Contacts of the helix formed by residues 251 - 268 (chain A) in PDB entry 2P6U
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 THR 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A GLU* 3.2 3.4 + - - +
250A SER* 1.3 86.8 + - - +
252A ARG* 1.3 67.0 + - - +
253A ARG* 4.1 12.6 - - + +
254A GLY* 3.7 20.0 + - - +
255A ALA* 3.4 12.1 + - - +
329A THR* 3.0 21.5 - - - +
351A PHE* 5.7 6.8 - - + +
712A PO4 5.4 1.1 - - - -
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Residues in contact with ARG 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A THR* 1.3 75.3 - - - +
253A ARG* 1.3 67.2 + - - +
254A GLY 3.3 0.2 - - - -
255A ALA* 3.4 2.1 + - - +
256A GLU* 3.1 32.3 + - - +
303A HIS* 3.6 27.1 - - + +
304A ALA* 2.9 31.3 - - - +
305A GLY* 3.5 14.6 - - - +
329A THR* 4.6 0.9 - - + -
586A ALA* 4.1 6.9 - - - +
589A ASP* 2.8 43.0 + - - -
592A ARG* 4.0 4.2 - - - +
712A PO4 3.0 34.7 + - - +
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Residues in contact with ARG 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A THR* 4.1 10.2 - - + +
252A ARG* 1.3 80.1 - - - +
254A GLY* 1.3 57.4 + - - +
256A GLU* 3.4 11.3 + - - +
257A LYS* 2.9 38.0 + - + +
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Residues in contact with GLY 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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249A GLU* 3.5 12.0 - - - +
251A THR* 3.7 18.3 - - - -
252A ARG 3.3 0.2 - - - -
253A ARG* 1.3 80.2 - - - +
255A ALA* 1.3 64.7 + - - +
257A LYS* 3.6 10.5 - - - +
258A THR* 3.1 28.2 + - - -
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Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A GLU* 4.0 4.5 - - + +
251A THR 3.4 20.8 + - - +
252A ARG* 3.4 5.3 + - - +
253A ARG 3.3 0.6 - - - -
254A GLY* 1.3 75.9 - - - +
256A GLU* 1.3 58.6 - - - +
259A ALA* 2.8 31.5 + - - +
301A PHE* 4.1 4.7 - - + -
302A HIS 5.6 0.4 - - - +
303A HIS* 4.9 4.5 - - + +
327A VAL* 3.4 34.9 - - + +
328A ALA* 4.3 3.4 - - - +
329A THR* 4.1 13.0 - - + -
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Residues in contact with GLU 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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252A ARG* 3.1 19.3 + - - +
253A ARG* 3.9 7.1 - - - +
255A ALA* 1.3 74.1 - - - +
257A LYS* 1.3 66.5 + - - +
259A ALA* 3.2 1.6 + - - +
260A VAL* 3.1 29.3 + - - +
287A MET* 3.5 14.7 - - - +
290A LYS* 4.1 24.7 + - + +
301A PHE* 3.4 42.6 - - + -
303A HIS* 3.2 31.1 + - + +
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Residues in contact with LYS 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 ARG* 2.9 26.6 + - + +
254A GLY* 3.6 10.1 - - - +
256A GLU* 1.3 76.6 - - - +
258A THR* 1.3 64.9 + - - +
260A VAL* 3.2 21.5 - - - +
261A LYS* 3.4 27.8 + - + +
290A LYS* 5.6 1.1 - - - +
346A ARG* 5.8 3.0 - - - +
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Residues in contact with THR 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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231A PHE* 4.6 18.2 - - + -
247A VAL* 4.9 2.2 - - + -
249A GLU* 2.6 29.3 + - - +
254A GLY 3.1 7.9 + - - -
255A ALA 4.0 2.0 - - - -
257A LYS* 1.3 78.8 - - - +
259A ALA* 1.3 59.0 + - - +
260A VAL 2.8 11.8 + - - -
261A LYS* 3.2 21.7 + - + +
262A LEU* 3.2 34.3 + - + +
327A VAL* 3.9 10.3 - - + -
346A ARG* 3.6 14.3 + - - +
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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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255A ALA 2.8 24.1 + - - +
256A GLU 3.2 5.1 + - - +
258A THR* 1.3 73.2 - - - +
260A VAL* 1.3 57.8 + - - +
262A LEU* 4.4 1.3 - - - -
263A SER 3.6 0.3 + - - -
294A CYS* 3.3 7.3 - - - -
299A ALA* 3.2 28.9 - - - +
300A ALA* 3.4 16.6 - - - +
301A PHE* 3.3 31.2 - - + -
327A VAL* 3.6 12.8 - - + +
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Residues in contact with VAL 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 GLU 3.1 14.6 + - - +
257A LYS* 3.2 13.5 - - - +
258A THR 2.8 1.4 + - - -
259A ALA* 1.3 75.9 - - - +
261A LYS* 1.3 64.8 + - + +
262A LEU 3.1 1.1 - - - -
263A SER* 2.1 42.7 + - - +
264A ALA* 3.5 0.9 + - - +
290A LYS* 4.0 23.3 - - + -
293A GLU* 5.3 3.8 - - - +
294A CYS* 3.7 16.4 - - - -
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Residues in contact with LYS 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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231A PHE* 5.2 4.6 - - - -
232A GLU* 4.7 17.2 - - - +
257A LYS* 3.8 32.6 - - + +
258A THR* 3.2 14.5 + - - +
260A VAL* 1.3 82.5 - - + +
262A LEU* 1.3 61.1 + - + +
264A ALA* 2.9 32.9 + - - +
265A ILE* 4.0 2.9 + - - +
346A ARG* 3.2 29.1 - - - +
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Residues in contact with LEU 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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231A PHE* 4.9 6.7 - - + -
232A GLU* 5.3 6.5 - - - +
235A VAL* 3.5 35.2 - - + -
247A VAL* 4.3 8.7 - - + -
258A THR* 3.2 31.1 + - + +
259A ALA 4.4 3.6 - - - +
260A VAL 3.1 0.8 - - - -
261A LYS* 1.3 80.4 - - + +
263A SER* 1.3 67.2 + - - +
265A ILE* 2.7 31.9 + - + +
266A THR* 2.8 14.7 + - + +
299A ALA* 4.5 3.4 - - + -
325A VAL* 3.3 37.5 - - + -
327A VAL* 3.9 9.0 - - + -
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Residues in contact with SER 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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259A ALA 3.8 2.7 - - - -
260A VAL* 2.1 40.1 + - - +
262A LEU* 1.3 72.8 - - - +
264A ALA* 1.3 52.8 + - - -
266A THR* 2.9 10.9 + - - -
267A ALA* 2.7 37.2 + - - +
293A GLU* 4.4 1.9 + - - -
294A CYS* 3.9 16.0 - - - -
297A LYS* 3.3 26.6 + - - +
299A ALA* 3.4 19.0 - - - +
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Residues in contact with ALA 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 VAL 3.5 0.4 + - - +
261A LYS* 2.9 19.1 + - - +
263A SER* 1.3 83.8 + - - +
265A ILE* 1.3 63.7 + - + +
267A ALA* 3.3 14.3 - - - +
268A LYS* 3.7 9.9 + - - +
297A LYS* 4.4 8.7 - - - +
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Residues in contact with ILE 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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232A GLU* 3.4 48.7 - - + +
235A VAL* 5.0 2.7 - - + -
236A GLU* 3.4 43.5 - - + +
239A VAL* 4.8 5.8 - - + -
261A LYS 4.6 2.7 - - - +
262A LEU* 2.7 35.0 + - + +
264A ALA* 1.3 69.1 - - + +
266A THR* 1.3 61.0 + - + +
267A ALA 2.9 9.8 + - - -
268A LYS* 3.0 35.3 - - - +
269A TYR* 3.0 10.5 - - + -
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Residues in contact with THR 266 (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 VAL* 5.8 0.2 - - + -
239A VAL* 4.3 7.6 - - + -
262A LEU* 2.8 10.0 + - + +
263A SER* 2.9 18.7 - - - -
265A ILE* 1.3 74.0 - - + +
267A ALA* 1.3 59.9 + - - +
268A LYS 3.5 0.2 - - - -
269A TYR* 3.4 9.8 + - - +
270A VAL* 3.3 20.6 + - - +
297A LYS 2.5 24.2 + - - +
298A GLY* 3.7 6.1 - - - -
299A ALA* 3.0 15.8 + - - +
324A LYS* 3.3 30.0 - - + +
325A VAL* 3.4 25.1 - - + -
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Residues in contact with ALA 267 (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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263A SER 2.7 24.9 + - - +
264A ALA* 3.3 9.9 - - - +
265A ILE 2.9 1.8 + - - -
266A THR* 1.3 69.1 - - - +
268A LYS* 1.3 57.9 + - - +
269A TYR 2.9 8.9 + - - -
270A VAL 2.8 22.6 + - - +
271A GLU* 4.9 1.9 - - - +
297A LYS* 3.5 31.6 - - + +
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Residues in contact with LYS 268 (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 GLU* 3.3 29.0 + - - -
264A ALA 4.1 5.2 - - - +
265A ILE* 3.0 33.3 - - - +
267A ALA* 1.3 76.4 - - - +
269A TYR* 1.3 67.9 + - + +
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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