Contacts of the strand formed by residues 229 - 239 (chain G) in PDB entry 3JCA
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 TRP 229 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220G MET* 3.7 36.8 - - + +
221G TRP* 3.4 10.5 - - - -
222G LYS* 3.3 39.4 - - + +
227G GLY 4.5 6.4 + - - -
228G SER* 1.3 83.3 + - - +
230G LYS* 1.3 62.8 + - - +
231G GLY 5.1 1.2 - - - +
260G PHE* 3.1 31.0 - + - -
262G ARG* 3.5 42.4 - - + -
8J G 2.8 38.2 + - - -
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Residues in contact with LYS 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220G MET* 3.2 4.0 - - - +
221G TRP* 2.8 67.8 + - + +
223G ASP* 3.8 31.4 - - + -
226G THR* 4.5 1.9 + - - +
228G SER* 3.5 25.1 + - - +
229G TRP* 1.3 77.4 - - - +
231G GLY* 1.3 62.0 + - - +
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Residues in contact with GLY 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220G MET* 4.1 6.5 - - - +
221G TRP* 4.3 1.4 - - - -
229G TRP 4.3 1.6 + - - +
230G LYS* 1.3 76.6 - - - +
232G PRO* 1.3 78.6 - - - +
233G ASP* 3.7 12.3 - - - -
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Residues in contact with PRO 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218G MET* 3.2 31.0 - - + +
219G VAL 3.2 19.5 - - - +
220G MET* 3.8 21.3 - - + +
231G GLY* 1.3 83.5 - - - +
233G ASP* 1.3 63.7 + - - +
262G ARG 5.0 0.2 - - - +
264G PHE* 3.7 39.3 - - + -
265G THR 5.0 1.3 - - - +
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Residues in contact with ASP 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217G PRO 2.6 26.9 - - - +
218G MET* 3.2 15.8 - - - +
219G VAL* 2.9 17.2 + - - +
221G TRP* 3.6 24.7 - - + -
231G GLY* 4.0 4.3 - - - -
232G PRO* 1.3 76.9 - - - +
234G VAL* 1.3 79.3 + - - +
235G LEU 3.0 2.6 + - - -
247G PRO* 3.6 21.5 - - + +
248G GLN* 4.8 6.8 + - - +
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Residues in contact with VAL 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217G PRO 4.0 4.5 - - - -
218G MET* 4.8 7.9 - - - -
233G ASP* 1.3 86.7 + - - +
235G LEU* 1.3 62.5 + - - +
236G ILE* 3.7 16.8 - - + -
245G VAL* 3.9 2.8 - - - +
246G PHE 2.9 39.0 + - - +
247G PRO* 3.6 20.1 - - + +
248G GLN* 5.0 3.8 - - - +
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Residues in contact with LEU 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217G PRO* 2.9 53.7 + - + +
219G VAL* 3.7 26.5 - - + -
233G ASP 3.0 1.6 + - - -
234G VAL* 1.3 75.9 - - - +
236G ILE* 1.3 62.5 + - - +
237G THR* 3.3 23.8 - - - +
238G ALA* 4.9 4.9 - - + -
243G ALA* 3.7 22.2 - - + -
244G CYS 3.3 27.6 - - - +
245G VAL* 3.7 11.7 - - + +
261G ILE* 5.6 2.5 - - + -
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Residues in contact with ILE 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217G PRO* 5.5 2.4 - - - +
234G VAL* 3.6 13.9 + - + -
235G LEU* 1.3 76.0 - - - +
237G THR* 1.3 73.3 + - + +
244G CYS* 2.9 16.0 + - - +
246G PHE* 3.3 48.5 - - + +
217H PRO* 4.3 24.9 - - + -
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Residues in contact with THR 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235G LEU* 3.3 12.2 - - - +
236G ILE* 1.3 85.5 - - + +
238G ALA* 1.3 73.6 + - - +
244G CYS* 2.7 33.0 + - + -
255G TRP* 3.7 24.5 - - + -
217H PRO* 4.1 21.5 - - + -
235H LEU* 4.8 2.9 - - + -
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Residues in contact with ALA 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E LEU 5.3 0.2 - - - +
225E LEU* 3.7 31.6 - - - +
226E THR* 5.2 6.5 - - - +
235G LEU* 4.9 7.4 - - + -
237G THR* 1.3 90.9 + - - +
239G GLY* 1.3 60.0 + - - +
242G TYR 3.1 14.8 - - - +
243G ALA* 4.1 7.2 - - + -
255G TRP* 4.0 9.2 - - - -
238H ALA* 5.2 2.3 - - - +
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Residues in contact with GLY 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E LEU 3.4 11.2 + - - -
225E LEU* 3.9 11.7 - - - -
238G ALA* 1.3 76.2 - - - +
240G ARG* 1.3 73.6 + - - +
241G GLY 3.1 2.2 - - - -
242G TYR* 2.9 28.3 + - - +
255G TRP* 4.1 7.2 - - - -
238H ALA* 5.5 7.6 - - - -
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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