Contacts of the helix formed by residues 229 - 246 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9E ILE* 4.4 1.2 - - - +
10E LYS* 4.7 1.4 + - - +
70E ALA* 4.1 2.7 - - - -
226E ASP* 3.3 28.1 + - - +
228E MET* 1.3 78.7 - - - +
230E ILE* 1.3 56.0 + - - +
231E LEU 2.8 19.8 + - - -
232E CYS* 2.8 32.5 + - - -
233E VAL* 3.2 9.3 + - - +
290E LEU* 4.6 11.6 - - + +
294E ARG* 2.8 43.1 + - - -
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Residues in contact with ILE 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E TYR* 4.2 29.4 - - + -
39E MET* 4.1 24.2 - - + -
70E ALA* 3.6 18.5 - - + +
73E VAL* 3.9 21.3 - - + +
74E GLY* 3.7 25.5 - - - +
77E ALA* 5.4 0.9 - - + -
228E MET 3.6 1.0 + - - +
229E ASP* 1.3 73.4 - - - +
231E LEU* 1.3 66.2 + - + +
233E VAL* 3.7 2.7 + - - +
234E ARG* 3.0 24.4 + - + +
287E PRO 4.7 4.9 - - - +
290E LEU* 5.9 1.6 - - + -
291E LEU* 3.9 29.4 - - + -
294E ARG* 5.1 1.8 - - - +
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Residues in contact with LEU 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PHE* 4.4 6.1 - - + -
9E ILE* 3.9 9.6 - - + +
25E THR* 4.3 13.8 - - + +
27E LEU* 4.2 32.1 - - + -
35E TYR* 4.7 4.0 - - + -
229E ASP* 2.8 10.3 + - - -
230E ILE* 1.3 89.2 - - + +
232E CYS* 1.3 60.0 + - - +
233E VAL 3.4 0.2 - - - -
234E ARG* 3.8 34.5 + - - +
235E GLU* 3.2 27.9 + - - +
291E LEU* 5.0 3.6 - - + -
294E ARG* 3.2 43.3 - - + +
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Residues in contact with CYS 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ILE* 3.6 21.1 - - - -
10E LYS* 3.6 27.4 - - - -
12E CYS* 6.0 2.7 - - - -
225E VAL* 3.8 20.2 - - + -
226E ASP* 4.0 10.3 - - - +
229E ASP* 2.8 29.9 + - - +
231E LEU* 1.3 75.3 - - - +
233E VAL* 1.3 59.7 + - - +
234E ARG 3.1 0.2 - - - -
235E GLU* 3.2 5.4 + - - +
236E ALA* 2.7 37.6 + - - +
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Residues in contact with VAL 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E ALA 3.5 20.4 - - - +
71E CYS* 4.0 1.1 - - - +
74E GLY* 3.4 16.4 - - - -
75E LEU* 3.1 35.7 - - + -
225E VAL* 4.6 5.6 - - + -
226E ASP 4.0 12.3 - - - +
227E GLY* 4.1 13.9 - - - -
229E ASP 3.2 10.0 + - - +
230E ILE 3.8 5.2 - - - +
232E CYS* 1.3 81.1 - - - +
234E ARG* 1.3 62.1 + - - +
236E ALA* 4.0 2.3 - - - +
237E THR* 3.0 29.2 + - - +
253E MET* 5.4 0.2 - - + -
255E LEU* 4.4 15.5 - - + -
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Residues in contact with ARG 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E THR* 3.3 16.8 + - - -
26E VAL 2.9 30.1 + - - -
27E LEU* 4.1 5.9 - - - +
28E THR* 5.4 0.8 - - - +
31E ASP* 4.0 11.3 + - - -
35E TYR* 2.9 40.6 + - + -
74E GLY 3.6 11.0 - - - +
77E ALA* 3.7 27.6 - - + +
230E ILE 3.0 18.4 + - - +
231E LEU* 4.0 24.0 + - - +
232E CYS 3.1 0.4 - - - -
233E VAL* 1.3 77.9 - - - +
235E GLU* 1.3 60.3 + - - +
237E THR* 3.7 1.5 - - - -
238E ARG* 3.0 65.3 + - - +
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Residues in contact with GLU 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ILE* 3.2 31.9 - - + -
21E PRO* 4.1 8.7 - - + +
22E PRO* 3.2 32.5 - - - +
25E THR* 2.8 28.6 + - - -
231E LEU 3.2 8.9 + - - +
232E CYS* 3.2 7.9 + - - +
234E ARG* 1.3 85.6 + - - +
236E ALA* 1.3 56.5 + - - +
238E ARG* 3.3 15.9 + - - +
239E PHE* 2.8 31.0 + - - +
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Residues in contact with ALA 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E CYS* 4.9 0.9 - - - -
21E PRO* 4.4 10.6 - - + +
223E LEU* 4.5 5.9 - - + +
225E VAL* 3.6 33.2 - - + -
232E CYS 2.7 20.8 + - - +
233E VAL* 4.0 3.1 - - - +
235E GLU* 1.3 74.5 - - - +
237E THR* 1.3 56.4 + - - +
239E PHE* 3.5 7.6 + - - +
240E ALA* 2.9 28.9 + - - +
253E MET* 3.7 14.3 - - + +
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Residues in contact with THR 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E LEU* 3.6 23.3 - - - +
78E GLY* 3.5 15.5 - - - +
79E ILE* 3.4 31.6 - - + -
162E LEU* 4.6 8.1 - - + -
190E ILE* 5.9 1.1 - - + -
233E VAL 3.0 22.0 + - - -
234E ARG 3.7 3.4 - - - -
235E GLU 3.2 0.2 - - - -
236E ALA* 1.3 73.0 - - - +
238E ARG* 1.3 58.8 + - - +
240E ALA* 3.7 3.0 - - - +
241E ALA* 2.7 32.9 + - - +
253E MET* 3.5 22.0 - - + +
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Residues in contact with ARG 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ASP* 5.8 0.2 + - - -
35E TYR* 4.8 2.0 + - - -
77E ALA 2.8 26.7 + - - -
78E GLY* 3.6 23.5 - - - -
234E ARG* 3.0 57.7 + - - +
235E GLU* 3.6 16.9 + - - +
237E THR* 1.3 74.4 - - - +
239E PHE* 1.3 65.4 + - - +
241E ALA* 3.9 2.4 - - - +
242E ALA* 3.0 25.1 + - - +
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Residues in contact with PHE 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E LEU* 4.4 13.2 - - + -
19E GLU* 3.7 19.7 - - + -
20E GLY* 3.8 17.9 - - - -
21E PRO* 3.7 25.4 - - + -
22E PRO* 5.2 4.7 - - + -
223E LEU* 3.8 28.0 - - + -
235E GLU 2.8 17.9 + - - +
236E ALA 3.6 2.9 - - - +
238E ARG* 1.3 78.2 - - - +
240E ALA* 1.3 66.7 + - + +
242E ALA* 3.2 6.9 + - + +
243E TYR* 3.0 33.1 + + + +
251E ILE* 4.2 17.7 - - + -
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Residues in contact with ALA 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E ILE* 3.9 22.9 - - + -
223E LEU* 5.3 1.3 - - + -
236E ALA 2.9 18.4 + - - +
237E THR* 3.7 4.3 - - - +
239E PHE* 1.3 81.3 - - + +
241E ALA* 1.3 67.7 + - - +
243E TYR* 3.0 9.0 + - - +
244E CYS* 3.0 23.0 + - - +
251E ILE* 4.1 19.7 - - + -
253E MET* 4.2 9.9 - - - -
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Residues in contact with ALA 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E GLY 4.3 10.8 - - - +
79E ILE* 4.7 3.8 - - + -
160E VAL* 4.2 10.2 - - + +
190E ILE* 3.7 13.0 - - + +
237E THR 2.7 20.4 + - - +
238E ARG* 3.9 3.6 - - - +
240E ALA* 1.3 72.1 - - - +
242E ALA* 1.3 53.6 + - - +
244E CYS* 3.1 3.1 + - - +
245E ARG* 2.8 66.8 + - - +
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Residues in contact with ALA 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E ARG 3.0 14.1 + - - +
239E PHE* 3.3 12.3 - - + +
241E ALA* 1.3 75.8 - - - +
243E TYR* 1.3 65.0 - - - +
245E ARG* 3.2 9.9 + - - +
246E SER* 2.8 26.0 + - - -
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Residues in contact with TYR 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E LEU* 4.0 24.9 - - + +
221E PRO* 3.2 26.0 - - + +
239E PHE* 3.0 24.2 + + + +
240E ALA* 3.4 10.8 - - - +
242E ALA* 1.3 76.9 - - - +
244E CYS* 1.3 63.9 + - - +
246E SER* 3.2 21.4 + - - -
248E LYS* 3.4 53.5 + - + +
249E GLY 3.1 24.0 - - - -
250E PRO 3.4 12.8 + - - -
251E ILE* 4.1 20.6 - - + -
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Residues in contact with CYS 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E VAL* 3.7 18.4 - - + -
188E PRO* 3.9 28.0 - - + +
189E CYS 4.1 7.0 - - - -
190E ILE* 3.6 28.3 - - + -
240E ALA 3.0 9.8 + - - +
241E ALA 3.7 5.6 - - - +
243E TYR* 1.3 72.6 - - - +
245E ARG* 1.3 61.2 + - - +
246E SER 3.1 1.1 - - - -
247E GLY* 2.8 24.1 + - - -
248E LYS 4.1 0.2 + - - -
249E GLY 3.6 22.5 + - - -
251E ILE* 4.2 9.0 - - - -
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Residues in contact with ARG 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E GLY 4.8 1.4 + - - -
79E ILE* 4.7 4.6 - - - +
80E ASN* 3.6 14.9 + - - +
83E ASP* 3.0 38.2 + - - -
158E ASP* 3.1 57.4 + - - +
160E VAL* 3.8 13.8 - - + +
188E PRO* 5.7 0.9 - - - -
241E ALA* 2.8 47.0 + - - +
242E ALA* 3.7 6.4 - - - +
244E CYS* 1.3 66.0 - - - +
246E SER* 1.3 56.0 + - - +
247E GLY* 2.9 13.1 + - - -
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Residues in contact with SER 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E ALA 2.8 16.9 + - - -
243E TYR* 3.2 5.3 + - - -
244E CYS 3.1 0.6 - - - -
245E ARG* 1.3 73.7 - - - +
247E GLY* 1.3 58.9 + - - +
248E LYS* 2.9 35.6 + - - +
18Q GLU* 5.1 5.2 - - - +
19Q GLU* 3.3 40.4 + - - +
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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