Contacts of the helix formed by residues 229 - 246 (chain G) in PDB entry 3EXG
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 229 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G ILE* 4.3 5.5 - - - -
10G LYS 4.7 1.4 + - - -
70G ALA* 4.1 2.9 - - - -
226G ASP* 3.4 21.6 + - - +
227G GLY 3.3 1.0 - - - -
228G MET* 1.3 78.3 - - - +
230G ILE* 1.3 65.5 + - - +
231G LEU* 2.7 28.4 + - - +
232G CYS* 3.1 33.2 + - + +
233G VAL* 3.1 13.2 + - - +
290G LEU* 5.2 6.1 - - + -
294G ARG* 3.1 39.5 + - - -
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Residues in contact with ILE 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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35G TYR* 4.0 31.9 - - + -
39G MET* 4.2 18.6 - - + -
70G ALA* 3.7 16.7 - - - +
73G VAL* 3.7 19.7 - - + +
74G GLY* 3.2 41.0 - - - +
77G ALA* 5.1 0.9 - - + -
228G MET 3.8 1.8 + - - -
229G ASP* 1.3 73.2 - - - +
231G LEU* 1.3 65.4 + - + +
233G VAL 3.7 0.2 + - - -
234G ARG* 3.3 20.4 + - - +
287G PRO 4.9 2.9 - - - +
291G LEU* 4.0 35.7 - - + -
294G ARG* 5.4 1.8 - - - +
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Residues in contact with LEU 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G PHE* 4.0 28.0 - - + -
9G ILE* 3.7 11.7 - - + -
25G THR* 4.3 7.1 - - + +
27G LEU* 4.2 20.6 - - + -
35G TYR* 4.8 5.8 - - + -
229G ASP* 2.7 15.8 + - - +
230G ILE* 1.3 79.8 - - + +
232G CYS* 1.3 57.1 + - - +
234G ARG* 3.8 37.8 - - - +
235G GLU* 3.2 32.2 + - - +
291G LEU* 5.5 4.9 - - + -
294G ARG* 3.1 31.0 - - - +
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Residues in contact with CYS 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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9G ILE* 3.8 12.9 - - - +
10G LYS* 3.7 34.5 - - - -
12G CYS* 6.2 2.0 - - - -
225G VAL* 3.6 8.2 - - + +
226G ASP* 3.5 29.6 - - - +
229G ASP* 3.1 27.1 + - - +
231G LEU* 1.3 73.4 - - - +
233G VAL* 1.3 67.8 + - - +
234G ARG 3.2 0.4 - - - -
235G GLU* 3.9 3.7 - - - +
236G ALA* 3.0 27.2 + - - +
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Residues in contact with VAL 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G ALA 3.3 23.1 - - - +
71G CYS* 3.8 4.5 - - - +
74G GLY* 3.5 5.4 - - - -
75G LEU* 3.3 48.0 - - + +
225G VAL* 4.3 6.5 - - + -
226G ASP 3.7 14.1 - - - +
227G GLY* 3.9 13.7 - - - -
229G ASP 3.1 12.9 + - - +
230G ILE 4.1 0.2 - - - +
232G CYS* 1.3 81.0 - - - +
234G ARG* 1.3 55.5 + - - +
236G ALA* 3.6 2.4 - - - +
237G THR* 2.6 36.2 + - - -
253G MET* 4.7 0.2 - - - +
255G LEU* 4.4 14.1 - - + -
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Residues in contact with ARG 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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25G THR* 3.0 27.3 + - - +
26G VAL 3.3 19.6 + - - -
27G LEU* 3.8 13.3 - - - +
31G ASP* 4.6 6.7 + - - -
35G TYR* 3.2 43.5 + - - -
74G GLY 3.4 14.6 + - - +
77G ALA* 3.6 19.7 - - + +
230G ILE 3.3 16.3 + - - +
231G LEU* 3.8 22.5 + - - +
232G CYS 3.2 0.2 - - - -
233G VAL* 1.3 80.6 - - - +
235G GLU* 1.3 61.6 + - - +
237G THR* 3.2 3.4 + - - -
238G ARG* 2.9 68.2 + - + +
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Residues in contact with GLU 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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9G ILE* 3.4 29.2 - - + -
21G PRO* 4.0 8.8 - - + +
22G PRO* 3.8 20.1 - - - +
25G THR* 2.9 30.7 + - - -
231G LEU 3.2 22.9 + - - +
232G CYS 3.9 2.0 - - - +
233G VAL 3.3 0.2 - - - -
234G ARG* 1.3 83.6 + - - +
236G ALA* 1.3 62.1 + - - +
238G ARG* 3.4 29.8 + - - +
239G PHE* 3.1 21.8 + - - +
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Residues in contact with ALA 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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12G CYS* 4.7 0.7 - - - -
21G PRO* 4.1 17.8 - - + +
223G LEU* 4.3 6.5 - - + +
225G VAL* 3.6 30.7 - - + -
232G CYS 3.0 18.5 + - - +
233G VAL 3.6 3.6 - - - +
235G GLU* 1.3 75.5 - - - +
237G THR* 1.3 52.2 + - - +
239G PHE* 3.2 4.5 + - - +
240G ALA* 2.7 35.2 + - - +
253G MET* 4.0 12.7 - - + +
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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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74G GLY 4.7 0.4 - - - -
75G LEU* 3.4 27.8 - - - +
78G GLY* 3.4 13.5 - - - -
79G ILE* 3.4 32.1 - - + -
162G LEU* 4.7 8.1 - - + -
190G ILE* 5.7 1.6 - - + -
233G VAL* 2.6 23.6 + - - +
234G ARG* 3.5 5.6 - - - -
235G GLU 3.2 0.2 - - - -
236G ALA* 1.3 73.6 - - - +
238G ARG* 1.3 61.9 + - - +
240G ALA* 3.7 6.7 - - + +
241G ALA* 2.9 28.7 + - + +
253G MET* 3.6 8.5 - - + +
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Residues in contact with ARG 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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25G THR* 4.7 0.8 + - - -
26G VAL 5.0 1.8 + - - -
35G TYR* 4.6 3.8 + - - -
77G ALA 3.7 18.2 + - - -
78G GLY* 3.9 19.3 - - - +
234G ARG* 2.9 65.6 + - - +
235G GLU* 3.4 21.2 + - - +
237G THR* 1.3 75.9 - - - +
239G PHE* 1.3 57.8 + - - +
241G ALA* 3.9 1.8 - - - +
242G ALA* 2.9 29.2 + - - +
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Residues in contact with PHE 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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17G LEU* 4.0 26.9 - - + -
19G GLU* 3.4 28.9 - - + -
20G GLY* 3.6 13.5 - - - -
21G PRO* 3.7 31.0 - - + -
22G PRO* 5.3 3.1 - - + -
223G LEU* 4.3 7.0 - - + -
235G GLU 3.1 13.1 + - - +
236G ALA 3.3 10.1 - - - +
238G ARG* 1.3 74.1 - - - +
240G ALA* 1.3 63.4 + - - +
242G ALA* 3.2 7.7 + - + +
243G TYR* 2.9 35.5 + + + +
251G ILE* 4.4 10.3 - - + -
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Residues in contact with ALA 240 (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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190G ILE* 3.8 31.1 - - + +
223G LEU* 5.5 1.6 - - + -
236G ALA 2.7 19.4 + - - +
237G THR* 3.7 4.9 - - - +
239G PHE* 1.3 75.7 - - + +
241G ALA* 1.3 67.6 + - - +
243G TYR* 3.1 7.4 + - - +
244G CYS* 3.1 25.6 + - - +
251G ILE* 4.4 11.3 - - + +
253G MET* 4.1 13.0 - - - -
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Residues in contact with ALA 241 (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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78G GLY 4.4 9.9 - - - +
79G ILE* 4.8 5.2 - - + -
160G VAL* 4.5 6.1 - - + -
190G ILE* 3.8 15.3 - - + -
237G THR 2.9 21.1 + - - +
238G ARG* 4.2 2.9 - - - +
240G ALA* 1.3 74.4 - - - +
242G ALA* 1.3 63.4 + - - +
244G CYS* 3.9 2.3 - - - +
245G ARG* 3.0 56.8 + - - +
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Residues in contact with ALA 242 (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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238G ARG 2.9 20.1 + - - +
239G PHE* 3.3 9.6 - - + +
240G ALA 3.1 0.2 - - - -
241G ALA* 1.3 79.9 - - - +
243G TYR* 1.3 66.6 + - - +
244G CYS 3.0 1.2 + - - -
245G ARG* 3.1 12.4 + - - +
246G SER* 3.2 13.3 + - - -
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Residues in contact with TYR 243 (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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17G LEU* 3.6 27.9 - - + +
221G PRO* 3.1 25.0 - - + +
239G PHE* 2.9 27.4 + + + +
240G ALA* 3.1 11.6 + - - +
242G ALA* 1.3 71.0 - - - +
244G CYS* 1.3 58.9 + - - +
246G SER* 2.7 23.8 + - - -
248G LYS* 3.3 59.9 + - + +
249G GLY 3.4 13.9 - - - -
250G PRO 3.4 20.1 + - - -
251G ILE* 4.1 19.7 - - + -
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Residues in contact with CYS 244 (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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160G VAL* 4.0 17.0 - - + -
188G PRO* 4.0 14.4 - - + +
189G CYS 3.8 23.8 - - - -
190G ILE* 3.7 27.1 - - + -
240G ALA 3.1 12.8 + - - +
241G ALA 3.9 3.4 - - - +
243G TYR* 1.3 74.4 - - - +
245G ARG* 1.3 60.7 + - - +
246G SER 3.2 1.6 - - - -
247G GLY* 3.0 19.8 + - - -
248G LYS 4.1 0.2 + - - -
249G GLY 3.4 24.2 + - - -
251G ILE* 4.1 8.1 - - - -
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Residues in contact with ARG 245 (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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280A GLU* 3.8 15.9 - - - +
284A LYS* 4.1 6.4 - - + -
78G GLY 5.0 1.6 + - - -
79G ILE* 4.7 2.2 - - - +
80G ASN* 3.7 17.5 + - - +
83G ASP* 2.8 40.4 + - - -
158G ASP* 2.8 63.0 + - - +
159G GLU* 4.0 0.2 - - - +
160G VAL* 3.5 18.6 - - + +
188G PRO* 5.8 0.4 - - - -
241G ALA* 3.0 38.1 + - - +
242G ALA* 3.8 4.9 - - - +
244G CYS* 1.3 72.4 - - - +
246G SER* 1.3 59.3 + - - +
247G GLY* 2.8 10.8 + - - -
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Residues in contact with SER 246 (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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280A GLU* 5.1 2.0 - - - +
284A LYS* 4.4 16.7 + - - +
242G ALA 3.2 8.0 + - - -
243G TYR* 2.7 23.0 + - - -
245G ARG* 1.3 78.7 - - - +
247G GLY* 1.3 57.7 + - - +
248G LYS* 3.4 23.7 + - - +
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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
------------------------------------------------------------
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