Contacts of the helix formed by residues 248 - 265 (chain A) in PDB entry 2AA0
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 ASN 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A LEU* 4.0 14.6 - - + +
245A SER* 3.2 15.6 + - - +
246A THR 2.9 0.6 - - - -
247A ALA* 1.3 76.9 - - - +
249A LYS* 1.3 66.2 + - - +
250A GLU* 3.3 15.7 + - - +
251A HIS* 2.8 49.6 + - - +
252A ALA* 3.0 10.0 + - - +
279A ARG* 3.8 2.2 - - - -
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Residues in contact with LYS 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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247A ALA 3.6 1.4 + - - -
248A ASN* 1.3 70.8 + - - +
250A GLU* 1.3 66.3 + - - +
252A ALA* 3.0 4.8 + - - +
253A VAL* 2.9 39.7 + - + +
279A ARG* 3.5 18.2 - - - +
285A ILE* 3.9 10.7 - - + +
297A VAL* 4.9 6.2 - - - +
299A GLU* 3.3 50.9 + - - +
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Residues in contact with GLU 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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248A ASN* 3.0 16.8 + - - +
249A LYS* 1.3 80.8 - - - +
251A HIS* 1.3 61.3 + - - +
253A VAL* 3.4 6.7 + - - +
254A GLU* 3.0 33.6 + - + +
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Residues in contact with HIS 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ALA* 6.3 0.8 - - - +
231A ALA* 6.3 0.2 - - + -
237A VAL* 4.6 8.1 - - + -
241A LYS* 3.1 35.2 + - + +
242A THR* 5.1 3.4 + - - -
244A LEU* 3.3 55.0 + - + +
245A SER 3.5 14.1 - - - +
246A THR* 3.6 20.9 - - + +
248A ASN* 2.8 16.6 + - - +
250A GLU* 1.3 70.9 - - - +
252A ALA* 1.3 66.1 + - - +
254A GLU* 3.3 12.9 + - - +
255A VAL* 3.0 49.3 + - + +
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Residues in contact with ALA 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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246A THR* 3.6 25.5 - - - +
248A ASN 3.0 7.2 + - - +
249A LYS 3.5 7.2 - - - +
251A HIS* 1.3 77.2 - - - +
253A VAL* 1.3 57.3 + - - +
255A VAL* 3.4 3.5 + - - +
256A CYS* 3.0 34.6 + - - -
277A MET* 3.8 18.5 - - - +
279A ARG* 3.7 18.8 - - - +
285A ILE* 4.3 8.3 - - + -
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Residues in contact with VAL 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 LYS* 2.9 38.5 + - + +
250A GLU* 3.7 6.5 - - - +
252A ALA* 1.3 75.0 - - - +
254A GLU* 1.3 58.1 + - + +
256A CYS* 3.9 2.2 - - + +
257A THR* 2.7 42.1 + - - +
285A ILE* 4.0 15.5 - - + -
297A VAL* 3.7 44.6 - - + -
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Residues in contact with GLU 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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236A LEU 5.2 0.3 - - - +
237A VAL* 4.5 15.8 - - + +
241A LYS* 2.9 44.0 + - - +
244A LEU* 5.8 0.9 - - - +
250A GLU* 3.0 22.7 + - - +
251A HIS* 3.3 12.4 + - - +
253A VAL* 1.3 77.9 - - + +
255A VAL* 1.3 57.5 + - - +
257A THR* 3.6 5.4 + - - -
258A GLY* 3.0 24.8 + - - -
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Residues in contact with VAL 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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227A PHE* 3.9 31.9 - - + +
228A ALA* 5.5 1.3 - - - -
231A ALA* 4.2 13.7 - - + -
236A LEU* 4.2 4.8 - - + +
237A VAL* 4.5 12.3 - - + -
246A THR* 4.7 5.6 - - + -
251A HIS* 3.0 50.4 + - + +
252A ALA 3.7 3.8 - - - +
254A GLU* 1.3 74.3 - - - +
256A CYS* 1.3 60.5 + - - +
258A GLY* 3.3 1.8 + - - -
259A ALA* 2.9 27.5 + - - +
277A MET* 3.8 18.4 - - + -
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Residues in contact with CYS 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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227A PHE* 5.3 3.6 - - - -
252A ALA 3.0 20.6 + - - +
253A VAL* 3.9 6.1 - - - +
255A VAL* 1.3 77.5 - - - +
257A THR* 1.3 57.6 + - - +
259A ALA* 3.3 4.8 + - - +
260A LEU* 3.0 23.6 + - - +
275A VAL* 3.1 31.9 - - + +
276A VAL 5.2 0.4 - - - -
277A MET* 3.6 37.2 - - - -
285A ILE* 4.0 21.1 - - + -
287A ALA* 3.9 9.6 - - + +
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Residues in contact with THR 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 VAL* 2.7 32.9 + - - +
254A GLU* 3.9 6.1 - - - -
256A CYS* 1.3 76.5 - - - +
258A GLY* 1.3 61.9 + - - +
260A LEU* 3.4 15.9 + - + +
261A ARG* 3.7 28.7 + - - +
287A ALA* 4.0 14.2 - - - +
295A VAL* 4.8 18.5 - - + +
297A VAL* 4.6 4.7 - - - +
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Residues in contact with GLY 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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236A LEU* 3.5 32.9 - - - +
254A GLU 3.0 15.5 + - - -
255A VAL 3.3 3.1 + - - -
256A CYS 3.2 0.2 - - - -
257A THR* 1.3 78.8 - - - +
259A ALA* 1.3 61.7 + - - +
261A ARG* 3.2 35.7 + - - +
262A LEU 3.9 1.0 + - - -
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Residues in contact with ALA 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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220A LEU* 4.8 2.0 - - + -
227A PHE* 3.9 27.6 - - + -
230A LEU* 3.9 9.0 - - + -
236A LEU* 3.6 17.8 - - + +
255A VAL 2.9 17.0 + - - +
256A CYS 3.3 4.7 + - - +
258A GLY* 1.3 73.4 - - - +
260A LEU* 1.3 61.1 + - - +
262A LEU* 2.9 29.9 + - - +
263A LEU* 3.3 8.8 - - - +
275A VAL* 4.0 7.4 - - + -
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Residues in contact with LEU 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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256A CYS 3.0 13.4 + - - +
257A THR* 3.5 12.1 - - + +
259A ALA* 1.3 76.8 - - - +
261A ARG* 1.3 58.1 + - + +
263A LEU* 2.9 9.2 + - + +
264A THR* 2.9 42.3 + - + +
273A LYS* 3.7 31.2 - - + +
274A LEU 4.0 2.7 - - - +
275A VAL* 3.6 14.5 - - + +
287A ALA* 3.9 20.6 - - + +
289A GLN* 4.0 11.0 - - + +
295A VAL* 3.9 39.0 - - + -
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Residues in contact with ARG 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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215A LEU* 5.2 0.7 - - - +
236A LEU* 5.0 7.6 + - + -
257A THR* 3.7 28.0 + - - +
258A GLY* 3.3 22.8 - - - +
259A ALA 3.1 0.6 - - - -
260A LEU* 1.3 77.0 - - + +
262A LEU* 1.3 59.1 + - + +
264A THR* 3.5 11.4 - - - +
265A ALA* 2.9 28.4 + - - -
266A GLY* 5.2 3.4 - - - +
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A GLN* 4.6 14.5 - - + +
214A LEU* 3.5 45.7 - - + +
215A LEU* 3.5 17.3 + - - +
230A LEU* 4.1 19.5 - - + -
234A HIS* 4.2 27.6 - - + +
236A LEU* 3.9 30.3 - - + -
258A GLY 5.1 0.2 - - - +
259A ALA 2.9 13.2 + - - +
261A ARG* 1.3 78.6 - - + +
263A LEU* 1.3 59.1 + - + +
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Residues in contact with LEU 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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214A LEU* 3.3 28.9 - - + +
215A LEU* 3.7 10.3 - - - +
217A THR* 3.6 32.3 - - + +
218A ASN 3.9 11.0 - - - +
220A LEU* 4.2 8.7 - - + -
259A ALA 3.3 18.4 - - - +
260A LEU* 2.9 7.4 + - + +
262A LEU* 1.3 84.1 - - + +
264A THR* 1.3 62.2 + - + +
265A ALA* 3.6 0.6 - - - +
273A LYS* 3.0 28.3 + - + -
274A LEU 3.7 28.3 - - - +
275A VAL* 4.0 15.5 - - + -
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Residues in contact with THR 264 (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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260A LEU* 2.9 29.4 + - + +
261A ARG* 3.5 10.4 - - - +
263A LEU* 1.3 77.9 - - - +
265A ALA* 1.3 71.7 + - - +
266A GLY* 3.4 10.2 + - - -
267A GLN* 2.9 33.3 + - - +
273A LYS* 3.8 22.0 - - + +
289A GLN* 3.7 30.3 - - + +
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Residues in contact with ALA 265 (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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215A LEU* 3.7 25.1 - - + -
261A ARG 2.9 18.0 + - - -
263A LEU 3.6 1.2 - - - +
264A THR* 1.3 78.8 - - - +
266A GLY* 1.3 57.5 + - - +
267A GLN* 3.2 22.0 + - - +
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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