Contacts of the helix formed by residues 229 - 246 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9W ILE* 4.3 5.5 - - - -
10W LYS 4.5 1.9 + - - -
70W ALA* 4.1 2.7 - - - -
226W ASP* 3.3 27.7 + - - +
228W MET* 1.3 76.7 - - - +
230W ILE* 1.3 65.4 + - - +
231W LEU* 2.7 31.6 + - - -
232W CYS* 3.0 27.1 + - + +
233W VAL* 3.3 12.5 + - - +
290W LEU* 5.1 6.1 - - + -
294W ARG* 3.1 36.3 + - - -
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Residues in contact with ILE 230 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35W TYR* 4.4 27.1 - - + -
39W MET* 4.2 16.8 - - + -
70W ALA* 3.7 17.4 - - + +
73W VAL* 3.9 18.6 - - + +
74W GLY* 3.2 33.9 - - - +
77W ALA* 5.2 1.8 - - + -
228W MET 3.7 1.6 + - - +
229W ASP* 1.3 72.1 - - - +
231W LEU* 1.3 65.7 + - + +
233W VAL* 3.6 1.6 + - - +
234W ARG* 3.3 20.4 + - + +
287W PRO 4.6 4.5 - - - +
290W LEU* 6.5 0.2 - - + -
291W LEU* 4.0 36.3 - - + -
294W ARG* 5.2 2.7 - - - +
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Residues in contact with LEU 231 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7W PHE* 4.0 26.9 - - + -
9W ILE* 3.7 15.2 - - + +
25W THR* 4.2 5.3 - - + +
27W LEU* 4.2 22.2 - - + -
35W TYR* 4.9 5.2 - - + -
229W ASP* 2.7 17.0 + - - +
230W ILE* 1.3 81.6 - - + +
232W CYS* 1.3 56.5 + - - -
234W ARG* 3.8 40.7 + - - +
235W GLU* 3.4 29.1 + - - +
291W LEU* 5.3 5.4 - - + -
294W ARG* 3.2 31.2 - - - +
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Residues in contact with CYS 232 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9W ILE* 3.7 11.2 - - - -
10W LYS* 3.7 34.5 - - - -
12W CYS* 5.9 3.4 - - - -
225W VAL* 3.7 8.7 - - + +
226W ASP* 3.7 32.1 - - - +
229W ASP* 3.0 19.7 + - - +
231W LEU* 1.3 74.5 - - - +
233W VAL* 1.3 67.7 + - - +
234W ARG 3.1 1.6 - - - -
235W GLU* 3.9 4.2 - - - +
236W ALA* 2.9 28.9 + - - +
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Residues in contact with VAL 233 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70W ALA 3.3 30.3 - - - +
71W CYS* 3.8 4.7 - - - +
74W GLY 3.4 11.0 - - - -
75W LEU* 3.4 31.4 - - + +
225W VAL* 4.2 9.2 - - + -
226W ASP 3.5 15.9 - - - +
227W GLY* 3.9 14.4 - - - -
229W ASP 3.3 13.2 + - - +
230W ILE 3.8 5.2 - - - +
232W CYS* 1.3 79.4 - - - +
234W ARG* 1.3 54.0 + - - +
236W ALA* 3.9 1.8 - - - +
237W THR* 2.6 36.6 + - - -
253W MET* 5.1 0.3 - - - +
255W LEU* 4.7 7.0 - - + -
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Residues in contact with ARG 234 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25W THR* 2.9 27.7 + - - -
26W VAL 3.3 18.4 + - - -
27W LEU* 4.0 10.9 - - - +
28W THR* 5.5 0.4 - - - +
31W ASP* 4.5 6.7 + - - -
35W TYR* 3.3 41.5 + - - -
74W GLY* 3.6 11.7 - - - +
77W ALA* 3.7 25.8 - - + +
230W ILE* 3.3 15.1 + - - +
231W LEU* 3.8 24.1 + - - +
233W VAL* 1.3 77.7 - - - +
235W GLU* 1.3 64.7 + - - +
237W THR* 3.1 3.3 + - - -
238W ARG* 2.9 65.0 + - - +
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Residues in contact with GLU 235 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9W ILE* 3.3 32.1 - - + -
21W PRO* 4.0 9.3 - - + +
22W PRO* 3.7 22.4 - - + +
25W THR* 3.0 28.8 + - - -
231W LEU 3.4 14.9 + - - +
232W CYS 3.3 3.2 + - - +
234W ARG* 1.3 94.1 + - - +
236W ALA* 1.3 58.4 + - - +
238W ARG* 3.4 17.8 + - - +
239W PHE* 3.0 27.7 + - - +
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Residues in contact with ALA 236 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12W CYS* 4.5 4.5 - - - -
21W PRO* 4.2 7.9 - - - +
223W LEU* 4.2 8.8 - - + +
225W VAL* 3.6 30.3 - - + -
232W CYS 2.9 20.8 + - - +
233W VAL 3.9 3.6 - - - +
235W GLU* 1.3 73.2 - - - +
237W THR* 1.3 52.6 + - - +
239W PHE* 3.2 9.8 - - - +
240W ALA* 2.7 35.0 + - - +
253W MET* 4.0 10.5 - - - +
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Residues in contact with THR 237 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74W GLY 4.5 1.1 - - - -
75W LEU* 3.4 28.6 - - - +
78W GLY* 3.5 22.4 - - - -
79W ILE* 3.5 23.3 - - + -
162W LEU* 4.8 7.2 - - + -
190W ILE* 5.7 2.2 - - + -
233W VAL 2.6 22.8 + - - -
234W ARG* 3.1 4.9 + - - -
236W ALA* 1.3 74.4 - - - +
238W ARG* 1.3 67.6 + - - +
240W ALA* 4.4 5.2 - - - -
241W ALA* 2.9 24.9 + - + +
253W MET* 3.8 8.6 - - + +
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Residues in contact with ARG 238 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26W VAL 5.5 0.6 + - - -
31W ASP* 5.8 0.8 + - - -
35W TYR* 4.8 3.2 + - - -
77W ALA 3.3 17.0 + - - -
78W GLY* 3.8 22.0 - - - +
234W ARG* 2.9 65.2 + - - +
235W GLU* 3.9 20.3 + - - +
237W THR* 1.3 75.1 - - - +
239W PHE* 1.3 57.8 + - - +
241W ALA* 3.9 1.6 - - - +
242W ALA* 2.9 30.8 + - - +
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Residues in contact with PHE 239 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17W LEU* 4.3 10.1 - - + -
19W GLU* 3.7 19.3 - - + -
20W GLY* 3.5 22.4 - - - -
21W PRO* 3.5 29.4 - - + -
22W PRO* 5.4 2.9 - - + -
223W LEU* 4.1 24.5 - - + -
235W GLU 3.0 15.7 + - - +
236W ALA 3.2 10.5 - - - +
237W THR 3.1 0.2 - - - -
238W ARG* 1.3 77.2 - - - +
240W ALA* 1.3 62.4 + - - +
242W ALA* 3.0 9.9 - - + +
243W TYR* 2.9 34.2 + + + +
251W ILE* 4.2 11.7 - - + -
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Residues in contact with ALA 240 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190W ILE* 3.5 31.0 - - + -
223W LEU* 5.6 1.6 - - + -
236W ALA 2.7 19.4 + - - +
237W THR* 3.2 3.6 + - - +
239W PHE* 1.3 77.4 - - + +
241W ALA* 1.3 66.9 + - - +
242W ALA 3.1 0.9 - - - -
243W TYR* 3.1 17.0 + - - +
244W CYS* 3.1 17.7 + - - -
251W ILE* 4.2 12.2 - - + +
253W MET* 4.4 11.0 - - + -
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Residues in contact with ALA 241 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78W GLY 4.2 10.5 - - - +
79W ILE* 4.9 4.3 - - + -
160W VAL* 4.3 13.2 - - + -
190W ILE* 3.5 11.8 - - + +
237W THR 2.9 15.6 + - - +
238W ARG* 4.1 2.5 - - - +
240W ALA* 1.3 76.3 - - - +
242W ALA* 1.3 64.1 + - - +
244W CYS* 3.9 0.9 - - - +
245W ARG* 3.0 56.4 + - - +
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Residues in contact with ALA 242 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238W ARG 2.9 17.3 + - - +
239W PHE* 3.0 17.5 - - + +
240W ALA 3.1 0.2 - - - -
241W ALA* 1.3 79.5 - - - +
243W TYR* 1.3 60.6 + - - +
245W ARG* 3.2 4.6 + - - +
246W SER* 3.1 22.5 + - - -
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Residues in contact with TYR 243 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17W LEU* 3.7 26.6 - - + +
221W PRO* 3.1 26.1 - - + +
239W PHE* 2.9 21.2 + + + +
240W ALA* 3.2 13.0 - - - +
242W ALA* 1.3 75.4 - - - +
244W CYS* 1.3 59.8 + - - +
246W SER* 3.0 23.4 + - - -
248W LYS* 3.3 56.9 + - + +
249W GLY 3.3 24.7 - - - -
250W PRO 3.4 10.1 - - - -
251W ILE* 3.9 22.0 - - + -
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Residues in contact with CYS 244 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160W VAL* 4.0 14.1 - - + -
188W PRO* 3.9 23.4 - - + +
189W CYS 3.9 27.6 - - - -
190W ILE* 3.9 14.4 - - - -
240W ALA 3.1 14.5 + - - +
243W TYR* 1.3 77.2 - - - +
245W ARG* 1.3 62.5 + - - +
246W SER 3.2 0.7 - - - -
247W GLY* 2.9 19.3 + - - +
248W LYS 4.6 0.7 - - - +
249W GLY 3.6 24.0 + - - -
251W ILE* 4.1 9.0 - - - -
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Residues in contact with ARG 245 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78W GLY 4.9 1.0 + - - -
79W ILE* 4.7 2.8 - - - +
80W ASN* 3.5 17.3 + - - +
83W ASP* 2.7 42.2 + - - -
158W ASP* 3.0 60.4 + - - +
159W GLU* 3.9 0.4 - - - +
160W VAL* 3.4 22.0 - - + +
188W PRO* 5.9 0.4 - - - -
241W ALA* 3.0 37.3 + - - +
242W ALA* 3.8 5.3 - - - +
244W CYS* 1.3 72.8 - - - +
246W SER* 1.3 63.7 + - - +
247W GLY* 2.9 6.8 + - - -
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Residues in contact with SER 246 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242W ALA 3.1 12.5 + - - -
243W TYR* 3.0 16.2 + - - -
244W CYS 3.2 0.2 - - - -
245W ARG* 1.3 77.2 - - - +
247W GLY* 1.3 57.3 + - - +
248W LYS* 3.1 27.8 + - - +
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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