Contacts of the helix formed by residues 230 - 245 (chain J) in PDB entry 5G04
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 ASN 230 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227J LEU* 3.7 25.7 - - + +
228J GLN 2.9 12.5 + - - +
229J GLU* 1.3 76.9 - - - +
231J LEU* 1.3 81.4 + - - +
232J ASP* 2.8 18.3 + - - +
233J VAL* 3.3 5.1 - - + +
234J VAL* 3.3 14.9 + - - +
27K ASP* 3.7 13.7 + - - +
28K LYS* 3.8 32.5 - - - +
31K SER* 3.1 38.3 + - - +
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Residues in contact with LEU 231 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229J GLU 4.0 9.4 - - - +
230J ASN* 1.3 76.5 + - - +
232J ASP* 1.3 60.0 + - - +
234J VAL* 3.2 14.3 + - + +
235J VAL* 2.8 32.2 + - - +
257J VAL* 4.7 14.7 - - + +
260J LYS* 3.9 33.0 - - + +
261J ASP* 3.6 42.4 - - + +
264J HIS* 4.3 16.8 - - + +
27K ASP* 5.6 3.1 - - - +
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Residues in contact with ASP 232 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207J ASN* 4.8 0.4 + - - -
208J LYS* 4.1 15.6 + - - +
230J ASN* 2.8 17.9 + - - +
231J LEU* 1.3 74.4 - - - +
233J VAL* 1.3 61.6 + - - +
235J VAL* 3.3 10.7 - - - +
236J SER* 3.2 21.5 + - - -
264J HIS* 3.2 29.3 + - - -
266J SER* 5.3 1.8 - - - -
24K PHE* 4.2 13.9 - - - +
27K ASP* 4.4 15.6 - - - +
28K LYS* 3.5 33.4 + - - +
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Residues in contact with VAL 233 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203J PHE* 4.4 23.8 - - + -
207J ASN* 4.6 5.2 - - - +
220J ILE* 5.4 4.7 - - + +
227J LEU* 3.3 32.1 - - + +
228J GLN* 2.9 38.4 - - + +
230J ASN* 3.3 11.2 + - + +
231J LEU 3.2 0.4 - - - -
232J ASP* 1.3 75.9 - - - +
234J VAL* 1.3 70.7 + - + +
236J SER* 3.2 8.5 + - - -
237J LEU* 3.1 20.3 + - - +
28K LYS* 4.6 8.7 - - - +
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Residues in contact with VAL 234 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228J GLN 3.8 12.3 - - - +
229J GLU* 4.8 5.2 - - - +
230J ASN 3.3 9.4 + - - +
231J LEU* 3.2 27.3 + - + +
233J VAL* 1.3 78.9 - - + +
235J VAL* 1.3 56.9 + - - +
237J LEU* 3.2 19.9 + - + +
238J ALA* 3.0 25.7 + - - +
253J LEU* 4.8 13.2 - - + +
256J VAL* 5.5 5.8 - - + -
257J VAL* 3.7 22.9 - - + -
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Residues in contact with VAL 235 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208J LYS* 5.2 3.8 - - - +
231J LEU 2.8 19.5 + - - +
232J ASP* 3.3 19.5 - - - +
234J VAL* 1.3 70.5 - - - +
236J SER* 1.3 69.5 + - - +
238J ALA* 3.3 4.4 + - + +
239J GLU* 3.0 25.2 + - + +
254J THR* 4.6 8.5 - - - +
257J VAL* 4.7 8.7 - - + -
264J HIS* 4.5 7.2 - - - +
266J SER* 3.6 19.5 - - - +
267J CYS* 3.4 39.7 - - + +
270J VAL* 4.4 9.9 - - + -
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Residues in contact with SER 236 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207J ASN* 3.3 34.4 + - - +
208J LYS* 5.0 5.8 - - - +
211J LYS* 2.9 30.7 + - - +
220J ILE* 4.8 4.8 - - - +
232J ASP 3.2 14.1 + - - -
233J VAL 3.2 11.4 + - - -
235J VAL* 1.3 78.5 - - - +
237J LEU* 1.3 61.3 + - - +
239J GLU* 3.1 9.9 + - - +
240J ARG* 3.0 21.0 + - - +
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Residues in contact with LEU 237 (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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218J THR 5.1 3.1 - - - +
219J VAL* 4.2 32.3 - - + -
220J ILE* 5.1 17.2 - - + +
233J VAL 3.1 8.7 + - - +
234J VAL* 3.2 17.0 + - + +
236J SER* 1.3 79.3 - - - +
238J ALA* 1.3 55.7 + - - +
240J ARG* 3.3 9.8 + - + +
241J HIS* 3.0 50.8 + - + -
249J MET* 6.1 0.2 - - + -
253J LEU* 4.0 31.6 - - + -
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Residues in contact with ALA 238 (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 3.0 13.2 + - - +
235J VAL* 3.6 11.0 - - - +
236J SER 3.3 0.2 - - - -
237J LEU* 1.3 72.9 - - - +
239J GLU* 1.3 66.3 + - - +
241J HIS* 3.3 6.8 + - - +
242J TYR* 2.9 24.4 + - - +
250J CYS* 3.5 21.0 - - - +
253J LEU* 4.1 14.8 - - + +
254J THR* 3.9 22.0 - - - +
257J VAL* 5.9 0.7 - - + -
270J VAL* 4.2 5.2 - - + -
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Residues in contact with GLU 239 (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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208J LYS* 5.7 6.1 + - - +
211J LYS* 3.6 29.4 - - + +
235J VAL* 3.0 14.2 + - - +
236J SER* 3.2 13.6 - - - +
238J ALA* 1.3 76.0 - - - +
240J ARG* 1.3 62.8 + - - +
242J TYR* 3.2 2.1 + - - +
243J TYR* 3.0 46.5 + - + -
266J SER* 4.7 10.4 + - - +
270J VAL* 3.9 32.0 - - + +
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Residues in contact with ARG 240 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206J GLU* 4.1 18.2 + - - +
207J ASN* 4.1 13.3 + - - +
211J LYS* 4.0 29.4 - - + +
217J GLU* 3.6 43.8 + - + +
218J THR 3.2 24.7 + - - +
220J ILE* 3.3 40.7 - - - +
236J SER 3.0 7.0 + - - +
237J LEU* 3.4 13.2 - - + +
239J GLU* 1.3 80.2 - - - +
241J HIS* 1.3 63.6 - - - +
243J TYR* 3.2 5.3 + - - +
244J ASN* 3.1 30.1 + - - +
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Residues in contact with HIS 241 (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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218J THR 6.3 0.9 - - - -
219J VAL* 4.9 13.9 - - + +
237J LEU* 3.0 44.4 + - + +
238J ALA 3.6 7.0 - - - +
240J ARG* 1.3 75.3 - - - +
242J TYR* 1.3 62.0 + - - +
244J ASN* 3.1 16.8 + - - +
245J CYS 3.2 0.2 + - - -
246J ASP* 3.0 43.8 + - + +
249J MET* 3.5 49.2 - - + +
250J CYS* 3.9 16.6 - - + +
253J LEU* 3.6 11.0 - - + +
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Residues in contact with TYR 242 (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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1G MET 2.9 35.4 + - - -
2G LEU* 3.8 5.0 + - - +
3G ARG* 3.2 14.8 + - - -
238J ALA 2.9 17.7 + - - +
239J GLU 3.6 2.5 - - - +
240J ARG 3.1 0.2 - - - -
241J HIS* 1.3 77.3 - - - +
243J TYR* 1.3 105.7 + + - +
245J CYS* 3.2 12.7 + - - +
246J ASP 4.9 2.0 - - - +
247J PHE* 3.3 42.0 - + - -
250J CYS* 3.5 15.0 - - - -
269J PRO 5.4 0.4 - - - -
270J VAL* 4.3 14.6 - - + -
273J GLY* 3.5 10.8 + - - -
274J THR* 3.5 29.8 - - - -
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Residues in contact with TYR 243 (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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1G MET* 3.9 33.4 + - + +
3G ARG* 2.7 48.8 + - - +
211J LYS* 4.2 16.8 - - + -
212J TYR* 3.4 50.2 - + + +
215J PRO* 4.0 13.2 - - + +
239J GLU* 3.0 46.3 + - + +
240J ARG 3.2 4.0 + - - +
242J TYR* 1.3 98.6 - + - +
244J ASN* 1.3 63.4 + - - +
245J CYS* 3.1 1.5 - - - -
369J LEU* 6.0 1.3 - - + -
403J PHE* 5.6 1.0 - - - -
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Residues in contact with ASN 244 (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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215J PRO* 3.0 29.8 - - - +
217J GLU 3.7 17.1 + - - +
218J THR* 4.8 7.7 - - - +
240J ARG* 3.1 20.4 + - - +
241J HIS* 3.1 15.7 + - - +
243J TYR* 1.3 75.9 - - - +
245J CYS* 1.3 66.5 + - - +
246J ASP* 3.5 23.5 + - - +
432J ILE* 4.7 0.5 - - - +
435J ILE* 3.7 26.6 - - + +
441J VAL* 3.5 15.4 - - - +
444J TRP* 4.3 5.7 + - - -
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Residues in contact with CYS 245 (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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3G ARG* 3.3 27.6 - - - -
241J HIS 3.2 1.6 + - - -
242J TYR 3.2 1.7 + - - -
243J TYR 3.1 5.0 - - - -
244J ASN* 1.3 80.9 - - - +
246J ASP* 1.4 58.7 + - - +
247J PHE* 3.0 35.0 + - + -
403J PHE* 4.6 3.8 - - - -
441J VAL* 3.7 23.5 - - + +
443J LYS* 3.5 46.6 - - + +
444J TRP* 4.4 9.4 - - - +
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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
------------------------------------------------------------
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