234A LYS* 2.8 67.3 + - - +
259A THR* 2.4 41.9 + - + +
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Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LYS* 5.9 1.1 - - - +
229A ALA* 3.3 3.0 - - + +
230A ASP* 1.3 81.6 - - + +
232A SER* 1.3 58.3 + - - +
234A LYS* 3.7 7.2 - - + +
235A GLN* 2.8 56.5 + - + +
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Residues in contact with SER 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLY* 3.2 35.4 - - - +
208A LYS* 3.6 21.4 + - - +
227A ASP* 4.6 4.0 - - - -
229A ALA* 3.1 24.5 + - - +
230A ASP 3.1 0.2 - - - -
231A VAL* 1.3 77.6 - - - +
233A VAL* 1.3 55.4 + - - +
235A GLN* 3.2 8.7 + - - +
236A CYS 2.7 30.7 + - - -
500A SAH 4.8 2.9 + - - -
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Residues in contact with VAL 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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206A CYS* 4.9 2.9 - - - -
207A GLY 4.6 1.6 - - - -
225A CYS 4.6 2.7 - - - +
226A THR 4.7 0.4 - - - -
227A ASP* 3.7 37.2 - - + +
229A ALA 3.1 14.6 + - - +
230A ASP* 3.5 7.2 - - - +
232A SER* 1.3 75.5 - - - +
234A LYS* 1.3 60.2 + - + +
236A CYS* 3.1 8.7 + - - +
237A GLN* 2.8 27.8 + - - +
257A PHE* 3.8 29.3 - - + +
258A ILE 3.8 14.1 - - - +
259A THR* 3.9 20.0 - - - +
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Residues in contact with LYS 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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230A ASP* 2.8 49.9 + - - +
231A VAL* 3.7 7.6 - - + +
233A VAL* 1.3 74.8 - - + +
235A GLN* 1.3 59.0 + - + +
237A GLN* 3.2 18.7 + - - +
238A GLN* 3.0 27.0 + - - +
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Residues in contact with GLN 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LYS* 3.5 43.9 + - + +
231A VAL* 2.8 36.8 + - + +
232A SER* 3.7 3.6 - - - +
234A LYS* 1.3 73.5 - - + +
236A CYS* 1.3 66.5 + - - +
238A GLN* 3.2 7.1 + - - +
239A ARG* 3.0 25.1 + - - +
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Residues in contact with CYS 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A CYS* 4.1 5.8 - - - -
207A GLY 3.5 11.9 - - - +
208A LYS 3.5 12.7 + - - -
209A GLY* 3.7 20.9 - - - -
212A LEU* 3.4 10.9 - - - +
225A CYS* 3.7 34.1 - - - -
232A SER 2.7 22.0 + - - +
233A VAL* 3.3 8.5 - - - +
235A GLN* 1.3 73.2 - - - +
237A GLN* 1.3 56.3 + - - +
239A ARG 3.5 0.2 + - - -
240A TYR* 3.0 24.4 + - - +
257A PHE* 3.7 7.0 - - + -
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Residues in contact with GLN 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 VAL* 2.8 16.5 + - - +
234A LYS* 3.4 23.3 + - - +
236A CYS* 1.3 74.0 - - - +
238A GLN* 1.3 57.5 + - - +
240A TYR* 3.0 5.2 + - - +
241A GLU* 2.8 41.9 + - + +
257A PHE* 3.5 44.9 - - + +
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Residues in contact with GLN 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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234A LYS 3.0 15.5 + - - +
235A GLN* 3.2 7.6 + - - +
237A GLN* 1.3 75.6 - - - +
239A ARG* 1.3 59.3 + - - +
241A GLU* 3.1 14.2 + - - +
242A ASP* 2.3 73.7 + - - +
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Residues in contact with ARG 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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208A LYS 4.5 8.7 - - - +
209A GLY 5.6 0.4 - - - +
212A LEU* 4.0 13.7 - - + -
235A GLN 3.0 16.3 + - - +
236A CYS 3.9 3.6 - - - +
238A GLN* 1.3 76.0 - - - +
240A TYR* 1.3 62.4 + - - +
242A ASP* 3.5 10.8 + - - +
243A MET* 3.0 24.9 + - + +
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Residues in contact with TYR 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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212A LEU* 3.7 13.2 - - + +
236A CYS 3.0 15.1 + - - +
237A GLN 3.0 7.6 + - - +
239A ARG* 1.3 77.2 - - - +
241A GLU* 1.3 87.1 + - - +
243A MET* 3.0 19.1 + - + +
244A LYS* 3.5 7.2 + - + +
252A ILE* 3.6 25.2 - - + +
253A PHE* 2.8 51.5 + + - -
254A SER* 3.7 2.8 - - - -
255A ALA* 3.7 22.4 + - + -
257A PHE* 3.6 26.9 - + + -
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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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237A GLN* 2.8 30.3 + - + +
238A GLN* 3.4 21.3 - - - +
240A TYR* 1.3 99.2 - - - +
242A ASP* 1.3 56.8 + - - +
243A MET 3.3 0.2 + - - -
244A LYS* 3.6 1.6 + - - +
245A ASN* 2.9 51.9 + - - +
257A PHE* 5.4 0.3 - - - -
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Residues in contact with ASP 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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238A GLN* 2.3 54.1 + - - +
239A ARG* 3.7 9.2 - - - +
241A GLU* 1.3 72.6 - - - +
243A MET* 1.3 63.1 + - - +
245A ASN* 3.6 12.7 + - - -
246A ARG* 3.6 18.7 + - - +
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Residues in contact with MET 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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212A LEU* 3.5 36.1 - - + +
213A LEU* 3.5 28.0 - - + +
216A LYS* 3.6 43.8 - - + -
239A ARG* 3.0 13.0 + - + +
240A TYR* 3.0 14.0 + - - +
242A ASP* 1.3 76.1 - - - +
244A LYS* 1.3 58.7 + - - +
246A ARG* 3.5 22.5 - - - +
249A SER* 4.3 5.0 - - - -
252A ILE* 3.9 11.9 - - + -
253A PHE* 4.6 4.0 - - - -
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Residues in contact with LYS 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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216A LYS* 5.9 0.2 - - - -
240A TYR* 3.5 8.4 + - + +
241A GLU* 3.9 1.1 - - - +
242A ASP 3.4 0.2 - - - -
243A MET* 1.3 77.9 - - - +
245A ASN* 1.3 64.3 + - - +
246A ARG 3.2 6.5 + - - +
249A SER* 3.8 17.9 + - - +
252A ILE* 3.4 42.8 - - + -
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Residues in contact with ASN 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* 2.9 43.5 + - - +
242A ASP* 3.6 9.0 + - - +
243A MET 3.5 0.4 - - - -
244A LYS* 1.3 80.5 - - - +
246A ARG* 1.3 64.8 + - - +
247A ARG* 5.1 3.1 - - - +
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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