Contacts of the helix formed by residues 246 - 261 (chain J) in PDB entry 5A31
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 246 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241J HIS* 3.0 34.7 + - + +
244J ASN* 3.3 19.9 + - - +
245J CYS* 1.3 70.8 - - - +
247J PHE* 1.3 63.0 + - - +
248J LYS 3.4 2.2 - - - -
249J MET* 3.2 11.7 + - + +
250J CYS* 3.1 20.4 + - - +
435J ILE* 3.9 15.0 - - - +
441J VAL* 3.2 26.1 - - - +
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Residues in contact with PHE 247 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G ARG* 5.4 2.5 - - - -
242J TYR* 3.8 46.9 - + - +
245J CYS* 3.1 49.8 + - + -
246J ASP* 1.3 71.1 - - - +
248J LYS* 1.3 61.7 + - - +
250J CYS* 3.4 5.3 - - - +
251J TYR* 2.9 24.1 + - - +
273J GLY 4.7 0.2 - - - -
274J THR* 3.3 17.1 + - - +
277J GLU* 3.1 61.9 - - + +
278J LEU* 3.4 9.8 - - + +
441J VAL 5.5 0.9 - - - -
443J LYS* 4.3 18.6 - - + -
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Residues in contact with LYS 248 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246J ASP 3.4 0.4 - - - -
247J PHE* 1.3 75.0 - - - +
249J MET* 1.3 66.3 + - - +
251J TYR* 3.2 8.0 + - + +
252J LYS* 2.9 33.9 + - + +
278J LEU* 4.2 20.1 - - + +
280J LYS* 4.5 19.3 - - - +
122P ARG* 5.0 10.1 - - - +
153P GLU* 3.4 42.8 + - + +
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Residues in contact with MET 249 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237J LEU* 6.2 0.4 - - + -
241J HIS* 3.7 39.5 - - + +
246J ASP* 3.2 16.8 + - + +
248J LYS* 1.3 75.9 - - - +
250J CYS* 1.3 63.4 + - - +
252J LYS* 3.2 44.7 + - - +
253J LEU* 3.3 29.0 + - + +
160P LYS* 6.3 0.9 - - - +
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Residues in contact with CYS 250 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238J ALA* 4.0 7.7 - - - +
241J HIS* 4.0 18.6 - - + +
242J TYR* 3.7 26.2 - - - +
246J ASP 3.1 9.3 + - - +
247J PHE* 3.4 11.0 - - - +
249J MET* 1.3 79.8 - - - +
251J TYR* 1.3 55.2 + - - +
253J LEU* 3.4 8.2 + - - +
254J THR* 2.9 30.4 + - - -
270J VAL* 4.0 12.1 - - - -
274J THR* 3.5 30.1 - - - -
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Residues in contact with TYR 251 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247J PHE 2.9 18.5 + - - +
248J LYS* 3.2 8.9 + - + +
250J CYS* 1.3 73.0 - - - +
252J LYS* 1.3 64.9 + - + +
254J THR* 3.9 8.7 - - + -
255J SER* 2.9 52.3 + - - -
271J HIS* 4.5 5.3 + - - -
274J THR* 3.8 11.0 - - + +
275J LEU* 3.4 32.3 - - + -
278J LEU* 3.6 19.5 - - + -
280J LYS* 3.2 32.2 + - + +
283J GLU* 4.2 13.5 - - - +
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Residues in contact with LYS 252 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248J LYS* 2.9 23.4 + - + +
249J MET* 3.2 36.5 + - + +
251J TYR* 1.3 79.0 - - + +
253J LEU* 1.3 63.0 + - + +
255J SER* 3.1 16.4 + - - -
256J VAL* 3.5 15.4 + - - +
107P HIS* 5.2 20.2 - - + +
157P GLU* 5.1 8.7 + - - -
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Residues in contact with LEU 253 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234J VAL* 4.2 24.0 - - + +
237J LEU* 4.1 23.3 - - + -
238J ALA* 4.0 22.0 - - + -
241J HIS* 3.7 26.0 - - + +
249J MET* 3.3 27.9 + - + +
250J CYS 3.5 4.9 - - - +
252J LYS* 1.3 78.4 - - + +
254J THR* 1.3 60.0 - - - +
256J VAL* 3.0 27.9 + - + +
257J VAL* 3.0 16.1 + - + +
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Residues in contact with THR 254 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235J VAL* 5.0 0.7 - - - +
238J ALA* 4.3 10.8 - - - +
250J CYS* 2.9 17.7 + - - +
251J TYR* 3.9 5.2 - - + +
253J LEU* 1.3 78.4 - - - +
255J SER* 1.3 59.8 - - - +
257J VAL* 3.3 11.1 + - - +
258J MET* 3.0 24.1 + - - +
267J CYS* 4.1 13.2 + - - +
270J VAL* 3.9 13.5 - - - +
271J HIS* 3.1 51.1 + - + +
274J THR* 3.7 21.5 - - + -
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Residues in contact with SER 255 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251J TYR* 2.9 48.2 + - - -
252J LYS* 3.1 12.6 + - - -
254J THR* 1.3 79.6 - - - +
256J VAL* 1.3 63.3 + - - +
258J MET* 3.4 6.0 + - - +
259J GLU* 3.2 20.6 + - - +
271J HIS* 4.4 8.5 - - - -
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Residues in contact with VAL 256 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234J VAL* 5.9 2.9 - - + -
252J LYS 3.5 12.1 + - - +
253J LEU* 3.0 21.2 + - + +
255J SER* 1.3 77.4 + - - +
257J VAL* 1.3 70.0 + - + +
259J GLU* 3.3 5.5 + - - +
260J LYS* 3.1 44.5 + - + +
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Residues in contact with VAL 257 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231J LEU* 4.3 15.7 - - + -
234J VAL* 3.5 32.1 - - + +
235J VAL* 4.7 10.8 - - + +
238J ALA* 6.0 0.2 - - + -
253J LEU 3.0 16.1 + - - +
254J THR* 3.3 14.6 + - - +
256J VAL* 1.3 77.9 - - + +
258J MET* 1.3 57.3 + - - +
260J LYS* 3.2 7.0 + - - +
261J ASP* 2.9 27.4 + - - +
264J HIS* 4.1 13.7 - - + -
267J CYS* 3.6 29.4 - - + -
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Residues in contact with MET 258 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254J THR 3.0 6.7 + - - +
255J SER* 3.6 11.0 - - - +
256J VAL 3.3 0.4 - - - -
257J VAL* 1.3 80.7 - - - +
259J GLU* 1.3 61.6 + - - +
261J ASP 3.0 15.4 - - - +
262J PRO* 3.2 33.8 - - + +
264J HIS 4.8 0.7 - - - -
267J CYS* 3.3 23.8 - - - -
268J LEU* 3.7 17.9 - - + -
271J HIS* 3.0 55.4 - - + +
283J GLU* 5.8 2.0 - - - +
287J LEU* 4.1 7.9 - - + -
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Residues in contact with GLU 259 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C LYS* 5.0 25.3 - - + +
255J SER 3.2 13.0 + - - +
256J VAL* 3.3 6.0 + - - +
257J VAL 3.3 0.4 - - - -
258J MET* 1.3 80.3 - - - +
260J LYS* 1.3 62.1 + - - +
261J ASP 4.9 0.2 - - - -
262J PRO* 4.9 0.9 - - - +
58K HIS* 4.6 8.1 + - - -
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Residues in contact with LYS 260 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229J LYS* 3.8 25.9 + - - +
231J LEU* 3.6 25.9 - - + +
234J VAL* 5.5 8.3 - - - +
256J VAL* 3.1 32.1 + - + +
257J VAL* 3.6 7.2 - - - +
259J GLU* 1.3 80.1 - - - +
261J ASP* 1.4 58.1 + - - +
262J PRO 4.2 0.2 - - - -
58K HIS* 3.9 16.3 + - - -
62K SER* 4.9 1.9 + - - -
63K ARG* 6.0 0.3 + - - -
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Residues in contact with ASP 261 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231J LEU* 3.5 21.5 - - + +
257J VAL 2.9 15.5 + - - +
258J MET* 3.0 12.0 - - - +
260J LYS* 1.4 72.5 - - - +
262J PRO* 1.3 77.2 - - - +
263J PHE 3.3 2.1 + - - -
264J HIS* 3.5 19.7 + - + +
47K LEU* 5.8 0.6 - - - +
55K ARG* 3.1 53.2 + - - +
58K HIS* 4.8 1.9 - - - -
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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