Contacts of the helix formed by residues 281 - 295 (chain A) in PDB entry 1FPQ
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 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280A TRP* 1.3 77.0 - - - +
282A ASP* 1.3 67.1 + - - +
283A GLU* 3.4 6.9 + - - +
284A LYS* 3.8 27.2 + - - +
285A CYS* 3.0 21.0 + - - +
336A ARG* 3.6 18.0 - - - +
338A ARG* 3.3 2.2 - - - +
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Residues in contact with ASP 282 (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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281A SER* 1.3 73.5 - - - +
283A GLU* 1.3 65.8 + - + +
285A CYS* 3.2 2.5 + - - +
286A ILE* 2.9 35.2 + - + +
336A ARG* 5.5 1.2 - - - -
338A ARG* 2.9 25.0 + - - +
345A LYS* 5.2 8.8 - - - +
346A LEU* 4.0 21.8 - - + +
349A LEU* 6.0 1.5 - - + +
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Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A SER* 3.3 8.8 + - - +
282A ASP* 1.3 80.6 - - + +
284A LYS* 1.3 68.1 + - + +
286A ILE* 3.3 10.6 + - - +
287A GLU* 3.1 30.5 + - - +
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Residues in contact with LYS 284 (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 PHE* 3.6 16.2 - - + -
280A TRP* 3.3 43.2 - - + -
281A SER* 3.4 16.9 + - - +
282A ASP 3.4 0.6 - - - -
283A GLU* 1.3 75.5 - - + +
285A CYS* 1.3 65.8 + - - +
287A GLU* 3.1 29.1 + - - +
288A PHE* 3.2 16.4 + - - -
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Residues in contact with CYS 285 (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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277A CYS* 3.4 34.3 - - - -
280A TRP* 3.6 8.3 - - - -
281A SER 3.0 23.0 + - - +
282A ASP* 3.5 3.8 - - - +
284A LYS* 1.3 77.1 - - - +
286A ILE* 1.3 63.7 + - - +
287A GLU 3.2 0.3 + - - -
288A PHE* 3.3 23.2 + - + -
289A LEU* 2.9 33.9 + - + +
338A ARG* 3.8 11.4 - - - -
346A LEU* 4.0 18.2 - - + -
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Residues in contact with ILE 286 (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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282A ASP* 2.9 31.3 + - + +
283A GLU* 3.5 9.6 - - - +
285A CYS* 1.3 74.6 - - - +
287A GLU* 1.3 57.8 + - + +
289A LEU* 4.0 6.0 - - - +
290A SER* 2.8 43.0 + - - +
346A LEU* 4.4 16.2 - - + +
349A LEU* 3.7 58.3 - - + +
350A SER* 4.2 2.5 - - - -
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Residues in contact with GLU 287 (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 PHE* 3.6 26.4 - - + +
283A GLU* 3.1 24.7 + - - +
284A LYS* 3.1 21.8 - - - +
285A CYS 3.1 0.4 - - - -
286A ILE* 1.3 79.5 - - + +
288A PHE* 1.3 61.3 + - - +
290A SER* 3.7 4.7 - - - -
291A ASN* 3.1 27.8 + - - +
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Residues in contact with PHE 288 (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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216A VAL* 5.7 0.4 - - + -
261A MSE 3.5 55.8 - - + +
262A PHE* 3.6 9.6 - + + -
265A VAL* 4.8 0.2 - - - +
273A LEU* 3.8 28.9 - - + -
276A VAL* 4.1 9.9 - - + -
277A CYS* 4.1 7.6 - - - -
280A TRP* 3.6 31.0 - + - -
284A LYS 3.2 22.5 + - - -
285A CYS* 3.6 29.2 - - - -
287A GLU* 1.3 77.4 - - - +
289A LEU* 1.3 73.5 + - + +
291A ASN* 3.2 3.6 + - - +
292A CYS* 2.9 31.8 + - - -
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Residues in contact with LEU 289 (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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273A LEU* 4.1 26.2 - - + -
277A CYS* 4.6 5.2 - - - -
285A CYS* 2.9 32.0 + - + +
286A ILE 4.6 0.4 - - - +
288A PHE* 1.3 79.8 - - + +
290A SER* 1.3 61.6 + - - +
292A CYS* 3.0 8.6 + - + +
293A HIS 2.8 24.1 + - - -
302A VAL* 4.6 6.1 - - + -
304A ILE* 4.4 15.0 - - + -
346A LEU* 4.2 36.6 - - + +
350A SER* 3.7 15.5 - - - +
352A PHE* 3.4 12.5 - - + -
370A PHE* 4.2 18.8 - - + -
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Residues in contact with SER 290 (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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286A ILE* 2.8 29.3 + - - +
287A GLU* 3.7 5.4 - - - -
289A LEU* 1.3 76.2 - - - +
291A ASN* 1.3 63.6 + - - +
293A HIS* 3.0 4.3 + - - +
294A LYS* 2.9 33.5 + - - +
349A LEU 4.6 0.7 + - - -
350A SER* 3.6 29.7 + - - -
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Residues in contact with ASN 291 (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 MSE 3.1 24.7 + - - +
262A PHE* 3.2 22.4 + - - +
263A ALA 3.9 13.3 - - - +
264A SER* 4.5 10.1 - - - -
265A VAL* 3.5 11.9 + - + +
287A GLU* 3.1 18.5 + - - +
288A PHE 3.2 7.1 + - - +
289A LEU 3.2 0.6 - - - -
290A SER* 1.3 77.6 - - - +
292A CYS* 1.3 62.1 + - - +
294A LYS* 3.4 30.2 + - - +
295A ALA* 3.2 18.0 + - - +
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Residues in contact with CYS 292 (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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216A VAL* 4.1 22.2 - - - -
265A VAL* 3.7 17.5 - - - -
271A MSE 3.6 23.0 - - - +
273A LEU* 4.4 16.8 - - - -
288A PHE* 2.9 23.0 + - - -
289A LEU* 3.0 13.6 + - - +
291A ASN* 1.3 73.4 - - - +
293A HIS* 1.3 66.5 + - - +
295A ALA 3.4 0.5 + - - -
296A LEU* 3.0 27.9 + - - +
302A VAL* 4.1 14.4 - - + -
352A PHE* 4.5 0.4 - - - -
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Residues in contact with HIS 293 (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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289A LEU 2.8 8.2 + - - +
290A SER* 3.0 9.8 + - - +
292A CYS* 1.3 77.2 - - - +
294A LYS* 1.3 67.5 + - - +
296A LEU* 3.1 12.2 + - - +
350A SER 3.9 8.5 - - - +
351A GLY* 3.4 29.5 + - - -
352A PHE* 3.6 35.4 - + + -
372A LYS* 3.3 61.1 + - + -
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Residues in contact with LYS 294 (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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267A GLN* 5.0 4.2 + - - -
290A SER* 2.9 23.6 + - - +
291A ASN* 3.5 31.0 + - - +
292A CYS 3.3 0.2 - - - -
293A HIS* 1.3 81.8 + - + +
295A ALA* 1.3 60.6 + - - +
296A LEU 3.4 5.0 + - - +
372A LYS* 4.5 3.4 + - - +
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Residues in contact with ALA 295 (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 VAL* 3.3 43.5 - - + +
266A PRO 3.7 3.6 - - - +
267A GLN* 3.5 25.3 + - + +
268A GLY 3.5 18.2 + - - +
271A MSE 3.6 8.7 - - + -
291A ASN 3.2 4.8 + - - +
294A LYS* 1.3 77.3 - - - +
296A LEU* 1.3 63.9 + - - +
297A SER* 3.7 0.5 + - - -
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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