Contacts of the helix formed by residues 233 - 249 (chain A) in PDB entry 5J3S
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 HIS 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A MET* 5.2 4.0 - - + -
228A GLU* 4.4 6.6 - - + +
230A THR* 3.3 34.0 - - + +
231A ARG 3.3 0.4 - - - -
232A GLY* 1.3 71.1 - - - +
234A ALA* 1.3 62.9 + - - +
235A ALA 3.5 2.0 - - - +
236A GLU* 3.8 16.1 - - + +
237A ARG* 3.1 21.1 + - - +
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Residues in contact with ALA 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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231A ARG 3.7 12.1 + - - +
232A GLY 2.8 11.7 + - - +
233A HIS* 1.3 71.3 - - - +
235A ALA* 1.3 55.0 + - - +
237A ARG* 3.0 14.4 + - - +
238A MET* 2.7 43.2 + - - +
269A GLU* 3.7 25.1 - - + +
272A ARG* 5.1 5.8 - - - +
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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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232A GLY 4.8 0.4 + - - -
233A HIS* 4.6 0.2 - - - +
234A ALA* 1.3 77.8 - - - +
236A GLU* 1.3 57.9 + - - +
238A MET* 3.1 13.2 + - + +
239A ASN* 2.7 32.4 + - - +
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Residues in contact with GLU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A SER* 4.7 12.3 - - - +
228A GLU* 4.9 2.7 - - + -
233A HIS* 3.6 22.2 + - + +
234A ALA 3.2 0.2 - - - -
235A ALA* 1.3 78.7 - - - +
237A ARG* 1.3 61.7 + - - +
239A ASN* 3.8 6.2 + - - +
240A GLN* 3.2 37.6 + - - +
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Residues in contact with ARG 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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227A LEU* 3.6 22.4 - - + +
228A GLU* 3.2 24.5 + - + +
229A SER 4.4 1.8 + - - -
230A THR 2.4 33.3 + - - -
231A ARG* 4.0 8.5 + - - +
233A HIS 3.1 11.3 + - - +
234A ALA* 3.0 19.1 + - - +
236A GLU* 1.3 76.1 - - - +
238A MET* 1.3 59.1 + - - +
240A GLN* 3.0 13.4 + - - +
241A LEU* 2.8 24.1 + - - +
263A THR 3.5 11.2 - - - +
264A ASN 2.8 27.4 + - - -
265A LEU* 4.2 5.4 - - + +
266A ARG* 4.3 12.0 - - - +
269A GLU* 2.7 40.0 + - - -
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Residues in contact with MET 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 ALA* 2.7 28.8 + - - +
235A ALA* 3.1 10.1 + - + +
237A ARG* 1.3 69.8 - - - +
239A ASN* 1.3 64.4 + - - +
241A LEU* 3.1 10.9 + - + +
242A LYS* 3.1 34.7 + - - +
265A LEU* 5.4 2.7 - - + -
269A GLU* 4.0 40.6 - - + +
272A ARG* 3.5 48.9 - - + +
273A SER* 3.6 12.2 - - - +
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Residues in contact with ASN 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 ALA 2.7 19.1 + - - +
236A GLU* 4.0 7.9 - - - +
238A MET* 1.3 72.7 - - - +
240A GLN* 1.3 61.2 - - - +
242A LYS* 3.4 20.9 + - + +
243A MET* 3.4 13.2 + - - +
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Residues in contact with GLN 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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199A PHE* 4.2 20.8 - - + +
200A PRO* 5.9 2.2 - - + -
201A SER 4.5 4.6 + - - -
202A THR* 4.0 30.1 + - - +
206A ARG* 5.1 4.3 - - - +
208A LEU* 5.1 6.4 - - + +
227A LEU* 3.7 16.6 - - + -
228A GLU* 2.8 40.0 + - - +
236A GLU* 3.2 26.6 + - - +
237A ARG* 3.0 11.0 + - - +
239A ASN* 1.3 74.4 - - - +
241A LEU* 1.3 62.8 + - - +
243A MET* 3.5 7.1 + - - +
244A VAL* 3.3 24.3 + - - +
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Residues in contact with LEU 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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227A LEU* 3.7 13.9 - - + +
237A ARG 2.8 11.8 + - - +
238A MET* 3.1 12.1 + - - +
240A GLN* 1.3 78.1 - - - +
242A LYS* 1.3 62.8 + - + +
244A VAL* 3.2 18.6 + - + +
245A LEU* 3.3 28.1 + - + +
259A PHE* 6.2 0.7 - - + -
263A THR* 5.8 0.9 - - + -
265A LEU* 3.7 30.3 - - + -
269A GLU 4.7 0.4 - - - +
270A VAL* 3.7 30.1 - - + +
273A SER* 3.7 21.1 - - - +
319A PHE* 4.2 21.8 - - + -
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Residues in contact with LYS 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 MET* 3.1 25.3 + - - +
239A ASN* 3.8 11.9 - - + +
240A GLN 3.3 0.4 - - - -
241A LEU* 1.3 77.4 - - + +
243A MET* 1.3 56.4 + - - +
245A LEU* 3.4 8.0 + - - +
246A LYS* 2.9 30.8 + - - +
272A ARG 5.4 1.0 + - - -
273A SER* 3.5 40.6 + - - +
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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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200A PRO* 5.8 8.5 - - + -
208A LEU* 4.3 15.1 - - + +
239A ASN 3.4 10.3 + - - +
240A GLN* 4.0 9.0 - - - +
241A LEU 3.3 0.6 - - - -
242A LYS* 1.3 79.3 - - - +
244A VAL* 1.3 61.4 + - - +
246A LYS* 3.9 6.8 - - - +
247A LYS* 3.2 23.9 + - - +
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Residues in contact with VAL 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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208A LEU* 3.9 29.6 - - + -
223A MET* 4.8 3.6 - - - +
227A LEU* 4.6 13.5 - - + -
240A GLN 3.3 15.9 - - - +
241A LEU* 3.2 13.2 + - + +
242A LYS 3.2 0.8 - - - -
243A MET* 1.3 77.0 - - - +
245A LEU* 1.3 59.6 + - + +
247A LYS* 3.3 4.8 + - - +
248A MET* 3.0 40.7 + - + +
259A PHE* 3.9 41.3 - - + -
319A PHE* 4.8 7.2 - - + -
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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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241A LEU* 3.3 29.8 + - + +
242A LYS* 4.1 6.7 - - - +
244A VAL* 1.3 77.3 - - + +
246A LYS* 1.3 61.6 + - - +
248A MET* 3.5 14.7 + - - +
249A GLN* 3.3 32.0 + - - +
273A SER* 6.1 0.7 - - - +
275A GLY 4.4 12.8 - - - +
276A LEU* 4.5 4.9 - - + -
277A PRO* 4.0 33.9 - - + -
280A ILE* 4.4 8.7 - - + -
319A PHE* 4.1 28.9 - - + -
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Residues in contact with LYS 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 LYS 2.9 18.6 + - - +
243A MET* 4.1 7.2 - - - +
244A VAL 3.2 0.2 - - - -
245A LEU* 1.3 79.1 - - - +
247A LYS* 1.3 59.2 + - - +
249A GLN* 3.9 11.9 + - - +
250A GLU* 3.7 18.7 + - - +
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Residues in contact with LYS 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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208A LEU* 5.5 5.6 - - + -
223A MET* 3.9 19.1 - - + +
243A MET 3.2 19.3 + - - +
244A VAL* 3.3 5.1 + - - +
246A LYS* 1.3 77.0 - - - +
248A MET* 1.3 65.1 + - - +
250A GLU* 3.1 19.0 + - - +
251A ALA* 3.6 5.5 + - - +
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Residues in contact with MET 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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223A MET* 3.8 20.2 - - - -
244A VAL* 3.0 24.5 + - + +
245A LEU* 3.8 22.7 - - + +
246A LYS 3.4 0.2 - - - -
247A LYS* 1.3 77.8 - - - +
249A GLN* 1.3 64.6 + - + +
250A GLU 3.1 1.7 + - - -
251A ALA* 3.4 7.8 + - - +
257A VAL* 3.7 47.9 - - + +
259A PHE* 3.8 18.6 - - + -
280A ILE* 4.8 5.6 - - + -
319A PHE* 3.8 39.0 - - + +
320A PHE 4.3 9.6 - - - +
321A ARG* 4.6 1.3 - - - +
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Residues in contact with GLN 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 LEU* 3.3 23.1 + - - +
246A LYS* 4.3 9.6 - - - +
247A LYS 3.3 0.6 - - - -
248A MET* 1.3 77.0 - - + +
250A GLU* 1.3 58.1 + - - +
251A ALA 3.5 2.8 + - - +
277A PRO* 3.9 31.4 - - + +
279A ASN* 4.9 14.0 - - + +
280A ILE* 5.9 2.7 - - + -
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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