Contacts of the helix formed by residues 242 - 263 (chain A) in PDB entry 3D2I
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 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A PHE* 1.3 74.2 - - - +
243A GLU* 1.3 56.6 + - - +
244A GLN* 3.0 19.7 + - - +
245A ARG* 2.6 43.2 + - - +
246A THR* 2.7 34.4 + - - -
336A LEU* 4.0 1.3 - - - -
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Residues in contact with GLU 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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242A ASP* 1.3 75.2 - - - +
244A GLN* 1.3 64.4 + - - +
246A THR* 3.8 0.8 - - - -
247A ALA* 3.0 31.5 + - - +
336A LEU* 3.9 18.2 - - + +
366A THR* 2.6 45.0 + - - +
369A ALA* 4.2 3.1 - - - +
395A TRP* 2.8 31.7 + - + -
399A ASN* 3.4 20.2 + - - +
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Residues in contact with GLN 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ASP* 3.0 18.2 + - - +
243A GLU* 1.3 85.2 + - - +
245A ARG* 1.3 55.5 + - - +
248A THR* 2.6 33.6 + - - -
398A ALA 5.5 0.2 + - - -
399A ASN* 2.8 50.6 + - - +
401A SER* 4.8 2.9 + - - +
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Residues in contact with ARG 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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234A GLU* 2.9 32.5 + - - -
238A LEU* 3.8 22.3 - - - +
241A PHE* 3.5 31.2 - - + +
242A ASP* 2.6 27.5 + - - +
244A GLN* 1.3 70.7 - - - +
246A THR* 1.3 65.7 + - - +
248A THR* 3.4 6.6 + - - -
249A TYR* 3.1 48.8 + - + -
277A LEU* 5.5 0.2 - - - +
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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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241A PHE* 3.6 13.3 - - - +
242A ASP 2.7 21.5 + - - -
243A GLU* 3.8 4.0 - - - -
244A GLN 3.4 0.2 - - - -
245A ARG* 1.3 76.2 - - - +
247A ALA* 1.3 58.8 + - - +
249A TYR* 3.1 6.2 + - - +
250A ILE* 2.9 31.9 + - + +
332A CYS* 4.0 15.3 - - - +
335A PHE* 3.7 32.8 - - + +
336A LEU* 3.3 29.2 - - + +
395A TRP* 4.0 11.0 - - + -
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Residues in contact with ALA 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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243A GLU 3.0 18.3 + - - +
246A THR* 1.3 76.8 - - - +
248A THR* 1.3 57.6 + - - +
250A ILE* 3.8 2.0 - - - +
251A THR* 2.8 35.8 + - - -
395A TRP* 4.2 7.4 - - + -
396A ILE* 3.9 26.3 - - + +
399A ASN* 3.7 20.9 - - + +
400A SER* 3.7 13.2 - - - +
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Residues in contact with THR 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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244A GLN 2.6 23.2 + - - -
245A ARG* 3.4 8.4 + - - -
246A THR 3.2 0.6 - - - -
247A ALA* 1.3 75.6 - - - +
249A TYR* 1.3 60.5 + - + +
251A THR* 3.3 2.0 + - - -
252A GLU* 2.9 55.4 + - + +
400A SER* 4.0 8.3 + - - +
401A SER* 3.6 34.2 + - - +
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Residues in contact with TYR 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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231A VAL* 4.7 4.3 - - + -
234A GLU* 2.9 22.0 + - - -
241A PHE* 3.6 36.8 - + - -
245A ARG* 3.1 43.0 + - + -
246A THR 3.5 6.3 - - - +
248A THR* 1.3 80.6 - - + +
250A ILE* 1.3 57.9 + - - +
252A GLU* 3.5 8.3 + - - +
253A LEU* 2.9 30.9 + - - +
277A LEU* 3.4 34.0 - - + +
281A GLY 3.9 13.8 + - - -
283A LEU* 3.7 28.2 - - + +
335A PHE* 3.7 21.8 - + + -
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Residues in contact with ILE 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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246A THR* 2.9 23.7 + - + +
247A ALA 3.8 4.0 - - - +
249A TYR* 1.3 72.8 - - - +
251A THR* 1.3 59.9 + - - +
253A LEU* 3.7 5.6 - - + +
254A ALA* 2.9 29.6 + - - +
328A LEU* 3.9 27.3 - - + +
331A LEU* 4.8 2.5 - - + -
332A CYS* 3.8 44.4 - - + +
335A PHE* 4.3 13.7 - - + -
372A LEU* 4.9 4.5 - - + -
390A VAL* 3.9 21.8 - - + -
396A ILE* 3.8 22.2 - - + -
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Residues in contact with THR 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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247A ALA 2.8 23.3 + - - -
248A THR* 3.5 3.8 - - - -
250A ILE* 1.3 78.0 - - - +
252A GLU* 1.3 60.1 + - + +
254A ALA* 3.4 3.5 + - - +
255A ASN* 3.1 41.5 + - - +
390A VAL* 6.4 0.2 - - - -
391A LEU* 3.9 21.5 - - + +
396A ILE* 3.7 15.2 - - + +
400A SER* 2.9 25.5 + - - +
401A SER 6.5 0.2 - - - -
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Residues in contact with GLU 252 (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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205A ASN* 3.6 33.3 + - - +
248A THR* 2.9 37.3 + - + +
249A TYR* 3.9 11.9 - - - +
251A THR* 1.3 75.1 - - + +
253A LEU* 1.3 64.1 - - - +
255A ASN* 3.6 9.0 + - - +
256A ALA* 3.2 15.6 + - - +
281A GLY 4.7 0.3 - - - +
282A GLU* 3.4 22.7 - - - +
283A LEU* 3.1 34.9 + - + +
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Residues in contact with LEU 253 (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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249A TYR 2.9 18.6 + - - +
250A ILE* 3.7 7.4 - - + +
252A GLU* 1.3 74.3 - - - +
254A ALA* 1.3 54.7 + - - +
256A ALA* 3.0 4.7 + - + +
257A LEU* 2.8 54.2 + - + +
270A ILE* 4.0 22.2 - - + -
275A LEU* 4.2 7.2 - - + -
283A LEU* 3.9 20.3 - - + +
285A ILE* 4.3 11.0 - - + -
328A LEU* 3.5 24.2 - - + -
331A LEU* 3.5 31.9 - - + -
335A PHE* 5.8 0.4 - - + -
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Residues in contact with ALA 254 (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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250A ILE 2.9 18.4 + - - +
251A THR* 3.6 5.6 - - - +
253A LEU* 1.3 76.9 - - - +
255A ASN* 1.3 52.1 + - - +
257A LEU* 3.3 2.2 + - - +
258A SER* 2.7 40.3 + - - -
328A LEU* 4.5 3.1 - - + +
387A LEU* 4.0 25.4 - - + +
390A VAL* 4.7 9.2 - - + -
391A LEU* 3.9 24.5 - - + -
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Residues in contact with ASN 255 (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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203A HIS* 3.8 21.2 - - + +
205A ASN* 4.1 6.0 - - - +
251A THR* 3.1 31.5 + - - +
252A GLU* 3.7 11.3 - - - +
254A ALA* 1.3 75.9 - - - +
256A ALA* 1.3 56.4 + - - +
258A SER* 3.1 8.1 + - - -
259A TYR* 3.0 28.8 + - - +
391A LEU* 3.8 20.4 - - - +
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Residues in contact with ALA 256 (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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203A HIS* 3.8 11.4 + - - -
205A ASN* 3.4 28.5 - - + +
206A ILE* 4.0 6.1 - - + +
252A GLU 3.2 10.5 + - - +
253A LEU* 3.0 12.4 + - + +
255A ASN* 1.3 78.4 - - - +
257A LEU* 1.3 57.6 + - + +
259A TYR* 3.6 3.1 + - - +
260A CYS* 3.1 33.5 + - - -
283A LEU* 5.5 0.4 - - + -
285A ILE* 3.9 16.4 - - + -
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Residues in contact with LEU 257 (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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253A LEU* 2.8 37.9 + - + +
254A ALA 3.8 3.1 - - - +
256A ALA* 1.3 72.1 - - - +
258A SER* 1.3 57.2 + - - +
260A CYS* 4.0 6.7 - - + -
261A HIS* 2.7 43.9 + - + +
267A HIS* 4.5 4.0 - - + -
270A ILE* 3.7 26.0 - - + -
285A ILE* 4.3 7.2 - - + -
324A ASP* 3.7 46.4 - - + +
328A LEU* 4.4 9.9 - - + -
387A LEU* 3.7 26.2 - - + -
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Residues in contact with SER 258 (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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254A ALA 2.7 24.6 + - - -
255A ASN* 3.1 10.5 + - - -
257A LEU* 1.3 74.0 - - - +
259A TYR* 1.3 59.6 + - - +
261A HIS* 4.2 2.4 - - - +
262A SER* 3.2 24.4 + - - -
387A LEU* 3.6 23.8 - - - +
391A LEU* 4.5 9.3 - - - +
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Residues in contact with TYR 259 (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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200A HIS 3.9 5.4 + - - -
201A LEU* 3.6 26.0 - - + -
202A ARG* 2.8 49.1 + - - +
203A HIS* 3.8 22.4 - + + +
206A ILE* 3.7 19.3 - - + -
255A ASN 3.0 14.8 + - - +
256A ALA 3.7 4.0 - - - +
258A SER* 1.3 76.5 - - - +
260A CYS* 1.3 61.0 + - - +
262A SER* 2.8 21.6 + - - -
263A LYS* 3.3 26.2 - - + +
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Residues in contact with CYS 260 (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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201A LEU* 4.2 10.8 - - - -
206A ILE* 3.8 18.4 - - - -
256A ALA 3.1 24.0 + - - +
257A LEU* 3.5 14.4 - - + +
259A TYR* 1.3 78.3 - - - +
261A HIS* 1.3 58.5 + - + +
263A LYS* 3.4 3.5 + - - +
264A ARG 3.4 3.1 + - - -
265A VAL* 2.7 47.6 + - + +
267A HIS* 5.8 2.2 - - - +
285A ILE* 5.5 2.7 - - - -
288A PHE* 3.7 32.1 - - - -
324A ASP* 5.8 0.2 - - - +
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Residues in contact with HIS 261 (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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257A LEU* 2.7 25.6 + - + +
258A SER* 4.3 4.0 - - - +
260A CYS* 1.3 73.0 - - + +
262A SER* 1.3 59.7 + - - +
264A ARG* 2.9 19.1 + - - +
265A VAL 3.3 18.6 - - - +
266A ILE* 4.5 0.2 - - - -
321A GLU* 3.2 60.1 + - + +
324A ASP* 2.7 33.3 + - + +
325A LEU* 3.9 13.5 - - + +
387A LEU* 3.6 19.3 - - + +
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Residues in contact with SER 262 (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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258A SER 3.2 16.8 + - - -
259A TYR* 2.8 27.9 + - - -
261A HIS* 1.3 72.1 - - - +
263A LYS* 1.3 61.5 + - - +
264A ARG* 3.0 7.8 + - - +
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Residues in contact with LYS 263 (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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200A HIS* 5.7 7.4 - - + +
201A LEU* 4.2 21.1 - - + -
259A TYR* 3.3 33.4 - - + +
260A CYS 3.4 5.4 + - - +
261A HIS 3.3 0.4 - - - -
262A SER* 1.3 79.2 + - - +
264A ARG* 1.3 64.7 + - - +
265A VAL* 3.2 14.6 + - + +
293A HIS* 4.4 5.9 + - - -
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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
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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