Contacts of the helix formed by residues 224 - 241 (chain A) in PDB entry 5DO7
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 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A LEU* 1.3 81.5 - - - +
225A CYS* 1.3 70.0 + - + +
226A MET* 4.1 17.0 - - - +
227A THR* 2.6 34.3 + - - +
228A ALA* 2.8 25.8 + - - +
107B SER* 4.2 22.4 - - - +
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Residues in contact with CYS 225 (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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224A ASP* 1.3 73.4 - - + +
226A MET* 1.3 63.7 + - + +
228A ALA* 4.4 1.8 - - - +
229A ASN* 3.7 22.9 + - - +
253A ARG* 2.7 43.0 + - - +
106B SER* 3.9 27.1 - - - -
107B SER* 3.8 21.5 + - - -
287B THR* 6.2 0.4 - - - -
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Residues in contact with MET 226 (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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224A ASP* 3.2 17.8 + - - +
225A CYS* 1.3 81.5 - - + +
227A THR* 1.3 75.3 + - - +
228A ALA 3.6 0.2 + - - -
229A ASN* 3.6 4.4 + - - +
230A GLN* 3.3 27.4 + - - +
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Residues in contact with THR 227 (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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196A GLY* 3.5 32.1 + - - -
200A ARG* 6.0 0.9 - - - +
223A LEU* 3.8 14.8 - - + -
224A ASP* 2.6 39.9 + - - -
226A MET* 1.3 82.4 - - - +
228A ALA* 1.3 67.0 + - - +
230A GLN* 2.8 21.7 + - + +
231A ILE* 2.9 20.5 + - + +
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Residues in contact with ALA 228 (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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220A THR* 4.6 20.7 - - + +
223A LEU* 4.1 22.5 - - + +
224A ASP 2.8 22.4 + - - +
225A CYS* 4.4 1.6 - - - +
227A THR* 1.3 70.2 - - - +
229A ASN* 1.3 71.0 + - - +
231A ILE* 2.8 8.0 + - - +
232A VAL* 2.8 26.3 + - - +
253A ARG* 6.3 1.3 - - - +
256A LEU* 6.1 1.1 - - + -
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Residues in contact with ASN 229 (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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225A CYS 3.7 13.6 + - - +
226A MET 3.6 7.1 + - - +
227A THR 3.2 0.2 - - - -
228A ALA* 1.3 77.4 - - - +
230A GLN* 1.3 64.8 + - - +
232A VAL* 2.9 11.4 + - - +
233A VAL* 2.8 31.8 + - + +
253A ARG* 4.4 8.3 - - - +
255A GLU* 3.5 22.6 + - - +
256A LEU* 4.2 23.5 - - - +
259A LEU* 6.3 1.0 - - - +
319B ASP* 5.8 1.0 + - - -
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Residues in contact with GLN 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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200A ARG* 3.1 31.2 - - - +
226A MET* 3.3 19.5 + - - +
227A THR* 2.8 21.6 + - + +
229A ASN* 1.3 74.5 - - - +
231A ILE* 1.3 59.6 + - - +
233A VAL* 3.4 14.0 - - + +
234A LEU* 3.3 21.4 - - + +
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Residues in contact with ILE 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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196A GLY 4.0 19.7 - - - +
199A ARG* 4.4 16.4 - - + -
200A ARG* 4.1 26.2 - - + +
203A ILE* 5.1 11.9 - - + -
219A PRO* 4.2 20.0 - - + +
220A THR* 5.9 0.9 - - + -
223A LEU* 3.9 21.1 - - + -
227A THR* 2.9 20.8 + - + +
228A ALA* 2.8 7.8 + - - +
230A GLN* 1.3 75.0 - - + +
232A VAL* 1.3 70.0 + - + +
234A LEU* 2.8 20.7 + - + +
235A LEU* 3.2 20.3 + - + +
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Residues in contact with VAL 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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220A THR* 3.6 31.2 - - + -
228A ALA 2.8 12.4 + - - +
229A ASN* 2.9 9.6 + - - +
231A ILE* 1.3 75.1 - - + +
233A VAL* 1.3 67.5 + - - +
235A LEU* 2.8 31.4 + - + +
236A VAL* 3.1 24.0 + - + +
247A LEU* 5.8 2.2 - - + -
249A ILE* 6.2 0.4 - - + -
256A LEU* 4.0 18.6 - - + -
259A LEU* 4.5 20.4 - - + -
260A PHE* 4.9 17.9 - - + -
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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
----------------------------------------------------------
229A ASN* 2.8 24.8 + - + +
230A GLN* 3.4 12.6 - - + +
232A VAL* 1.3 72.3 - - + +
234A LEU* 1.3 60.8 + - + +
236A VAL* 2.8 32.2 + - - +
237A GLU* 2.8 37.5 + - + +
259A LEU* 6.5 1.8 - - + -
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Residues in contact with LEU 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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175A LEU* 4.3 20.2 - - + +
176A SER* 4.8 9.9 - - - +
200A ARG* 3.2 46.2 - - + +
203A ILE* 5.5 7.4 - - + -
230A GLN* 3.3 18.8 - - + +
231A ILE* 2.8 18.5 + - + +
233A VAL* 1.3 86.4 - - + +
235A LEU* 1.3 64.1 + - - +
237A GLU* 3.3 13.0 + - + +
238A LEU* 3.0 30.8 + - + +
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Residues in contact with LEU 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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81A ILE* 5.8 0.9 - - + -
203A ILE* 5.4 3.6 - - + +
216A PHE* 3.4 53.4 - - + -
219A PRO* 4.2 11.0 - - + -
231A ILE* 3.2 12.9 + - + +
232A VAL* 2.8 27.4 + - + +
234A LEU* 1.3 76.2 - - - +
236A VAL* 1.3 65.2 + - + +
238A LEU* 2.8 24.2 + - + +
239A ALA 3.0 8.7 + - - -
245A VAL* 4.1 21.2 - - + +
247A LEU* 3.4 34.5 - - + -
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Residues in contact with VAL 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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81A ILE* 4.4 22.6 - - + +
232A VAL* 3.2 30.5 - - + +
233A VAL* 2.8 14.5 + - - +
235A LEU* 1.3 72.7 - - + +
237A GLU* 1.3 64.5 + - + +
239A ALA* 2.8 15.2 + - + +
240A ARG* 2.8 18.1 + - - +
259A LEU* 4.7 20.0 - - + +
260A PHE* 6.0 2.2 - - + -
261A ASP* 5.6 2.5 - - - +
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Residues in contact with GLU 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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233A VAL* 2.8 40.5 + - + +
234A LEU* 3.6 15.0 - - + +
235A LEU 3.2 0.2 - - - -
236A VAL* 1.3 73.1 - - + +
238A LEU* 1.3 57.2 + - + +
240A ARG* 2.7 45.2 + - - +
241A ARG* 2.8 16.7 + - + +
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Residues in contact with LEU 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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174A GLU* 4.2 10.5 - - + +
175A LEU* 4.9 14.1 - - + -
203A ILE* 4.5 16.8 - - + -
207A LEU* 3.5 32.3 - - + -
214A MET* 4.0 18.2 - - + -
216A PHE* 4.7 4.0 - - + -
234A LEU* 3.0 24.7 + - + +
235A LEU* 2.8 16.0 + - + +
237A GLU* 1.3 75.3 - - + +
239A ALA* 1.3 56.3 + - - +
241A ARG* 2.8 25.4 + - - +
243A ARG* 3.3 38.0 - - + +
245A VAL* 5.0 2.7 - - + -
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Residues in contact with ALA 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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79A GLY* 2.9 42.0 - - - +
80A GLN 3.5 18.6 - - - +
81A ILE* 4.5 3.4 - - + -
235A LEU 3.0 4.8 + - - +
236A VAL* 2.8 21.6 + - + +
238A LEU* 1.3 72.9 - - - +
240A ARG* 1.3 64.1 + - - +
242A ASN 3.2 6.8 + - - -
243A ARG 4.0 9.9 - - - -
245A VAL* 3.7 12.4 - - + +
261A ASP* 5.6 0.2 - - - +
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Residues in contact with ARG 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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79A GLY 4.6 0.9 + - - -
236A VAL 2.8 7.4 + - - +
237A GLU* 2.7 39.1 + - - +
239A ALA* 1.3 72.1 - - - +
241A ARG* 1.3 81.1 + - + +
242A ASN* 2.9 7.3 + - - +
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Residues in contact with ARG 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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174A GLU* 4.1 24.7 - - + +
212A LYS* 5.5 2.1 + - - +
237A GLU* 2.8 17.7 + - + +
238A LEU* 2.8 14.2 + - - +
240A ARG* 1.3 105.1 + - + +
242A ASN* 1.3 69.4 + - - +
243A ARG* 3.8 12.9 + - - +
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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