Contacts of the helix formed by residues 255 - 270 (chain A) in PDB entry 5F0P
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 ASP 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A VAL* 4.0 18.6 - - + +
198A GLN* 4.1 12.1 - - - +
199A HIS* 5.5 0.9 - - - -
213A ARG* 2.9 43.7 + - - -
253A CYS* 3.1 19.5 - - - +
254A ARG* 1.3 76.7 - - - +
256A ALA* 1.3 59.4 + - - +
257A LEU* 3.4 3.5 + - - -
258A ALA* 3.0 19.2 + - - +
259A GLN* 2.8 34.9 + - - +
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Residues in contact with ALA 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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255A ASP* 1.3 72.9 - - - +
257A LEU* 1.3 57.4 + - - +
260A GLU* 2.9 34.9 + - - +
290A HIS* 3.5 33.0 + - + +
292A ASN* 4.1 19.1 - - + +
293A VAL* 3.5 22.7 - - + +
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Residues in contact with LEU 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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194A TRP* 4.1 15.9 - - + -
198A GLN* 6.2 0.2 - - - -
210A GLU* 4.1 28.3 - - + +
213A ARG* 3.7 46.2 - - + +
214A GLN* 3.2 35.4 - - + +
217A ARG* 5.7 0.4 - - + -
255A ASP* 3.3 8.1 + - - +
256A ALA* 1.3 77.4 - - - +
258A ALA* 1.3 62.4 + - - +
260A GLU* 4.1 3.1 - - - +
261A TYR* 3.2 22.0 + - + +
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Residues in contact with ALA 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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191A ASN* 3.9 12.6 - - - +
194A TRP* 3.5 28.5 - - + -
195A VAL* 4.2 2.9 - - + -
213A ARG* 3.9 5.8 - - - +
253A CYS* 4.0 13.7 - - - -
255A ASP* 3.0 19.2 + - - +
257A LEU* 1.3 75.0 - - - +
259A GLN* 1.3 56.4 + - - +
261A TYR* 3.2 1.9 + - - -
262A LEU* 2.7 42.8 + - + +
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Residues in contact with GLN 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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250A VAL* 3.1 39.7 + - + +
251A VAL* 3.6 18.2 + - - +
253A CYS* 3.9 4.5 - - - -
254A ARG* 3.8 14.3 - - - +
255A ASP 2.8 26.4 + - - +
256A ALA 3.9 2.7 - - - +
258A ALA* 1.3 72.6 - - - +
260A GLU* 1.3 63.2 + - - +
262A LEU* 4.2 0.8 - - - +
263A MET* 3.1 31.9 + - - +
289A LEU* 3.3 20.0 - - + +
290A HIS* 2.7 34.3 + - - +
293A VAL* 3.6 7.5 - - + +
504A GOL 3.9 8.1 + - - -
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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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214A GLN* 6.0 0.2 + - - -
256A ALA* 2.9 19.0 + - - +
257A LEU* 4.1 3.8 - - - +
259A GLN* 1.3 75.7 - - - +
261A TYR* 1.3 63.3 + - - +
263A MET* 4.3 1.0 - - - +
264A GLU* 3.3 43.4 + - - +
292A ASN 4.1 4.2 - - - +
293A VAL* 3.8 22.3 - - + +
294A ASN* 3.0 39.2 + - - +
297A ASN* 5.6 1.7 + - - -
298A ILE* 4.5 4.7 - - + +
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Residues in contact with TYR 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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194A TRP* 3.7 22.9 - + + -
214A GLN* 5.8 1.6 - - - +
217A ARG* 3.2 66.4 + - + -
218A ILE* 3.9 7.4 - - - +
221A GLY* 3.6 24.2 - - - -
257A LEU* 3.2 19.2 + - + +
258A ALA 3.2 2.1 + - - +
260A GLU* 1.3 81.6 - - - +
262A LEU* 1.3 70.2 + - + +
264A GLU* 3.4 9.1 + - + +
265A CYS* 2.8 42.2 + - + +
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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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187A PHE* 3.8 30.3 - - + -
191A ASN* 3.5 28.5 - - - +
194A TRP* 4.5 1.3 - - + -
220A VAL* 4.0 14.4 - - + -
221A GLY* 5.1 1.3 - - - -
224A LEU* 4.1 14.3 - - + +
250A VAL* 3.8 31.0 - - + -
253A CYS* 5.4 0.4 - - - -
258A ALA* 2.7 29.4 + - + +
259A GLN 4.2 1.1 - - - +
261A TYR* 1.3 89.4 - - + +
263A MET* 1.3 59.1 + - - +
265A CYS* 3.2 5.3 + - + +
266A ILE* 2.9 33.6 + - - +
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Residues in contact with MET 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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247A LEU* 3.9 21.3 - - - -
250A VAL* 3.9 17.0 - - + -
259A GLN 3.1 21.7 + - - +
262A LEU* 1.3 71.4 - - - +
264A GLU* 1.3 64.9 + - - +
266A ILE* 3.5 7.4 + - - +
267A ILE* 3.4 17.0 + - - +
282A PHE* 3.5 60.0 - - + +
285A ALA* 3.9 12.6 - - + -
286A CYS* 3.5 23.6 - - - +
289A LEU* 3.9 13.9 - - + -
298A ILE* 3.9 18.2 - - + -
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Residues in contact with GLU 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 GLU* 3.3 37.3 + - - +
261A TYR* 3.7 8.3 - - + +
263A MET* 1.3 78.4 - - - +
265A CYS* 1.3 60.0 + - - +
267A ILE* 3.2 11.6 + - - +
268A GLN* 3.1 25.0 + - - +
297A ASN* 3.8 28.5 + - - +
298A ILE* 4.1 18.1 + - + +
301A ALA* 5.2 7.6 - - + -
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Residues in contact with CYS 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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221A GLY* 4.1 15.9 - - - -
224A LEU* 4.0 17.5 - - + -
225A VAL* 5.3 1.6 - - - -
261A TYR* 2.8 44.6 + - + +
262A LEU* 3.2 11.2 + - - +
264A GLU* 1.3 73.4 - - - +
266A ILE* 1.3 64.1 + - - +
268A GLN* 3.6 9.4 + - - +
269A VAL* 3.1 45.8 + - - +
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Residues in contact with ILE 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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224A LEU* 4.2 8.0 - - + +
238A TYR* 3.3 26.0 - - - +
243A LEU* 4.0 15.9 - - + -
246A ILE* 3.7 30.1 - - + -
247A LEU* 4.3 3.4 - - + -
250A VAL* 5.1 1.3 - - + -
262A LEU 2.9 20.0 + - - +
263A MET* 3.7 28.5 - - - +
265A CYS* 1.3 74.4 - - - +
267A ILE* 1.3 65.1 + - - +
269A VAL 3.2 11.1 + - - -
270A PHE* 3.2 26.1 + - + -
275A HIS* 3.6 8.6 - - + +
282A PHE* 4.0 16.8 - - + -
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Residues in contact with ILE 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 MET 3.6 7.0 - - - +
264A GLU* 3.2 12.9 + - - +
266A ILE* 1.3 77.0 - - - +
268A GLN* 1.3 63.5 + - - +
270A PHE 3.4 1.2 - - - +
275A HIS* 2.9 27.6 + - + -
282A PHE* 3.5 35.2 - - + -
298A ILE* 3.4 30.7 - - + +
301A ALA* 4.0 24.2 - - + +
302A LEU* 4.0 22.4 - - + +
305A ARG* 3.2 29.7 + - - -
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Residues in contact with GLN 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 GLU 3.1 13.5 + - - +
265A CYS* 3.9 9.5 - - - +
267A ILE* 1.3 81.7 - - - +
269A VAL* 1.3 67.4 + - - +
305A ARG* 3.2 27.5 + - - +
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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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224A LEU* 3.4 22.0 - - + +
225A VAL* 3.7 29.6 - - + +
228A SER* 3.3 32.3 + - - +
265A CYS* 3.1 32.4 + - - +
266A ILE 3.2 1.1 + - - +
268A GLN* 1.3 89.1 - - + +
270A PHE* 1.3 69.5 + - + +
271A PRO* 4.2 1.2 - - - +
305A ARG* 5.0 1.1 + - - -
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Residues in contact with PHE 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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224A LEU* 3.9 20.0 - - + -
227A LEU* 4.2 4.0 - - + -
228A SER* 3.9 28.7 - - - -
233A VAL* 5.1 3.4 - - + -
238A TYR* 3.4 45.5 - + + +
242A VAL* 4.0 20.0 - - + -
246A ILE* 4.1 15.0 - - + -
266A ILE* 3.2 29.5 + - + +
267A ILE 3.4 2.4 - - - +
269A VAL* 1.3 86.6 - - + +
271A PRO* 1.4 69.3 - - + +
274A PHE* 4.1 11.7 - + + -
275A HIS* 3.1 25.6 + - + -
305A ARG* 3.3 13.1 + - - -
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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