Contacts of the helix formed by residues 227 - 245 (chain A) in PDB entry 4G17
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 SER 227 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 3.9 15.5 - - - +
161A ARG* 6.2 0.2 - - - +
192A TYR* 5.6 1.8 - - - -
200A HIS* 4.0 14.1 - - - -
201A ILE* 5.8 0.2 - - - -
226A GLN* 1.3 75.9 - - - +
228A ARG* 1.3 67.3 + - - +
229A ARG* 3.3 18.1 + - - +
230A ASP* 2.9 21.5 + - - +
231A ASP* 3.7 6.2 + - - -
295A PHE* 2.8 45.4 + - - -
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Residues in contact with ARG 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A HIS* 3.5 40.0 - - + +
159A ILE* 3.8 7.2 - - + +
192A TYR* 3.5 41.8 + - + -
193A ILE* 5.8 1.0 - - - +
200A HIS* 4.1 13.3 + - - -
227A SER* 1.3 78.1 - - - +
229A ARG* 1.3 62.6 + - - +
230A ASP 3.2 0.9 + - - -
231A ASP 3.2 10.0 + - - -
232A LEU* 3.5 9.4 + - - +
295A PHE 5.9 0.4 + - - +
296A PHE 2.9 27.3 + - - -
297A GLU 3.9 6.5 + - - +
298A LYS* 3.5 42.6 - - - +
299A PRO* 4.1 12.8 - - + -
301A TYR* 3.8 13.6 + - - -
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Residues in contact with ARG 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TYR* 4.7 4.6 - - - -
219A ASN* 3.6 37.3 - - - +
224A LYS* 4.5 10.7 - - - +
225A GLU 4.8 3.0 + - - -
227A SER* 3.5 10.8 + - - +
228A ARG* 1.3 77.9 - - - +
230A ASP* 1.3 78.7 + - - +
232A LEU* 3.2 7.2 + - - +
233A GLU* 2.9 28.5 + - - +
290A VAL* 4.1 9.0 - - - +
291A ARG 5.5 1.3 + - - -
293A LEU* 3.0 61.2 + - + -
294A ASP* 3.8 11.6 - - - +
295A PHE* 3.3 35.0 - - - +
297A GLU 5.2 2.5 + - - +
299A PRO* 4.7 1.2 - - - +
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Residues in contact with ASP 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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217A SER* 2.6 35.6 + - - +
219A ASN* 3.9 17.2 + - - +
220A THR* 3.8 10.9 + - - +
225A GLU 4.2 2.1 - - - +
226A GLN* 3.4 19.9 - - - +
227A SER 2.9 31.8 + - - +
229A ARG* 1.3 93.0 + - - +
231A ASP* 1.3 65.6 + - - +
233A GLU* 3.3 2.5 + - - +
234A ALA* 3.0 24.4 + - - +
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Residues in contact with ASP 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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150A MET* 3.9 13.7 - - + -
154A HIS* 2.9 23.9 + - - +
159A ILE* 3.5 7.4 - - - +
160A TYR* 2.9 30.6 + - - +
161A ARG* 2.8 31.3 + - - +
162A ASP 4.8 0.2 + - - -
163A VAL* 3.8 7.0 - - + +
226A GLN* 5.2 1.6 + - - -
227A SER 3.7 4.9 + - - -
228A ARG 3.2 9.4 + - - +
230A ASP* 1.3 78.2 - - - +
232A LEU* 1.3 62.8 + - - +
234A ALA* 3.4 7.0 + - - +
235A LEU* 3.1 25.6 + - - +
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Residues in contact with LEU 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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147A ILE* 5.2 7.4 - - + -
150A MET* 4.2 24.0 - - + -
154A HIS* 4.7 3.4 - - + -
228A ARG 3.8 8.1 - - - +
229A ARG 3.2 6.9 + - - +
230A ASP 3.2 0.4 - - - -
231A ASP* 1.3 74.3 - - - +
233A GLU* 1.3 65.8 + - - +
235A LEU* 3.2 10.7 + - + -
236A GLY 3.1 11.1 + - - -
286A TYR* 2.9 33.2 + - - +
290A VAL* 3.8 13.5 - - + -
293A LEU* 4.6 2.5 - - + -
299A PRO* 3.3 42.2 - - + -
301A TYR* 4.2 13.9 - - + -
304A LEU* 4.1 17.9 - - + -
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Residues in contact with GLU 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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217A SER* 3.0 22.5 - - - -
218A ILE* 2.8 26.1 + - - +
219A ASN* 5.1 6.6 + - - -
229A ARG 2.9 15.8 + - - +
230A ASP* 3.3 6.1 + - - +
232A LEU* 1.3 75.0 - - - +
234A ALA* 1.3 64.0 + - - +
236A GLY* 3.0 12.0 + - - -
237A HIS* 3.1 24.1 + - + +
287A LEU* 4.0 5.3 - - + +
290A VAL* 3.8 15.4 - - + +
291A ARG* 3.2 52.0 + - + +
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Residues in contact with ALA 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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163A VAL* 3.6 27.6 - - + +
215A TYR* 3.3 28.2 - - + +
216A MET* 4.7 5.6 - - - -
217A SER 4.9 1.7 - - - +
230A ASP 3.0 17.2 + - - +
231A ASP* 3.5 5.6 - - - +
233A GLU* 1.3 77.6 - - - +
235A LEU* 1.3 61.4 + - - +
237A HIS* 3.2 4.2 + - - +
238A MET* 3.1 21.0 + - - +
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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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146A LEU* 3.9 52.7 - - + +
147A ILE* 4.6 2.0 - - - +
150A MET* 3.9 23.3 - - + -
163A VAL* 4.0 17.5 - - + -
168A PHE* 4.1 11.2 - - + -
231A ASP 3.1 17.5 + - - +
232A LEU* 3.2 19.9 + - + +
234A ALA* 1.3 75.2 - - - +
236A GLY* 1.3 59.4 + - - +
238A MET* 3.1 9.4 + - + +
239A PHE* 2.8 47.4 + - + -
286A TYR* 3.8 4.9 - - - +
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Residues in contact with GLY 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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232A LEU 3.1 6.7 + - - -
233A GLU 3.0 8.7 + - - -
235A LEU* 1.3 77.1 - - - +
237A HIS* 1.3 62.9 + - - +
239A PHE* 3.0 25.2 + - - +
240A MET* 3.1 19.1 + - - +
283A MET* 5.4 1.0 - - - +
286A TYR* 3.7 17.4 - - - -
287A LEU* 4.0 11.9 - - - -
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Residues in contact with HIS 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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214A ARG 4.6 0.7 - - - +
215A TYR* 2.9 35.3 + - + +
216A MET 3.4 17.6 + - - -
217A SER* 4.2 0.6 + - - -
218A ILE 4.7 0.7 - - - -
233A GLU* 3.1 33.0 + - + +
234A ALA 3.2 7.2 + - - +
236A GLY* 1.3 74.3 - - - +
238A MET* 1.3 57.9 + - - +
240A MET* 3.4 4.3 + - - +
241A TYR* 3.0 27.4 + - - +
247A LEU* 3.7 8.6 - - + +
249A TRP* 4.0 23.4 - + + -
268A LYS* 4.3 13.4 - - + -
276A LEU* 4.6 2.0 - - + -
287A LEU* 4.3 13.5 - - + -
291A ARG* 3.0 32.5 + - - -
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Residues in contact with MET 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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123A LEU* 4.4 1.3 - - + -
146A LEU* 3.6 31.0 - - + -
163A VAL* 4.4 3.8 - - + -
164A LYS* 3.8 8.7 - - - -
165A PRO* 3.5 41.7 - - + -
168A PHE* 3.7 16.2 - - + -
215A TYR* 3.9 11.1 - - + -
234A ALA 3.1 12.5 + - - +
235A LEU* 3.4 17.3 - - + +
237A HIS* 1.3 75.9 - - - +
239A PHE* 1.3 70.4 + - + +
241A TYR* 3.2 8.8 + - + +
242A PHE* 3.0 50.2 + - + -
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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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139A VAL* 4.1 10.3 - - + +
142A ILE* 4.7 2.5 - - + -
143A ALA* 3.5 46.9 - - + -
146A LEU* 4.4 8.5 - - + -
147A ILE* 5.0 1.8 - - + -
235A LEU* 2.8 47.9 + - + -
236A GLY* 3.0 13.6 + - - +
238A MET* 1.3 96.3 - - + +
240A MET* 1.3 57.5 + - - +
242A PHE* 3.4 12.3 + + - +
243A LEU* 3.1 33.3 + - - +
283A MET* 3.9 28.7 - - + -
286A TYR* 4.1 16.6 - + - -
308A PHE* 4.4 6.5 - + - -
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Residues in contact with MET 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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236A GLY 3.1 13.2 + - - +
237A HIS* 3.8 8.1 - - - +
239A PHE* 1.3 73.2 - - - +
241A TYR* 1.3 61.3 + - - +
243A LEU* 4.2 4.0 - - + -
244A ARG* 2.9 59.6 + - + +
247A LEU* 4.1 6.7 - - + -
276A LEU* 3.5 34.5 - - + +
277A CYS* 3.7 23.8 - - - -
280A PHE* 4.0 17.7 - - + -
283A MET* 3.4 39.7 - - + -
287A LEU* 4.9 3.1 - - + -
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Residues in contact with TYR 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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124A GLU* 3.1 26.1 + - - -
127A PHE* 3.7 19.9 - + - -
132A ARG* 2.7 31.2 + - - -
165A PRO* 4.0 2.0 - - + -
214A ARG* 3.2 22.5 + - - -
215A TYR* 3.4 24.7 - + + -
237A HIS 3.0 15.3 + - - +
238A MET* 3.2 11.2 - - - +
240A MET* 1.3 77.5 - - - +
242A PHE* 1.3 77.7 + + - +
245A GLY* 2.9 28.5 + - - -
246A SER* 3.4 14.4 + - - -
247A LEU* 3.8 20.3 - - + +
250A GLN* 3.9 19.3 - - - -
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Residues in contact with PHE 242 (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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123A LEU* 4.0 24.0 - - + -
127A PHE* 3.5 27.6 - + - -
133A THR* 3.6 4.2 - - - -
134A PHE* 3.2 51.1 + + + -
139A VAL* 3.9 12.8 - - + -
142A ILE* 4.6 10.5 - - + -
165A PRO* 3.8 21.8 - - + -
238A MET* 3.0 53.9 + - + -
239A PHE* 3.7 13.2 - + - +
240A MET 3.3 0.2 - - - -
241A TYR* 1.3 101.2 - + - +
243A LEU* 1.3 59.4 + - - +
245A GLY 3.8 0.9 + - - -
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Residues in contact with LEU 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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133A THR* 4.1 9.2 + - - -
134A PHE 4.0 9.5 - - - +
136A LEU* 3.9 23.1 - - + +
139A VAL* 3.4 28.9 - - + -
239A PHE 3.1 21.6 + - - +
240A MET* 3.3 9.6 + - + +
242A PHE* 1.3 79.1 - - - +
244A ARG* 1.3 58.6 + - - +
280A PHE* 4.1 44.2 - - + -
283A MET* 3.9 37.2 - - + -
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Residues in contact with ARG 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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133A THR* 5.0 3.3 + - - -
240A MET* 2.9 44.1 + - + +
243A LEU* 1.3 74.8 - - + +
245A GLY* 1.3 58.6 + - - +
246A SER* 3.0 25.6 + - - +
247A LEU* 4.5 1.1 - - - -
248A PRO* 3.4 35.0 - - - +
275A VAL* 4.0 6.3 + - - +
276A LEU* 3.0 39.4 + - - +
278A GLU* 6.0 0.8 - - - +
280A PHE* 5.3 4.9 - - + -
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Residues in contact with GLY 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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127A PHE* 4.0 13.1 - - - -
132A ARG* 3.4 35.2 + - - +
133A THR* 4.9 1.6 - - - -
241A TYR* 2.9 17.0 + - - -
242A PHE 3.8 2.0 + - - -
243A LEU 3.5 1.8 - - - -
244A ARG* 1.3 79.0 - - - +
246A SER* 1.3 62.8 + - - +
250A GLN* 5.0 0.3 + - - -
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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