Contacts of the helix formed by residues 226 - 247 (chain A) in PDB entry 4XNW
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 PHE 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A TYR* 4.4 1.1 - - + -
139A ILE* 4.3 10.2 - - + +
221A THR 3.4 0.4 + - - -
222A THR* 3.2 13.1 + - + +
224A ALA 3.6 0.6 - - - -
225A MET* 1.3 80.7 - - - +
227A CYS* 1.3 87.9 + - - +
228A VAL 3.4 0.7 - - - -
229A PRO* 3.5 4.9 - - - +
230A LEU* 2.9 43.4 + - + +
269A PHE* 3.8 30.7 - + - -
273A TYR* 3.8 14.8 - - + -
274A ILE* 3.7 31.4 - - + -
277A HIS* 3.8 46.2 - + + +
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Residues in contact with CYS 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A THR* 2.7 33.0 + - - -
223A VAL* 3.5 19.5 - - + +
226A PHE* 1.3 87.7 - - - +
228A VAL* 1.3 70.3 + - + +
230A LEU* 3.3 7.2 + - - +
231A VAL* 3.0 27.0 + - + +
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Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A VAL* 2.9 28.3 + - + +
224A ALA* 3.8 9.6 - - - +
227A CYS* 1.3 73.3 - - + +
229A PRO* 1.3 76.4 - - + +
231A VAL* 2.9 11.4 + - + +
232A LEU* 2.8 38.4 + - + +
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Residues in contact with PRO 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 3.7 16.4 - - + -
140A LEU* 4.0 15.7 - - + -
143A THR* 3.6 19.5 - - + +
224A ALA 3.2 14.8 - - - +
225A MET 3.8 19.1 - - - +
226A PHE 3.5 9.2 - - - +
228A VAL* 1.3 97.0 - - + +
230A LEU* 1.3 53.1 + - - +
232A LEU* 3.0 13.9 + - + +
233A ILE* 2.6 40.8 + - + +
269A PHE* 5.5 0.2 - - + -
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Residues in contact with LEU 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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226A PHE* 2.9 47.2 + - + +
227A CYS* 3.3 6.9 + - - +
229A PRO* 1.3 72.4 - - - +
231A VAL* 1.3 59.1 + - + +
233A ILE* 3.3 9.7 + - + +
234A LEU* 3.0 61.7 + - + +
266A LEU* 5.6 3.1 - - + -
269A PHE* 3.8 31.4 - - + -
274A ILE* 4.2 17.7 - - + -
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Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A CYS* 3.0 18.6 + - + +
228A VAL* 2.9 11.7 + - + +
230A LEU* 1.3 75.2 - - + +
232A LEU* 1.3 65.6 + - + +
234A LEU* 3.4 9.2 + - + +
235A GLY* 2.9 26.9 + - - -
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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
----------------------------------------------------------
143A THR* 4.1 24.5 - - + -
228A VAL* 2.8 32.5 + - + +
229A PRO* 3.4 9.9 - - + +
231A VAL* 1.3 79.9 - - + +
233A ILE* 1.3 57.4 + - - +
235A GLY* 3.4 2.2 + - - +
236A CYS* 3.1 36.7 + - - -
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Residues in contact with ILE 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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139A ILE 4.6 0.2 - - - +
142A LEU* 4.3 5.2 - - + -
143A THR* 3.7 37.0 - - + +
146A SER* 3.8 16.4 - - - +
229A PRO* 2.6 20.5 + - + +
230A LEU* 3.7 8.7 - - + +
231A VAL 3.2 0.2 - - - -
232A LEU* 1.3 71.0 - - - +
234A LEU* 1.3 63.6 - - + +
235A GLY 3.3 0.2 + - - -
236A CYS* 3.4 5.6 + - - +
237A TYR* 2.9 61.2 + - + +
265A VAL* 4.6 5.6 - - + -
266A LEU* 5.0 4.3 - - + -
269A PHE* 3.9 32.1 - - + -
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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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230A LEU* 3.0 44.1 + - + +
231A VAL* 4.0 8.5 - - + +
233A ILE* 1.3 72.8 - - + +
235A GLY* 1.3 68.9 + - - +
237A TYR* 3.8 5.7 - - + +
238A GLY* 3.0 18.5 + - - -
266A LEU* 3.7 31.4 - - + -
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Residues in contact with GLY 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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231A VAL 2.9 16.9 + - - -
232A LEU* 3.7 2.5 - - - -
234A LEU* 1.3 78.6 - - - +
236A CYS* 1.3 63.5 + - - +
237A TYR 3.1 0.2 + - - -
238A GLY* 3.2 7.3 + - - -
239A LEU* 3.2 24.2 + - - +
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Residues in contact with CYS 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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143A THR* 5.5 1.6 - - - -
146A SER* 4.3 8.7 - - - +
147A ALA* 4.1 27.8 - - - -
150A TYR* 4.1 31.6 - - + -
232A LEU* 3.1 21.5 + - - -
233A ILE 3.6 6.5 - - - +
235A GLY* 1.3 72.2 - - - +
237A TYR* 1.3 66.5 + - + +
239A LEU* 3.3 5.1 + - - +
240A ILE* 2.8 34.5 + - - +
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Residues in contact with TYR 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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146A SER* 3.0 36.8 + - - -
233A ILE* 2.9 38.9 + - + +
234A LEU* 3.8 7.2 - - + +
236A CYS* 1.3 79.1 - - + +
238A GLY* 1.3 63.0 + - - +
240A ILE* 3.3 10.2 + - + +
241A VAL* 2.9 31.9 + - + +
261A LEU* 3.5 22.5 - - + +
262A VAL* 3.7 40.8 - - + -
265A VAL* 3.2 35.7 - - + +
266A LEU* 4.0 18.8 - - + -
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Residues in contact with GLY 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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234A LEU 3.0 14.3 + - - -
235A GLY 3.8 2.2 - - - -
237A TYR* 1.3 77.1 - - - +
239A LEU* 1.3 57.7 + - - +
241A VAL* 3.3 5.4 + - - +
242A ARG* 2.8 31.1 + - - +
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Residues in contact with LEU 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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150A TYR* 3.4 36.6 - - + +
154A VAL* 3.9 8.9 - - + +
235A GLY* 3.2 21.4 + - - +
236A CYS* 3.5 6.3 - - - +
238A GLY* 1.3 76.0 - - - +
240A ILE* 1.3 61.2 + - - +
242A ARG* 3.5 38.3 + - - +
243A ALA* 3.0 25.1 + - - +
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Residues in contact with ILE 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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146A SER 4.1 6.5 - - - +
149A ARG* 4.3 7.9 - - + -
150A TYR* 3.6 44.0 - - + +
153A VAL* 4.3 16.5 - - + +
154A VAL* 4.6 0.9 - - - -
236A CYS 2.8 28.3 + - - +
237A TYR* 3.7 19.1 - - + +
238A GLY 3.2 0.2 - - - -
239A LEU* 1.3 70.6 - - - +
241A VAL* 1.3 67.8 + - + +
243A ALA* 3.1 4.3 + - - +
244A LEU* 2.9 30.6 + - + +
258A SER* 3.9 26.9 - - - +
261A LEU* 5.5 2.2 - - + -
262A VAL* 5.1 8.7 - - + -
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Residues in contact with VAL 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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237A TYR* 2.9 23.2 + - + +
238A GLY* 3.6 5.8 - - - +
240A ILE* 1.3 76.6 - - + +
242A ARG* 1.3 63.7 + - - +
244A LEU* 3.1 10.2 + - + +
245A ILE* 2.9 46.0 + - + +
259A ILE* 6.3 2.9 - - + -
262A VAL* 4.6 20.9 - - + -
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Residues in contact with ARG 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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154A VAL* 6.1 3.4 - - - +
238A GLY 2.8 19.9 + - - +
239A LEU* 3.5 35.3 + - - +
240A ILE 3.2 0.2 - - - -
241A VAL* 1.3 74.2 - - - +
243A ALA* 1.3 65.4 + - - +
245A ILE* 3.3 4.9 + - - +
246A TYR* 2.9 53.1 + - + -
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Residues in contact with ALA 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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153A VAL* 4.0 20.2 - - + +
154A VAL* 4.2 17.9 - - + -
239A LEU 3.0 17.6 + - - +
240A ILE 3.6 4.3 - - - +
242A ARG* 1.3 79.1 - - - +
244A LEU* 1.3 57.9 + - - +
246A TYR* 3.5 4.9 + - - +
247A LYS* 3.0 31.0 + - - +
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Residues in contact with LEU 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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153A VAL* 4.2 17.7 - - + -
240A ILE* 2.9 33.3 + - + +
241A VAL* 3.5 11.9 - - + +
243A ALA* 1.3 77.3 - - - +
245A ILE* 1.3 64.3 + - + +
247A LYS* 3.8 8.7 + - + +
254A LEU 5.4 0.2 - - - -
255A ARG* 2.3 88.8 + - + +
258A SER* 4.1 5.4 - - - -
259A ILE* 4.0 17.5 - - + -
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Residues in contact with ILE 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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241A VAL* 2.9 39.9 + - + +
242A ARG* 3.3 6.3 + - - +
244A LEU* 1.3 78.6 - - + +
246A TYR* 1.3 72.5 + - + +
247A LYS 4.5 1.9 - - - +
255A ARG* 4.8 0.2 - - - +
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Residues in contact with TYR 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 ARG* 2.9 50.3 + - + +
243A ALA* 4.0 5.2 - - - +
245A ILE* 1.3 87.2 - - + +
247A LYS* 1.3 64.8 + - - +
1001A MET* 3.1 14.0 + - - +
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Residues in contact with LYS 247 (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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156A PRO* 5.7 9.1 - - - +
243A ALA 3.0 18.5 + - - +
244A LEU* 3.8 9.0 + - + +
245A ILE 3.6 2.3 - - - +
246A TYR* 1.3 74.2 - - - +
255A ARG* 3.3 28.6 + - - +
1001A MET* 1.3 72.3 + - - +
1002A LYS* 3.8 2.1 + - - +
1003A LYS* 3.6 29.6 - - - +
1016A GLU* 6.1 1.6 - - - +
1054A GLU* 4.6 9.4 - - - -
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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