Contacts of the helix formed by residues 244 - 261 (chain B) 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 244 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A SER* 3.3 31.1 + - - -
306A SER* 5.6 1.7 + - - -
308A ASP* 2.5 32.5 - - - +
243B LEU* 1.3 74.8 - - - +
245B SER* 1.3 77.2 + - - +
246B PHE* 4.2 8.0 - - + +
247B THR* 2.8 18.0 + - - +
248B ALA* 2.8 19.7 + - - -
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Residues in contact with SER 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ASP* 3.4 12.6 + - - -
243B LEU 4.1 1.0 + - - -
244B ASP* 1.3 79.2 + - - +
246B PHE* 1.3 69.0 + - - +
248B ALA* 3.0 20.8 + - - +
249B HIS* 3.2 19.9 + - - -
273B ARG* 3.0 43.1 + - - +
275B ASP* 4.5 7.0 - - - -
276B ILE* 4.8 2.6 - - - +
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Residues in contact with PHE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ASP 5.7 2.9 - - - -
306A SER* 4.7 9.2 - - - -
308A ASP* 3.1 57.0 - - + -
309A THR 4.4 0.2 - - - -
310A GLN* 3.8 30.1 - - + -
314A ARG* 3.8 46.2 + - + -
318A THR* 4.3 15.3 - - + -
321A ARG* 6.1 1.1 - - - -
244B ASP* 4.3 9.8 - - + +
245B SER* 1.3 84.4 + - - +
247B THR* 1.3 60.6 + - - +
249B HIS* 3.8 12.0 + - - +
250B ASN* 3.1 20.6 + - - +
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Residues in contact with THR 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ASP* 6.2 0.2 - - - -
310A GLN* 3.4 25.0 + - - +
216B GLY* 4.4 8.7 - - - -
220B ARG* 4.0 16.8 - - - +
243B LEU* 4.0 21.3 - - + -
244B ASP* 2.8 23.4 + - - +
246B PHE* 1.3 73.1 - - - +
248B ALA* 1.3 64.8 + - - -
249B HIS 3.2 2.5 - - - -
250B ASN* 2.8 9.1 + - + +
251B LEU* 2.8 21.1 + - - +
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Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B THR* 3.9 28.7 - - + +
243B LEU* 4.5 9.7 - - + +
244B ASP 2.8 16.6 + - - +
245B SER* 3.0 17.4 + - - +
247B THR* 1.3 70.2 - - - +
249B HIS* 1.3 54.6 + - - +
251B LEU* 3.1 7.6 + - - +
252B VAL* 2.8 39.0 + - - +
276B ILE* 4.1 12.8 - - + -
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Residues in contact with HIS 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ASP* 6.0 0.7 - - - -
314A ARG* 5.6 5.9 + - - -
245B SER 3.2 9.3 + - - -
246B PHE* 3.8 13.1 + - - +
248B ALA* 1.3 77.2 - - - +
250B ASN* 1.3 61.6 + - - +
252B VAL* 3.4 6.5 - - - +
253B LYS* 2.8 42.6 + - - +
275B ASP* 2.8 47.9 + - + +
276B ILE* 4.2 12.5 - - + +
279B LEU* 3.8 23.0 - - + +
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Residues in contact with ASN 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A GLN* 3.2 49.1 - - - +
314A ARG* 4.9 8.4 + - - +
23B LEU* 3.4 27.7 - - + +
196B ARG* 4.9 3.3 + - - -
220B ARG* 3.0 13.4 + - - +
246B PHE* 3.1 22.0 + - - -
247B THR* 2.8 10.5 + - - +
249B HIS* 1.3 81.3 - - - +
251B LEU* 1.3 51.2 + - - +
253B LYS* 4.3 6.3 - - - +
254B THR* 2.6 28.5 + - - -
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LEU* 6.4 0.4 - - + -
216B GLY 5.6 0.4 - - - +
219B ARG* 4.1 13.7 - - + -
220B ARG* 3.7 31.8 - - + +
223B ILE* 4.1 18.8 - - + -
239B PRO* 3.9 39.3 - - + +
240B THR* 4.4 6.1 - - + +
243B LEU* 4.1 18.6 - - + -
247B THR 2.8 10.4 + - - +
248B ALA 3.5 6.5 - - - +
250B ASN* 1.3 76.1 - - - +
252B VAL* 1.3 63.1 + - - +
253B LYS 3.1 1.1 - - - -
254B THR* 2.8 24.2 + - - -
255B LEU* 2.8 20.9 + - + +
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B MET* 4.6 7.6 - - + +
239B PRO* 6.3 0.7 - - + -
240B THR* 5.0 9.0 - - + -
248B ALA 2.8 17.8 + - - +
249B HIS* 3.4 12.1 - - - +
251B LEU* 1.3 74.2 - - + +
253B LYS* 1.3 60.1 + - - +
255B LEU* 3.2 14.4 + - + +
256B SER* 2.8 27.5 + - - -
267B ILE* 4.2 25.1 - - + -
269B LEU* 5.8 2.2 - - + -
276B ILE* 4.2 26.5 - - + -
279B LEU* 3.8 29.3 - - + +
280B PHE* 5.1 5.8 - - + -
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Residues in contact with LYS 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 3.1 48.8 - - + +
196B ARG* 5.8 4.7 - - - +
249B HIS* 2.8 21.5 + - - +
250B ASN* 4.6 5.8 - - - +
252B VAL* 1.3 76.7 - - - +
254B THR* 1.3 54.5 + - - +
256B SER* 3.4 8.9 + - - -
257B ARG* 2.8 30.9 + - - +
279B LEU* 4.3 28.7 - - + -
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Residues in contact with THR 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B GLU* 4.1 5.1 - - - +
195B LEU* 3.6 35.0 - - + +
196B ARG* 3.4 33.0 + - - +
220B ARG* 3.8 10.2 + - + -
250B ASN 2.6 24.9 + - - -
251B LEU* 2.8 18.9 + - + -
253B LYS* 1.3 71.2 - - - +
255B LEU* 1.3 61.4 + - - +
257B ARG* 3.3 6.6 - - + +
258B LEU* 2.8 30.0 + - - +
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B MET* 4.7 7.0 - - - -
195B LEU* 6.3 1.8 - - + -
223B ILE* 4.0 22.2 - - + -
234B LEU* 5.1 1.6 - - + -
236B LEU* 3.2 38.1 - - + -
239B PRO* 4.0 18.8 - - + -
251B LEU* 2.8 23.7 + - + +
252B VAL* 3.3 21.5 - - + +
254B THR* 1.3 75.0 - - + +
256B SER* 1.3 59.4 + - - +
258B LEU* 3.4 19.2 - - + +
259B ALA* 2.8 26.9 + - - +
265B VAL* 4.0 11.7 - - + +
267B ILE* 4.1 11.2 - - + -
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Residues in contact with SER 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B MET* 4.5 13.2 - - - +
252B VAL 2.8 14.7 + - - -
253B LYS* 3.5 14.1 - - - -
254B THR 3.3 0.2 - - - -
255B LEU* 1.3 73.0 - - - +
257B ARG* 1.3 53.4 + - - +
259B ALA* 2.9 12.4 + - - +
260B LYS* 2.8 41.0 + - - +
279B LEU* 4.6 16.6 + - - +
281B ASP* 5.8 3.3 - - - +
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Residues in contact with ARG 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU 5.4 1.0 + - - -
24B GLN 2.9 16.6 + - - +
25B ASP* 2.4 40.1 + - - +
26B ARG* 3.9 4.2 - - + +
27B LEU* 3.6 30.5 - - + +
28B PHE* 6.0 0.6 - - - -
193B ALA 5.1 1.6 + - - -
194B GLU* 2.9 28.7 + - - +
196B ARG* 3.0 51.8 - - - +
253B LYS 2.8 18.6 + - - +
254B THR* 3.2 9.4 + - - +
256B SER* 1.3 68.3 - - - +
258B LEU* 1.3 69.3 + - - +
260B LYS* 2.8 23.5 + - + +
261B GLY 3.3 5.9 + - - -
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Residues in contact with LEU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B SER* 5.1 1.5 - - - +
194B GLU* 4.1 24.3 + - + +
195B LEU* 4.9 6.1 - - + -
223B ILE* 4.8 5.8 - - + -
227B LEU* 3.6 31.0 - - + -
234B LEU* 3.5 29.6 - - + -
254B THR 2.8 15.8 + - - +
255B LEU* 3.4 16.6 - - + +
257B ARG* 1.3 71.2 - - - +
259B ALA* 1.3 58.3 + - - +
261B GLY* 2.8 20.4 + - - -
263B ARG* 2.9 55.4 - - + +
265B VAL* 5.2 1.3 - - + -
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Residues in contact with ALA 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLY* 3.2 23.7 - - - +
100B MET* 4.1 13.2 - - + +
255B LEU 2.8 17.0 + - - +
256B SER* 2.9 18.1 + - - +
258B LEU* 1.3 72.5 - - - +
260B LYS* 1.3 52.2 + - - +
261B GLY 2.4 21.8 - - - +
263B ARG 3.3 8.5 - - - +
265B VAL* 3.4 25.7 - - + +
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Residues in contact with LYS 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ARG* 6.1 3.6 - - - +
27B LEU* 4.4 8.5 - - + -
98B GLY* 4.7 3.6 - - - -
256B SER* 2.8 25.5 + - - +
257B ARG* 2.8 12.6 + - + +
259B ALA* 1.3 65.5 - - - +
261B GLY* 1.3 69.4 + - - +
262B ASN* 5.0 1.4 - - - +
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Residues in contact with GLY 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 3.8 11.0 - - - +
29B SER 4.5 0.2 - - - -
30B SER* 3.4 21.8 - - - -
98B GLY* 4.0 4.0 - - - -
257B ARG 3.3 3.2 + - - -
258B LEU 2.8 12.2 + - - -
259B ALA 2.4 23.4 - - - +
260B LYS* 1.3 83.1 - - - +
262B ASN* 1.3 61.8 + - - +
263B ARG* 2.9 7.5 + - - +
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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