Contacts of the helix formed by residues 248 - 260 (chain A) in PDB entry 2JAM
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 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A GLU* 2.7 33.8 + - - -
247A ILE* 1.3 76.1 - - - +
249A GLU* 1.3 63.3 + - - +
250A SER* 3.7 6.0 + - - -
251A ALA* 3.1 26.0 + - - +
252A LYS* 3.4 15.0 + - - +
277A TRP* 3.9 0.3 - - - -
282A THR 3.8 11.8 + - - -
284A LEU* 3.8 22.2 - - - +
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Residues in contact with GLU 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 ILE 3.8 1.0 + - - -
248A SER* 1.3 72.2 - - - +
250A SER* 1.3 58.3 + - - +
252A LYS* 3.2 23.8 + - - +
253A ASP* 2.9 41.1 + - + +
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Residues in contact with SER 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 SER* 3.2 8.4 + - - -
249A GLU* 1.3 79.4 - - - +
251A ALA* 1.3 56.9 + - - +
253A ASP* 3.3 6.0 + - - +
254A PHE* 2.9 25.5 + - - +
275A HIS* 3.4 22.8 - - - -
276A PRO* 4.3 1.7 - - - +
277A TRP* 3.7 3.7 + - - +
282A THR* 2.7 44.5 + - - +
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Residues in contact with ALA 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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118A GLU* 3.9 1.1 - - - +
210A THR* 5.4 0.2 - - - +
214A LEU* 3.6 25.8 - - + -
247A ILE* 3.7 8.7 - - + -
248A SER* 3.1 23.6 + - - +
250A SER* 1.3 74.3 - - - +
252A LYS* 1.3 57.8 + - - +
254A PHE* 3.4 2.6 + - - +
255A ILE* 3.0 35.5 + - - +
277A TRP* 3.6 28.6 - - + +
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Residues in contact with LYS 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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239A PHE* 3.9 49.1 + - + +
244A TRP* 3.4 35.2 + - + +
245A ASP* 5.2 2.0 + - - +
247A ILE* 3.5 28.7 + - - -
248A SER 3.5 8.7 - - - +
249A GLU* 3.2 23.1 + - - +
251A ALA* 1.3 72.1 - - - +
253A ASP* 1.3 60.9 + - - +
255A ILE* 3.4 2.6 + - - +
256A CYS* 2.9 37.2 + - - -
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Residues in contact with ASP 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 GLU* 2.9 30.2 + - + +
250A SER* 3.5 7.9 - - - +
252A LYS* 1.3 75.9 - - - +
254A PHE* 1.3 61.2 + - - +
256A CYS* 3.3 7.2 + - - +
257A HIS* 3.0 50.7 + - - -
275A HIS* 2.8 25.6 + - - +
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Residues in contact with PHE 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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125A ILE* 3.9 8.5 - - + -
129A LEU* 4.0 4.9 - - + -
210A THR* 3.8 27.6 - - + -
250A SER 2.9 16.8 + - - +
251A ALA 3.5 5.2 - - - +
253A ASP* 1.3 75.8 - - - +
255A ILE* 1.3 64.6 - - - +
257A HIS* 3.2 14.0 + - - +
258A LEU* 3.4 37.2 + - + +
267A TYR* 5.2 2.0 - + - -
272A ALA* 3.6 22.9 - - + -
275A HIS* 3.6 37.6 + + + +
277A TRP* 3.7 24.2 - + + -
278A ILE* 3.4 31.9 - - + -
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Residues in contact with ILE 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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207A GLY* 4.0 9.6 - - - +
210A THR* 3.6 28.7 - - + -
211A TYR* 3.9 20.4 - - + -
214A LEU* 4.1 6.7 - - + -
239A PHE* 4.2 9.6 - - + -
244A TRP* 3.6 35.0 - - + -
251A ALA 3.0 21.8 + - - +
252A LYS* 3.7 4.5 - - - +
254A PHE* 1.3 79.3 - - - +
256A CYS* 1.3 59.0 + - - +
258A LEU* 3.1 8.3 + - - +
259A LEU* 2.9 52.1 + - + +
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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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237A TYR* 4.8 13.5 - - - -
239A PHE* 3.6 28.0 - - - -
252A LYS 2.9 21.9 + - - +
253A ASP* 3.8 6.7 - - - +
255A ILE* 1.3 76.5 - - - +
257A HIS* 1.3 60.4 + - + +
259A LEU* 3.8 6.0 - - - +
260A GLU* 2.9 29.5 + - - +
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Residues in contact with HIS 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 ASP* 3.0 52.1 + - - -
254A PHE* 3.2 8.6 + - - +
256A CYS* 1.3 78.1 - - + +
258A LEU* 1.3 59.8 + - - +
260A GLU* 3.6 13.9 - - + +
265A GLU 4.7 4.4 - - - +
266A ARG* 3.6 0.5 - - - -
267A TYR* 3.0 76.9 + + + -
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Residues in contact with LEU 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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129A LEU* 4.8 3.8 - - + -
203A CYS* 3.6 21.3 - - + +
204A TRP* 3.4 10.7 - - - -
206A ILE* 4.1 11.2 - - + -
207A GLY* 3.7 31.4 - - - +
254A PHE* 3.4 41.8 + - + +
255A ILE* 3.1 5.8 + - - +
257A HIS* 1.3 76.5 - - - +
259A LEU* 1.3 58.6 + - - +
260A GLU 3.3 2.0 - - - -
266A ARG* 3.1 27.0 + - - -
267A TYR* 3.8 33.0 - - + +
272A ALA* 4.2 13.0 - - + -
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Residues in contact with LEU 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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204A TRP* 3.5 32.5 + - + +
207A GLY 3.7 4.7 - - - +
208A VAL* 3.5 41.3 - - + +
211A TYR* 4.6 3.1 - - + -
219A PRO* 4.5 9.2 - - + -
232A ILE 5.6 0.3 - - - +
235A GLY* 5.2 1.1 - - - -
237A TYR* 3.5 55.2 - - + +
255A ILE* 2.9 40.8 + - + +
256A CYS* 3.8 3.8 - - - +
258A LEU* 1.3 73.9 - - - +
260A GLU* 1.3 67.8 + - - +
261A LYS* 3.2 4.3 + - - +
189B PRO* 5.0 0.5 - - - +
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Residues in contact with GLU 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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235A GLY 5.8 2.2 - - - -
256A CYS 2.9 14.0 + - - +
257A HIS* 3.6 21.1 - - + +
258A LEU 3.3 0.4 - - - -
259A LEU* 1.3 72.1 - - - +
261A LYS* 1.3 76.3 + - - +
262A ASP* 3.0 43.9 + - - +
265A GLU* 3.8 15.1 - - + +
266A ARG* 2.9 46.3 + - - +
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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
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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