Contacts of the helix formed by residues 229 - 246 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9O ILE* 3.4 14.9 - - - +
10O LYS 4.8 0.3 + - - -
226O ASP* 3.5 11.4 + - - +
227O GLY 3.5 0.2 - - - -
228O MET* 1.3 75.7 - - - +
230O ILE* 1.3 55.4 + - - +
231O LEU* 2.2 59.7 + - - +
232O CYS* 2.9 39.5 + - - -
233O VAL* 3.1 15.7 + - - +
290O LEU* 4.7 12.7 - - + +
294O ARG* 3.0 31.8 + - - -
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Residues in contact with ILE 230 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O TYR* 4.4 26.7 - - + -
39O MET* 4.1 17.7 - - - -
70O ALA* 3.8 15.0 - - + +
73O VAL* 4.2 12.8 - - + +
74O GLY* 3.3 30.5 - - - +
77O ALA* 5.4 0.4 - - + -
228O MET 3.2 6.6 + - - +
229O ASP* 1.3 71.6 - - - +
231O LEU* 1.3 67.0 - - + +
234O ARG* 3.6 18.7 + - + +
287O PRO 4.6 7.0 - - - +
290O LEU* 5.8 1.6 - - + -
291O LEU* 4.0 37.0 - - + +
294O ARG* 5.1 2.0 - - - +
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Residues in contact with LEU 231 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7O PHE* 4.3 19.3 - - + -
9O ILE* 3.7 11.9 - - + -
25O THR* 4.8 8.5 - - + +
27O LEU* 4.2 15.7 - - + -
35O TYR* 5.3 2.2 - - + -
229O ASP* 2.2 31.4 + - - +
230O ILE* 1.3 85.3 - - + +
232O CYS* 1.3 65.1 + - - +
233O VAL 2.8 0.9 - - - -
234O ARG* 3.5 29.8 - - - +
235O GLU* 2.9 26.7 + - - +
291O LEU* 5.0 6.5 - - + -
294O ARG* 2.2 47.3 - - - +
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Residues in contact with CYS 232 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9O ILE* 3.7 20.6 - - - +
10O LYS* 3.9 19.7 - - - +
12O CYS* 5.6 2.7 - - - -
225O VAL* 3.5 20.8 - - + +
226O ASP* 3.6 23.1 - - - +
229O ASP* 2.9 28.9 + - - -
231O LEU* 1.3 77.9 - - - +
233O VAL* 1.3 60.7 + - - +
235O GLU* 2.9 8.5 - - - +
236O ALA* 2.8 30.3 + - - +
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Residues in contact with VAL 233 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70O ALA 3.6 25.4 - - - +
71O CYS* 4.4 5.6 - - - +
74O GLY* 4.4 0.2 - - - -
75O LEU* 3.9 31.6 - - + +
225O VAL* 4.2 9.0 - - + -
226O ASP 3.2 19.3 - - - +
227O GLY* 4.1 13.0 - - - +
229O ASP 3.1 17.7 - - - +
230O ILE 4.3 1.8 - - - -
231O LEU 2.8 0.6 - - - -
232O CYS* 1.3 74.1 - - - +
234O ARG* 1.3 63.3 + - - +
235O GLU 2.8 1.2 + - - -
236O ALA* 3.3 1.3 + - - +
237O THR* 2.3 31.5 + - - +
253O MET* 5.7 0.2 - - + -
255O LEU* 4.6 10.8 - - + -
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Residues in contact with ARG 234 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25O THR* 4.0 9.4 + - - +
26O VAL 3.1 24.7 + - - -
27O LEU* 4.2 10.8 - - - +
28O THR* 5.6 1.8 - - - +
31O ASP* 5.5 4.5 + - - +
35O TYR* 3.7 32.2 + - - -
74O GLY 3.3 19.9 + - - +
77O ALA* 3.8 11.0 - - + +
78O GLY* 4.1 0.6 - - - +
230O ILE 3.6 18.3 + - - +
231O LEU* 3.4 32.7 + - - +
233O VAL* 1.3 80.5 - - - +
235O GLU* 1.3 66.9 + - + +
237O THR* 3.2 3.3 - - - -
238O ARG* 2.9 69.4 + - - +
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Residues in contact with GLU 235 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O ILE* 3.4 29.6 - - + -
21O PRO* 4.3 6.0 - - + +
22O PRO* 3.4 34.3 - - - +
25O THR* 3.6 27.3 + - + -
231O LEU 2.9 11.5 + - - +
232O CYS* 2.9 11.2 - - - +
233O VAL 2.8 3.2 + - - -
234O ARG* 1.3 72.9 - - + +
236O ALA* 1.3 72.6 + - - +
238O ARG* 3.1 27.2 + - - +
239O PHE* 2.9 16.5 + - - +
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Residues in contact with ALA 236 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12O CYS* 4.8 0.2 - - - -
21O PRO* 4.2 12.1 - - + +
223O LEU* 4.0 9.9 - - + -
225O VAL* 3.7 31.2 - - + -
232O CYS 2.8 15.4 + - - +
233O VAL* 3.8 2.7 - - - +
235O GLU* 1.3 70.1 - - - +
237O THR* 1.3 74.3 + - - +
239O PHE* 2.4 23.7 + - - -
240O ALA* 2.7 10.9 + - - -
253O MET* 3.8 11.9 - - + -
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Residues in contact with THR 237 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75O LEU* 3.7 39.9 - - + +
78O GLY* 3.8 21.5 - - - -
79O ILE* 4.2 10.5 - - + -
162O LEU* 4.5 4.3 - - + -
190O ILE* 5.3 3.4 - - + -
233O VAL* 2.3 28.6 + - - +
234O ARG* 3.2 8.4 - - - -
236O ALA* 1.3 88.0 - - - +
238O ARG* 1.3 62.5 - - - +
240O ALA* 2.6 17.3 + - - -
241O ALA* 2.8 14.2 + - + -
253O MET* 4.2 7.7 - - + +
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Residues in contact with ARG 238 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25O THR* 4.7 1.8 + - - -
35O TYR* 4.9 1.8 + - - -
77O ALA 3.3 18.7 + - - -
78O GLY* 3.6 26.7 + - - +
234O ARG* 2.9 58.0 + - - +
235O GLU* 3.1 22.8 + - - +
236O ALA 3.0 0.6 + - - -
237O THR* 1.3 77.7 - - - +
239O PHE* 1.3 56.7 + - - +
241O ALA* 4.0 2.5 - - - +
242O ALA* 2.9 31.9 + - - +
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Residues in contact with PHE 239 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17O LEU* 4.1 26.9 - - + -
19O GLU 3.7 17.9 - - - -
20O GLY* 3.3 29.2 - - - -
21O PRO* 3.8 18.4 - - + -
22O PRO* 5.1 5.2 - - + -
223O LEU* 3.8 27.4 - - + -
235O GLU* 2.9 10.6 + - - +
236O ALA 2.4 21.4 + - - +
238O ARG* 1.3 70.4 - - - +
240O ALA* 1.3 63.1 + - - -
242O ALA* 3.5 5.0 + - + +
243O TYR* 3.1 29.8 + + + +
251O ILE* 4.5 7.0 - - + -
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Residues in contact with ALA 240 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190O ILE* 3.9 27.8 - - + -
223O LEU* 4.9 2.2 - - + -
236O ALA 2.7 7.0 + - - +
237O THR* 2.6 12.8 + - - +
239O PHE* 1.3 76.6 - - + +
241O ALA* 1.3 67.4 + - - +
242O ALA 3.1 0.5 + - - -
243O TYR* 3.1 9.3 + - - +
244O CYS* 2.9 23.7 + - - +
251O ILE* 4.3 17.3 - - + -
253O MET* 4.3 15.3 - - - -
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Residues in contact with ALA 241 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78O GLY 4.0 14.1 - - - +
79O ILE* 4.7 4.7 - - + -
160O VAL* 4.3 5.8 - - + +
190O ILE* 3.5 18.2 - - + +
237O THR 2.8 17.9 + - - +
238O ARG* 4.0 4.3 - - - +
240O ALA* 1.3 73.6 - - - +
242O ALA* 1.3 55.9 + - - +
244O CYS* 3.3 4.8 + - - +
245O ARG* 3.1 58.9 + - - +
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Residues in contact with ALA 242 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238O ARG 2.9 20.7 + - - +
239O PHE* 3.7 6.1 - - - +
240O ALA 3.1 0.2 - - - -
241O ALA* 1.3 72.3 - - - +
243O TYR* 1.3 65.4 + - - +
245O ARG* 3.1 11.9 + - - +
246O SER* 3.1 22.1 + - - -
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Residues in contact with TYR 243 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17O LEU* 4.0 26.9 - - + +
221O PRO* 3.3 24.7 - - + +
239O PHE* 3.1 22.7 + + + +
240O ALA* 3.1 11.6 + - - +
242O ALA* 1.3 74.3 - - - +
244O CYS* 1.3 67.1 + - - +
246O SER* 3.1 23.4 + - - -
248O LYS* 3.3 65.5 + - + +
249O GLY 3.8 15.7 - - - -
250O PRO 3.8 10.0 + - - -
251O ILE* 4.1 22.0 - - + -
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Residues in contact with CYS 244 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160O VAL* 3.9 15.3 - - + -
188O PRO* 4.0 16.4 - - + +
189O CYS 4.0 18.8 - - - -
190O ILE* 3.9 15.5 - - + -
240O ALA 2.9 11.5 + - - +
241O ALA* 3.5 11.0 - - - +
242O ALA 3.2 0.2 - - - -
243O TYR* 1.3 71.9 - - - +
245O ARG* 1.3 63.7 + - - +
246O SER 3.1 2.1 + - - -
247O GLY* 3.7 9.0 + - - -
248O LYS 4.8 0.3 + - - -
249O GLY 3.4 24.7 + - - +
251O ILE* 3.7 25.4 - - - -
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Residues in contact with ARG 245 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78O GLY 4.5 7.5 + - - -
79O ILE* 4.6 0.4 - - - +
80O ASN* 3.9 15.7 + - - +
83O ASP* 3.0 40.6 + - - -
158O ASP* 3.2 48.5 + - - +
159O GLU* 4.3 0.2 - - - +
160O VAL* 3.7 19.9 - - + +
188O PRO* 5.8 0.2 - - - -
241O ALA* 3.1 39.8 + - - +
242O ALA* 3.1 9.2 + - - +
244O CYS* 1.3 75.3 - - - +
246O SER* 1.3 62.1 + - - +
247O GLY 3.1 4.9 + - - -
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Residues in contact with SER 246 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242O ALA 3.1 11.4 + - - -
243O TYR* 3.1 16.2 + - - -
244O CYS 3.1 1.8 - - - -
245O ARG* 1.3 78.0 - - - +
247O GLY* 1.3 56.9 + - - +
248O LYS* 3.3 25.7 + - - +
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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
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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