Contacts of the helix formed by residues 232 - 251 (chain A) in PDB entry 2FJX
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 232 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A TRP* 3.3 15.3 - - - +
230A ALA* 3.7 2.0 - - - +
231A THR* 1.3 81.4 - - - +
233A GLU* 1.3 63.6 + - - +
234A LEU* 3.7 8.0 + - - +
235A ASP* 3.3 29.4 + - - +
236A CYS* 3.1 23.2 + - - +
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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
----------------------------------------------------------
145A TRP* 3.3 54.3 - - + +
232A SER* 1.3 73.5 - - - +
234A LEU* 1.3 60.2 + - - +
236A CYS* 3.4 2.8 + - - +
237A GLN* 3.0 34.9 + - + +
262A CYS* 4.2 12.2 - - + +
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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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232A SER* 3.2 8.4 - - - +
233A GLU* 1.3 74.9 - - - +
235A ASP* 1.3 64.3 + - - +
236A CYS 3.1 1.8 - - - -
237A GLN* 2.8 35.3 - - - +
238A GLN* 2.8 55.1 + - + +
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Residues in contact with ASP 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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216A ASP* 5.4 9.0 - - - +
217A LEU* 3.9 11.2 - - + +
230A ALA* 3.7 16.8 - - + -
231A THR* 4.7 9.3 + - - +
232A SER* 3.3 22.4 + - - +
234A LEU* 1.3 81.9 - - - +
236A CYS* 1.3 57.3 + - - +
238A GLN* 3.4 19.7 - - - +
239A GLY* 2.8 26.6 + - - -
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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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145A TRP* 3.5 27.1 - - + -
146A TYR 3.9 2.7 - - - -
147A THR* 3.2 28.7 - - - -
217A LEU* 5.3 0.7 - - - -
228A LEU* 4.6 6.6 - - - +
230A ALA* 3.5 11.2 - - + +
232A SER 3.1 17.8 + - - +
233A GLU* 3.6 4.7 - - - +
234A LEU 3.1 0.8 - - - -
235A ASP* 1.3 76.0 - - - +
237A GLN* 1.3 58.1 + - - +
239A GLY* 4.9 0.4 - - - -
240A THR* 2.6 39.2 + - - +
262A CYS* 3.3 25.4 - - + -
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Residues in contact with GLN 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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25A TRP* 3.5 16.3 - - + -
233A GLU* 3.0 23.2 + - + +
234A LEU* 2.8 48.3 - - + +
236A CYS* 1.3 72.6 - - - +
238A GLN* 1.3 64.5 + - - +
241A ARG* 2.9 63.0 + - - +
262A CYS* 3.3 12.3 - - - -
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Residues in contact with GLN 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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214A HIS* 6.2 0.7 - - - -
234A LEU* 2.8 44.7 + - + +
235A ASP* 3.4 25.8 - - - +
237A GLN* 1.3 80.3 - - + +
239A GLY* 1.3 62.0 - - - +
241A ARG* 3.4 13.1 + - - +
242A ALA* 3.1 23.0 + - - +
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Residues in contact with GLY 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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210A PHE* 4.0 2.4 - - - -
214A HIS* 5.4 1.6 - - - -
217A LEU* 3.7 24.2 - - - -
228A LEU* 3.6 8.8 - - - +
235A ASP 2.8 22.4 + - - -
236A CYS 3.8 0.4 - - - -
238A GLN* 1.3 72.3 - - - +
240A THR* 1.3 58.5 + - - +
242A ALA* 3.2 7.1 + - - +
243A LEU* 2.8 30.0 + - - +
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Residues in contact with THR 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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25A TRP* 3.6 23.8 - - + -
147A THR* 2.9 40.7 + - + -
149A LEU* 5.3 3.1 - - + -
228A LEU* 3.5 9.3 - - - +
236A CYS 2.6 28.9 + - - -
239A GLY* 1.3 71.8 - - - +
241A ARG* 1.3 63.8 + - - +
243A LEU* 3.7 3.0 - - - +
244A LEU* 2.8 39.3 + - + +
261A ILE* 4.0 12.1 - - + -
262A CYS* 3.9 1.2 - - - -
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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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25A TRP* 3.4 20.3 - - + -
29A PHE* 3.3 39.1 - - + -
237A GLN* 2.9 87.9 + - - +
238A GLN* 3.4 13.8 - - - +
240A THR* 1.3 77.5 - - - +
242A ALA* 1.3 57.9 + - - +
244A LEU 3.5 0.2 + - - -
245A GLN* 3.0 24.1 + - - +
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Residues in contact with ALA 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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210A PHE* 3.8 3.1 - - + -
214A HIS* 3.8 32.1 - - + +
238A GLN 3.1 11.3 + - - +
239A GLY 3.6 6.1 - - - +
241A ARG* 1.3 77.5 - - - +
243A LEU* 1.3 60.6 + - - +
245A GLN* 3.4 6.0 + - - +
246A THR* 2.8 34.3 + - - +
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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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147A THR* 5.8 0.4 - - + -
149A LEU* 4.1 19.5 - - + -
207A LEU* 4.4 20.4 - - + -
210A PHE* 3.4 31.3 - - + -
219A LEU* 4.4 19.3 - - + -
226A LEU* 4.8 7.6 - - + -
228A LEU* 4.2 21.3 - - + -
239A GLY 2.8 20.5 + - - +
240A THR* 3.7 5.4 - - - +
242A ALA* 1.3 70.6 - - - +
244A LEU* 1.3 61.4 + - - +
246A THR* 3.2 1.3 + - - -
247A LEU* 2.8 56.4 + - + +
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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
----------------------------------------------------------
25A TRP* 3.9 8.5 - - + -
29A PHE* 3.7 26.0 - - + -
32A ALA* 3.0 31.2 - - + +
33A TRP* 3.5 45.1 - - + -
149A LEU* 3.8 20.4 - - + -
240A THR* 2.8 37.7 + - + +
241A ARG 3.8 3.1 - - - +
243A LEU* 1.3 76.3 - - - +
245A GLN* 1.3 63.4 + - - +
247A LEU* 4.6 4.5 - - + -
248A GLY* 3.0 19.8 + - - -
254A ALA* 4.7 4.9 - - + -
261A ILE* 4.8 0.2 - - + -
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Residues in contact with GLN 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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28A ASP 4.8 2.2 + - - -
29A PHE* 3.3 27.3 - - + +
31A GLN* 4.8 10.7 + - - +
32A ALA* 5.2 0.2 - - - -
241A ARG 3.0 18.3 + - - +
242A ALA* 3.7 7.2 - - - +
244A LEU* 1.3 75.9 - - - +
246A THR* 1.3 63.8 + - - +
248A GLY* 4.0 0.6 - - - -
249A ASN* 3.0 27.3 + - + +
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Residues in contact with THR 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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206A ASP 4.9 2.2 - - - +
207A LEU* 4.2 12.6 - - + -
210A PHE* 3.8 24.5 - - + +
242A ALA* 2.8 22.2 + - - +
243A LEU 3.6 4.0 - - - -
245A GLN* 1.3 75.5 - - - +
247A LEU* 1.3 60.6 + - - +
249A ASN* 3.3 7.4 + - - +
250A LEU* 2.9 53.5 + - + +
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Residues in contact with LEU 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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32A ALA* 5.2 4.0 - - + +
149A LEU* 4.2 14.8 - - + -
151A LEU* 4.2 11.4 - - + -
203A LEU* 4.2 17.7 - - + -
207A LEU* 4.1 20.6 - - + -
226A LEU* 4.0 23.6 - - + -
243A LEU* 2.8 46.1 + - + +
244A LEU* 3.9 7.4 - - + +
246A THR* 1.3 71.5 - - - +
248A GLY* 1.3 64.9 + - - +
250A LEU* 3.1 6.4 + - - +
251A GLY 3.0 5.4 + - - -
252A TYR* 3.0 43.4 + - + +
254A ALA* 5.2 2.9 - - + +
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Residues in contact with GLY 248 (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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31A GLN* 3.4 39.1 - - - +
32A ALA* 3.8 7.8 - - - +
244A LEU 3.0 17.1 + - - -
245A GLN 4.0 0.4 - - - -
247A LEU* 1.3 75.7 - - - +
249A ASN* 1.3 61.5 + - - +
251A GLY* 3.1 11.1 + - - -
252A TYR 3.8 3.8 + - - -
253A ARG* 3.3 11.1 + - - -
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Residues in contact with ASN 249 (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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31A GLN* 3.4 15.3 + - - +
43A VAL* 4.2 10.4 - - - +
44A ARG* 3.5 22.2 + - - -
245A GLN* 3.0 23.3 + - + +
246A THR* 3.6 7.3 - - - +
247A LEU 3.3 0.2 - - - -
248A GLY* 1.3 75.9 - - - +
250A LEU* 1.3 62.7 + - - +
251A GLY* 3.5 0.5 + - - -
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Residues in contact with LEU 250 (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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42A ALA* 3.5 7.1 - - - +
43A VAL* 3.3 28.9 + - - +
44A ARG* 3.6 45.0 + - + +
206A ASP* 3.4 44.5 - - + +
207A LEU* 3.8 11.2 - - + -
246A THR* 2.9 37.0 + - + +
247A LEU* 3.1 5.8 + - - +
249A ASN* 1.3 78.6 - - - +
251A GLY* 1.3 57.6 + - - +
252A TYR* 3.7 17.4 - - + -
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Residues in contact with GLY 251 (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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40A GLY* 3.1 9.2 - - - -
41A LEU 2.8 41.7 + - - -
43A VAL* 5.2 2.0 - - - -
157A CYS* 3.9 1.7 - - - -
247A LEU 3.0 2.0 + - - -
248A GLY 3.1 11.1 + - - -
249A ASN 3.2 1.2 - - - -
250A LEU* 1.3 80.4 - - - +
252A TYR* 1.3 63.6 + - - +
253A ARG* 3.4 8.7 - - - -
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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