Contacts of the helix formed by residues 256 - 270 (chain A) in PDB entry 2PFQ
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 ILE 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A HIS* 5.2 0.4 - - + -
254A LEU* 2.6 30.6 + - + -
255A HIS* 1.3 79.8 + - + +
257A THR* 1.3 69.0 + - + +
258A GLU 3.0 1.3 - - - -
259A LYS* 2.8 24.6 + - - +
260A LEU* 3.1 17.1 + - + +
286A LEU* 4.7 6.3 - - + -
313A ILE* 3.1 61.7 - - + +
316A ILE* 3.5 31.2 - - + -
317A LEU* 5.4 6.1 - - + +
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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 ASN* 4.0 10.0 + - - -
254A LEU* 2.9 23.3 + - + +
256A ILE* 1.3 77.9 - - + +
258A GLU* 1.3 61.2 + - - +
259A LYS 2.9 4.9 - - - -
260A LEU* 3.0 11.9 + - - +
261A GLU* 3.0 42.7 + - - +
283A ILE* 4.2 18.1 - - - +
286A LEU* 3.3 47.3 - - + -
287A LYS* 5.0 2.2 - - - +
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Residues in contact with GLU 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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253A ASN* 4.2 17.1 + - - +
254A LEU 3.2 6.7 + - - +
255A HIS* 3.6 21.3 - - - +
257A THR* 1.3 84.0 + - - +
259A LYS* 1.3 58.0 + - + +
261A GLU* 3.9 16.3 - - - +
262A VAL* 3.1 21.3 + - - +
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Residues in contact with LYS 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 HIS* 3.1 29.8 - - + +
256A ILE 2.8 10.2 + - - +
258A GLU* 1.3 82.5 - - + +
260A LEU* 1.3 61.7 + - - +
261A GLU 3.5 0.4 - - - -
262A VAL* 3.4 10.7 - - + +
263A LEU* 3.8 0.7 + - - +
316A ILE* 3.8 36.6 - - + -
320A GLY 4.7 11.2 - - - +
322A LEU* 4.1 2.9 - - + +
325A LEU* 3.1 48.0 - - + +
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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 ILE* 3.5 18.6 - - + +
257A THR* 3.0 9.9 + - - +
259A LYS* 1.3 76.0 - - - +
261A GLU* 1.3 53.1 + - - +
262A VAL 3.0 1.8 - - - -
263A LEU* 2.7 11.2 + - + +
264A ALA* 2.6 32.7 + - - +
279A TYR* 4.2 22.7 - - + -
282A ALA 5.6 0.4 - - - +
283A ILE* 3.5 23.8 - - + +
286A LEU* 4.1 26.0 - - + -
309A MET* 4.6 20.6 - - + +
312A LYS* 5.3 11.0 - - + -
313A ILE* 5.2 3.6 - - + +
316A ILE* 4.8 5.4 - - + -
322A LEU* 4.2 19.5 - - + -
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Residues in contact with GLU 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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253A ASN* 4.9 6.1 - - - +
257A THR* 3.0 24.3 + - - +
258A GLU* 3.9 14.4 - - - +
259A LYS 3.5 0.2 - - - -
260A LEU* 1.3 75.4 - - - +
262A VAL* 1.3 58.2 + - + +
264A ALA* 3.6 5.5 - - + +
265A LYS* 2.9 34.0 + - - +
283A ILE* 3.3 36.1 - - + +
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Residues in contact with VAL 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 GLU 3.1 24.5 - - - +
259A LYS* 3.4 14.8 - - - +
261A GLU* 1.3 80.4 - - + +
263A LEU* 1.3 57.8 + - - +
265A LYS* 4.7 3.1 - - - +
266A ALA* 3.5 16.3 + - - +
325A LEU* 3.9 15.9 - - + -
328A ILE* 4.4 10.7 - - + +
332A VAL* 5.4 1.9 - - - +
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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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259A LYS 4.8 0.7 - - - +
260A LEU* 2.7 11.8 + - + +
262A VAL* 1.3 78.3 - - - +
264A ALA* 1.3 57.9 + - - +
265A LYS 3.2 1.6 - - - -
266A ALA* 2.6 27.7 + - + +
267A TYR* 2.9 38.6 + - + +
279A TYR* 3.8 29.6 - - + +
312A LYS* 5.3 3.1 - - + -
322A LEU* 4.3 18.2 - - + -
324A LYS* 3.6 33.7 - - + -
325A LEU* 3.8 11.4 - - + -
328A ILE* 3.9 19.5 - - + -
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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 LEU 2.6 17.9 + - - +
261A GLU* 3.6 11.9 - - - +
263A LEU* 1.3 73.2 - - - +
265A LYS* 1.3 62.2 + - - +
267A TYR* 3.4 1.4 + - - -
268A SER* 3.0 22.6 + - - -
276A ALA* 3.6 16.8 - - - +
279A TYR* 3.8 28.2 - - + +
280A ALA* 4.9 2.2 - - + +
283A ILE* 4.1 7.2 - - + -
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Residues in contact with LYS 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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261A GLU 2.9 15.9 + - - +
262A VAL* 4.7 3.4 - - - +
264A ALA* 1.3 76.9 - - - +
266A ALA* 1.3 58.0 + - - +
268A SER* 4.0 7.0 - - - -
269A VAL* 2.9 39.7 + - + +
332A VAL* 5.1 1.1 - - + -
336A GLU* 4.8 16.2 - - - +
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Residues in contact with ALA 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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262A VAL 3.5 14.8 + - - +
263A LEU* 2.6 29.5 + - + +
265A LYS* 1.3 73.6 - - - +
267A TYR* 1.3 55.9 + - + +
269A VAL* 3.1 2.6 - - - +
270A GLN* 2.8 47.3 + - - +
328A ILE* 4.5 9.0 - - + -
332A VAL* 3.8 25.3 - - + +
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Residues in contact with TYR 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 LEU* 2.9 46.1 + - + +
266A ALA* 1.3 72.0 - - + +
268A SER* 1.3 59.9 + - - +
270A GLN* 3.2 20.8 + - - +
271A GLY 3.3 1.9 + - - -
272A ASP* 2.6 49.4 + - + +
275A ARG* 3.7 38.4 + - + -
276A ALA* 3.8 19.3 - - + +
279A TYR* 3.9 27.8 + + - -
324A LYS* 5.1 5.4 - - - +
1D G 3.3 12.2 + - - -
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Residues in contact with SER 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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264A ALA 3.0 18.4 + - - -
265A LYS* 3.4 9.9 - - - -
266A ALA 3.1 0.2 - - - -
267A TYR* 1.3 74.4 - - - +
269A VAL* 1.3 64.6 + - - +
271A GLY* 2.8 22.3 + - - -
272A ASP 4.7 1.8 - - - +
273A LYS* 5.1 2.7 + - - +
276A ALA* 3.5 11.6 - - - +
346A THR* 4.2 4.9 + - - +
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Residues in contact with VAL 269 (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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265A LYS* 2.9 18.1 + - + +
266A ALA 3.1 13.5 - - - +
268A SER* 1.3 77.4 - - - +
270A GLN* 1.3 58.5 + - + +
271A GLY 3.0 0.2 - - - -
332A VAL* 3.8 22.0 - - + +
335A LEU* 4.1 30.2 - - + +
336A GLU* 4.1 28.7 - - + +
339A SER* 4.1 11.8 - - - +
346A THR* 2.6 30.9 + - - +
349A ALA* 5.4 0.5 - - - +
350A GLN* 4.6 2.8 - - - +
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Residues in contact with GLN 270 (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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266A ALA* 2.8 30.1 + - - +
267A TYR* 3.2 36.1 - - - +
268A SER 3.1 0.2 - - - -
269A VAL* 1.3 81.0 - - + +
271A GLY* 1.3 60.1 + - - +
272A ASP* 3.4 4.4 + - + +
328A ILE* 4.7 2.1 - - - +
329A SER* 5.2 5.4 + - - -
331A SER* 5.5 1.6 - - - +
332A VAL* 3.2 23.7 - - + +
335A LEU* 4.3 16.6 - - + -
346A THR* 3.5 2.5 - - - -
350A GLN* 3.3 23.1 + - - +
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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