Contacts of the helix formed by residues 239 - 257 (chain W) in PDB entry 5O9G
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 LEU 239 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179W ILE* 4.0 11.2 - - + -
230W TYR* 4.3 22.0 + - + -
233W ILE* 5.0 1.8 - - + -
234W GLY 4.9 7.6 - - - +
235W GLN* 4.0 20.9 - - - +
236W VAL* 3.7 34.1 - - + +
238W GLY* 1.3 82.0 - - - +
240W LYS* 1.3 65.0 + - - +
241W ARG 3.3 2.5 - - - -
242W LEU* 3.7 7.4 + - + +
243W ASP* 2.9 31.7 + - - +
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Residues in contact with LYS 240 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-11I G 3.0 30.8 + - - +
-10I C 3.5 36.4 + - - +
-9I A 5.9 3.6 - - - -
10J G 6.3 0.2 - - - +
11J C 4.9 4.9 - - - +
12J G 4.7 22.4 + - - +
239W LEU* 1.3 76.1 - - - +
241W ARG* 1.3 60.1 + - - +
242W LEU 3.3 0.2 - - - -
243W ASP* 3.2 11.9 + - + +
244W ASN* 2.9 51.3 + - - +
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Residues in contact with ARG 241 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J G 3.4 68.8 + - - +
13J T 4.0 19.1 + - - +
179W ILE* 4.2 15.1 + - + -
180W ASP* 2.4 57.5 + - - +
181W ILE* 4.5 6.2 - - - +
182W VAL* 4.7 8.0 - - + +
238W GLY* 6.0 3.4 - - - -
239W LEU 3.3 2.4 - - - +
240W LYS* 1.3 77.0 - - - +
242W LEU* 1.3 58.1 + - - +
244W ASN* 3.3 9.0 + - - +
245W TYR* 2.9 29.9 + - - +
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Residues in contact with LEU 242 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179W ILE* 4.9 16.9 - - + +
182W VAL* 3.8 20.3 - - + +
213W PHE* 4.2 20.2 - - + -
215W ILE* 3.7 35.4 - - + -
228W GLU 5.1 0.7 - - - +
229W THR 4.7 6.1 - - - +
230W TYR* 3.5 37.2 - - + +
239W LEU* 3.7 7.8 + - - +
240W LYS 3.3 0.2 - - - -
241W ARG* 1.3 76.0 - - - +
243W ASP* 1.3 58.8 + - - +
245W TYR* 4.3 4.0 - - + -
246W CYS* 2.9 51.7 + - - -
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Residues in contact with ASP 243 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204W LEU* 4.6 16.5 - - + +
230W TYR* 2.3 36.5 + - - -
239W LEU* 2.9 22.9 - - - +
240W LYS* 3.2 14.4 + - + +
242W LEU* 1.3 78.7 - - - +
244W ASN* 1.3 60.0 + - - +
246W CYS* 3.5 4.5 + - - +
247W LYS* 2.9 28.6 + - - +
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Residues in contact with ASN 244 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J G 5.2 9.1 + - - -
13J T 5.2 8.7 - - - -
240W LYS* 2.9 50.3 + - - +
241W ARG* 3.9 6.6 - - - +
243W ASP* 1.3 75.8 - - - +
245W TYR* 1.3 61.3 + - - +
247W LYS* 3.2 12.0 + - - +
248W GLN* 2.9 41.2 + - + +
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Residues in contact with TYR 245 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182W VAL* 3.7 45.3 - - + -
183W ILE 4.1 11.3 + - - -
185W HIS* 2.9 46.3 + + + -
213W PHE* 5.4 2.2 - + - -
241W ARG 2.9 18.1 + - - +
242W LEU* 4.0 8.3 - - + +
244W ASN* 1.3 76.8 - - - +
246W CYS* 1.3 60.9 + - - +
248W GLN* 3.3 18.4 + - + +
249W PHE* 2.9 27.5 + - + +
277W ARG* 5.9 7.4 - - + +
281W PHE* 5.7 3.0 - + - -
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Residues in contact with CYS 246 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204W LEU* 6.2 4.3 - - + -
207W CYS* 4.7 15.3 - - + -
213W PHE* 3.5 40.6 - - + -
230W TYR* 4.8 6.1 - - - +
242W LEU* 2.9 40.9 + - - +
243W ASP* 3.9 5.4 - - - +
245W TYR* 1.3 75.2 - - - +
247W LYS* 1.3 59.6 + - - +
249W PHE* 3.2 10.0 + - - +
250W ILE* 2.9 35.5 + - + +
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Residues in contact with LYS 247 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243W ASP 2.9 18.9 + - - +
244W ASN* 3.2 13.2 + - - +
246W CYS* 1.3 74.4 - - - +
248W GLN* 1.3 61.4 + - + +
250W ILE* 3.0 12.8 + - + +
251W ILE* 2.9 50.3 + - + +
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Residues in contact with GLN 248 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244W ASN* 2.9 29.0 + - - +
245W TYR* 3.7 16.7 - - + +
247W LYS* 1.3 76.1 - - + +
249W PHE* 1.3 57.7 + - - +
251W ILE* 3.9 11.8 - - + +
252W GLU* 2.9 29.7 + - - +
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Residues in contact with PHE 249 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185W HIS* 3.3 42.6 - + + -
186W ARG* 6.5 0.4 - - - -
202W PRO* 6.6 0.2 - - + -
207W CYS* 5.1 9.9 - - - -
211W TYR* 4.5 33.4 - + - -
213W PHE* 5.0 13.2 - + + -
245W TYR* 2.9 21.5 + - + +
246W CYS* 3.5 12.3 - - - +
247W LYS 3.1 0.4 - - - -
248W GLN* 1.3 75.7 - - - +
250W ILE* 1.3 60.5 + - + +
252W GLU* 3.5 15.6 - - - +
253W ASP* 2.9 68.8 + - - +
274W ARG* 4.4 11.0 - - - -
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Residues in contact with ILE 250 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201W VAL* 3.9 9.4 - - + -
202W PRO* 3.3 32.0 - - + +
203W ASP* 4.2 15.7 - - - +
204W LEU* 4.6 3.4 - - + +
207W CYS* 4.3 13.7 - - - -
246W CYS* 2.9 19.9 + - + +
247W LYS* 3.0 15.2 + - + +
249W PHE* 1.3 76.4 - - + +
251W ILE* 1.3 61.6 + - + +
253W ASP* 3.2 11.2 + - - +
254W GLN* 2.9 46.1 + - - +
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Residues in contact with ILE 251 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247W LYS* 2.9 39.5 + - + +
248W GLN* 4.0 10.8 - - + +
250W ILE* 1.3 77.7 - - + +
252W GLU* 1.3 57.1 + - - +
254W GLN* 3.0 20.7 + - + +
255W GLN* 2.9 51.1 + - + +
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Residues in contact with GLU 252 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185W HIS* 4.9 4.9 + - - -
248W GLN 2.9 18.6 + - - +
249W PHE* 3.5 21.8 - - - +
250W ILE 3.2 0.2 - - - -
251W ILE* 1.3 76.3 - - - +
253W ASP* 1.3 58.2 + - - +
255W GLN* 2.8 22.8 + - - +
256W VAL* 2.9 24.7 + - + +
270W MET* 3.7 38.7 - - + +
273W GLU* 5.9 0.2 - - - +
274W ARG* 3.0 45.1 + - - +
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Residues in contact with ASP 253 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202W PRO* 4.7 23.0 - - + +
211W TYR* 5.3 1.9 + - - -
249W PHE* 2.9 58.5 + - - +
250W ILE* 3.5 10.7 - - - +
252W GLU* 1.3 75.8 - - - +
254W GLN* 1.3 60.8 + - + +
255W GLN 3.4 0.3 + - - -
256W VAL* 3.6 14.4 + - - +
257W ARG 3.9 1.6 + - - -
258W LEU* 3.3 28.9 + - + +
274W ARG* 4.6 7.4 + - - -
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Residues in contact with GLN 254 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200W THR 5.1 1.1 - - - +
201W VAL* 3.3 37.1 - - + +
202W PRO* 6.3 0.7 - - + -
250W ILE* 2.9 25.1 + - + +
251W ILE* 3.0 23.8 + - + +
253W ASP* 1.3 76.7 - - + +
255W GLN* 1.3 60.3 + - + +
256W VAL 3.6 0.2 - - - -
258W LEU* 3.2 32.6 - - + +
259W ASP* 3.2 13.0 - - - +
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Residues in contact with GLN 255 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251W ILE* 2.9 36.3 + - + +
252W GLU* 2.8 9.1 + - - +
254W GLN* 1.3 81.9 - - + +
256W VAL* 1.3 62.5 + - - +
259W ASP* 4.7 6.1 - - + -
262W VAL* 3.6 21.0 - - - +
266W ASP* 5.4 1.2 - - - +
267W ILE* 4.4 2.1 - - - +
270W MET* 3.8 37.3 - - + +
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Residues in contact with VAL 256 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252W GLU* 2.9 32.7 + - + +
253W ASP* 3.6 8.9 + - - +
255W GLN* 1.3 79.6 - - - +
257W ARG* 1.3 82.3 + - + +
259W ASP 5.4 0.2 - - - -
262W VAL* 3.9 11.1 - - - +
267W ILE* 3.3 33.7 - - + +
270W MET* 5.0 8.7 - - + -
271W ASP* 4.9 12.6 - - - +
274W ARG* 4.4 13.0 - - - +
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Residues in contact with ARG 257 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253W ASP 3.9 2.2 + - - -
256W VAL* 1.3 96.4 - - + +
258W LEU* 1.3 72.7 + - + +
259W ASP 3.4 8.8 + - - +
262W VAL* 5.4 2.5 - - - -
267W ILE* 5.8 0.9 - - + -
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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
------------------------------------------------------------
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