Contacts of the helix formed by residues 229 - 246 (chain A) in PDB entry 2OZL
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ILE* 4.0 7.2 - - - +
10A LYS* 5.0 7.4 + - - +
70A ALA* 4.0 2.5 - - - -
226A ASP* 3.4 19.7 + - - +
228A MET* 1.3 78.3 - - - +
230A ILE* 1.3 63.6 + - - +
231A LEU* 2.9 10.6 + - - +
232A CYS* 3.1 22.6 + - + +
233A VAL* 3.0 24.3 + - - +
290A LEU* 4.8 8.7 - - + -
294A ARG* 2.7 49.0 + - - -
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Residues in contact with ILE 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A TYR* 4.4 19.5 - - + -
39A MET* 4.2 16.4 - - + -
70A ALA* 3.7 20.7 - - + +
73A VAL* 3.6 21.8 - - + -
74A GLY* 3.1 41.5 - - - +
77A ALA* 5.4 0.9 - - + -
228A MET 3.8 1.2 + - - -
229A ASP* 1.3 72.8 + - - +
231A LEU* 1.3 75.0 + - + +
233A VAL* 3.4 1.9 + - - +
234A ARG* 3.0 27.3 + - + +
287A PRO 5.3 2.8 + - - +
291A LEU* 4.0 36.1 - - + +
294A ARG* 4.7 2.7 - - - +
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Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.9 36.8 - - + -
9A ILE* 3.9 11.0 - - + -
25A THR* 4.2 12.1 - - + -
27A LEU* 3.7 32.1 - - + -
35A TYR* 4.7 7.2 - - + -
229A ASP* 2.9 6.9 + - - +
230A ILE* 1.3 85.1 - - + +
232A CYS* 1.3 61.6 + - - +
234A ARG* 3.3 24.9 + - - +
235A GLU* 2.9 33.8 + - - +
291A LEU* 5.2 0.9 - - + -
294A ARG* 3.5 23.3 - - - +
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Residues in contact with CYS 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.9 19.7 - - + +
10A LYS* 3.9 24.5 - - - +
12A CYS* 4.7 6.7 - - - -
225A VAL* 3.5 21.8 - - - -
226A ASP* 3.8 18.4 - - + +
229A ASP* 3.1 31.8 + - + +
231A LEU* 1.3 77.4 - - - +
233A VAL* 1.3 63.3 + - - +
235A GLU* 3.8 1.6 - - - +
236A ALA* 3.0 23.6 + - - +
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ALA 3.7 22.9 - - - +
71A CYS* 4.1 5.6 - - - +
74A GLY 3.6 22.0 - - - -
75A LEU* 3.6 22.0 - - + +
225A VAL* 4.2 6.1 - - + -
226A ASP 3.7 14.4 - - - +
227A GLY* 4.0 13.0 - - - -
229A ASP 3.0 17.7 + - - +
230A ILE 3.7 4.5 - - - +
232A CYS* 1.3 76.7 - - - +
234A ARG* 1.3 58.7 + - - +
236A ALA* 3.4 2.0 + - - +
237A THR* 2.7 32.4 + - - -
255A LEU* 4.4 14.6 - - + -
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Residues in contact with ARG 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A THR* 3.3 18.0 + - - +
26A VAL 2.9 30.3 + - - -
27A LEU* 4.3 5.5 - - - +
31A ASP* 4.0 12.1 + - - -
35A TYR* 3.0 41.0 + - - -
74A GLY* 3.5 14.1 + - - +
77A ALA* 3.8 21.5 - - + +
78A GLY* 4.3 0.2 - - - -
230A ILE* 3.0 18.7 + - + +
231A LEU* 3.6 25.1 + - + +
233A VAL* 1.3 77.1 - - - +
235A GLU* 1.3 60.8 + - - +
237A THR* 3.3 2.3 + - - -
238A ARG* 3.0 70.4 + - - +
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Residues in contact with GLU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.4 32.8 - - + -
21A PRO* 4.0 11.4 - - + +
22A PRO* 3.3 26.5 - - + +
25A THR* 2.8 31.9 + - + -
231A LEU 2.9 15.2 + - - +
232A CYS 3.8 2.5 - - - +
234A ARG* 1.3 85.6 + - - +
236A ALA* 1.3 65.6 + - - +
238A ARG* 3.4 19.4 + - - +
239A PHE* 3.1 22.9 + - - +
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Residues in contact with ALA 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A CYS* 4.5 2.7 - - - -
21A PRO* 3.8 14.7 - - + +
223A LEU* 4.0 8.9 - - + +
225A VAL* 3.6 31.6 - - + -
232A CYS 3.0 18.3 + - - +
233A VAL* 3.9 2.9 - - - +
235A GLU* 1.3 74.4 - - - +
237A THR* 1.3 58.5 + - - +
239A PHE* 3.3 4.3 + - - +
240A ALA* 2.9 29.8 + - - +
253A MET* 3.8 10.5 - - - +
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Residues in contact with THR 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLY 4.5 0.9 - - - -
75A LEU* 3.1 50.5 - - + +
78A GLY* 3.8 8.3 - - - +
79A ILE* 3.8 19.1 - - + -
162A LEU* 4.6 5.8 - - + -
190A ILE* 4.9 2.6 - - + +
233A VAL* 2.7 22.7 + - - +
234A ARG* 3.6 5.6 - - - -
236A ALA* 1.3 75.4 - - - +
238A ARG* 1.3 59.1 + - - +
240A ALA* 3.8 1.8 - - - +
241A ALA* 2.8 29.9 + - + +
253A MET* 3.7 10.7 - - + +
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Residues in contact with ARG 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL 5.6 0.2 + - - -
31A ASP* 5.3 3.0 + - - -
35A TYR* 4.4 4.2 + - - -
77A ALA 3.4 22.0 + - - -
78A GLY* 3.8 19.4 - - - +
234A ARG* 3.0 60.3 + - - +
235A GLU* 3.4 19.8 + - - +
237A THR* 1.3 76.1 - - - +
239A PHE* 1.3 57.2 + - - +
241A ALA* 4.0 2.0 - - - +
242A ALA* 3.0 31.0 + - - +
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Residues in contact with PHE 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 4.3 15.9 - - + -
19A GLU* 3.5 21.1 - - + -
20A GLY* 3.6 20.9 - - - -
21A PRO* 3.6 32.1 - - + -
22A PRO* 5.4 3.1 - - + -
223A LEU* 4.3 6.5 - - + -
235A GLU 3.1 13.2 + - - +
236A ALA 3.4 9.2 - - - +
238A ARG* 1.3 74.3 - - - +
240A ALA* 1.3 65.7 + - - +
242A ALA* 3.4 5.5 + - - +
243A TYR* 2.9 36.0 + + + +
251A ILE* 4.1 21.1 - - + -
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Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ILE* 3.8 19.7 - - + -
223A LEU* 5.2 1.6 - - + -
236A ALA 2.9 16.7 + - - +
237A THR* 3.9 3.6 - - - +
239A PHE* 1.3 79.1 - - + +
241A ALA* 1.3 61.5 + - - +
243A TYR* 3.2 7.7 + - - +
244A CYS* 2.9 32.1 + - - -
251A ILE* 3.9 24.2 - - + +
253A MET* 4.3 11.4 - - + -
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Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A GLY 4.3 10.3 - - - +
79A ILE* 4.9 4.3 - - + -
160A VAL* 4.1 7.3 - - + +
190A ILE* 3.7 15.8 - - + +
237A THR 2.8 18.3 + - - +
238A ARG* 4.0 3.4 - - - +
240A ALA* 1.3 76.6 - - - +
242A ALA* 1.3 57.5 + - - +
244A CYS* 3.2 3.5 + - - +
245A ARG* 2.9 58.9 + - - +
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Residues in contact with ALA 242 (chain A).
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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238A ARG 3.0 20.3 + - - +
239A PHE* 3.7 5.2 - - - +
241A ALA* 1.3 73.5 - - - +
243A TYR* 1.3 66.2 + - - +
245A ARG* 3.4 9.8 + - - +
246A SER* 3.1 24.6 + - - -
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Residues in contact with TYR 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 4.2 20.6 - - + +
221A PRO* 3.2 25.2 - - + +
239A PHE* 2.9 24.0 + + + +
240A ALA* 3.3 12.3 - - - +
241A ALA 3.2 0.2 - - - -
242A ALA* 1.3 77.5 - - - +
244A CYS* 1.3 62.4 + - - +
246A SER* 2.5 25.9 + - - -
248A LYS* 3.6 48.0 + - + +
249A GLY 3.4 21.8 - - - -
250A PRO 3.6 11.6 + - - -
251A ILE* 4.0 22.4 - - + -
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Residues in contact with CYS 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A VAL* 3.8 18.6 - - + -
188A PRO* 3.9 30.7 - - + +
189A CYS 4.0 6.3 - - - -
190A ILE* 3.6 28.7 - - + -
240A ALA 2.9 13.4 + - - +
241A ALA 3.7 4.3 - - - +
243A TYR* 1.3 77.6 - - - +
245A ARG* 1.3 61.6 + - - +
247A GLY* 3.1 14.6 + - - -
248A LYS 4.3 0.4 + - - +
249A GLY 3.4 25.1 + - - -
251A ILE* 4.0 7.9 - - - -
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Residues in contact with ARG 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A GLY 5.0 1.0 + - - -
79A ILE* 4.6 3.4 - - - +
80A ASN* 3.7 21.0 + - - +
83A ASP* 2.8 43.4 + - - -
158A ASP* 3.1 51.3 + - - +
160A VAL* 3.8 18.3 - - + +
188A PRO* 5.7 0.2 - - - -
241A ALA* 2.9 42.5 + - - +
242A ALA* 4.0 7.7 - - - +
244A CYS* 1.3 73.6 - - - +
246A SER* 1.3 59.6 + - - +
247A GLY* 3.1 1.9 + - - -
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Residues in contact with SER 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ALA 3.1 11.8 + - - -
243A TYR* 2.5 23.3 + - - -
245A ARG* 1.3 77.9 - - - +
247A GLY* 1.3 58.6 - - - +
248A LYS* 3.1 35.0 + - - +
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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