Contacts of the helix formed by residues 247 - 261 (chain A) in PDB entry 2FO1
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 GLN 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A GLU 4.1 16.7 + - - +
212A LYS* 5.4 6.2 - - - +
246A GLY* 1.3 79.1 - - - +
248A GLY* 1.3 59.0 + - - +
249A TRP 3.0 6.1 - - - -
250A LYS* 3.2 30.3 + - - +
251A LEU* 3.5 4.9 + - - +
320A ASN* 5.5 13.7 - - + +
321A ILE 5.4 0.3 - - - -
322A TYR* 4.6 16.8 + - - -
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Residues in contact with GLY 248 (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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211A GLU 4.4 2.6 + - - -
212A LYS 4.9 0.2 - - - -
213A TYR* 3.1 30.5 - - - +
214A GLU 3.5 7.7 + - - -
215A CYS* 3.6 8.6 - - - -
246A GLY 3.3 1.6 - - - -
247A GLN* 1.3 77.8 - - - +
249A TRP* 1.3 54.0 + - - +
250A LYS 3.1 0.9 - - - -
251A LEU* 3.6 10.5 - - - +
252A LYS* 2.6 35.3 + - - +
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Residues in contact with TRP 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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214A GLU 4.7 0.2 + - - -
215A CYS* 3.7 15.1 - - + -
216A VAL 3.0 18.6 + - - -
217A ILE* 4.1 15.5 - - + -
244A LEU* 3.2 46.5 - - + +
245A ILE 3.3 20.4 + - - -
246A GLY 4.1 1.3 + - - +
247A GLN 3.0 0.2 - - - -
248A GLY* 1.3 78.5 - - - +
250A LYS* 1.3 60.0 + - - +
252A LYS* 3.7 26.4 - - + +
253A LYS* 3.4 13.7 + - - +
286A LEU* 5.3 10.6 - - + +
322A TYR* 3.2 46.4 + + + -
347A PHE* 6.2 2.9 - + + -
349A TYR* 4.0 12.7 + + - -
355A ILE* 4.6 17.9 - - + -
548A PHE* 3.9 29.8 - + - -
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Residues in contact with LYS 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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247A GLN* 3.2 23.9 + - + +
248A GLY 3.1 0.2 - - - -
249A TRP* 1.3 78.2 - - - +
251A LEU* 1.3 62.2 + - - +
253A LYS* 2.9 50.4 + - + +
254A ASP* 3.3 29.4 + - - +
322A TYR* 4.2 16.9 - - + -
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Residues in contact with LEU 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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212A LYS 4.7 13.5 - - - +
213A TYR* 4.8 10.1 - - + +
247A GLN 3.5 3.4 + - - +
248A GLY* 3.3 15.6 + - - +
250A LYS* 1.3 81.0 - - - +
252A LYS* 1.3 67.2 + - - +
253A LYS 3.1 0.3 + - - -
254A ASP* 3.1 15.8 + - + +
255A ARG* 3.0 77.4 + - + +
549A PHE* 4.7 16.4 - - + -
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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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215A CYS* 4.2 6.7 - - - -
248A GLY 2.6 22.2 + - - +
249A TRP* 3.7 25.1 - - + +
250A LYS 3.1 0.2 - - - -
251A LEU* 1.3 75.4 - - + +
253A LYS* 1.3 63.9 + - - +
255A ARG* 3.6 26.9 + - - +
256A VAL* 3.8 7.0 + - - +
349A TYR* 2.9 34.5 + - - +
355A ILE* 4.3 4.0 - - - -
548A PHE* 6.4 0.9 - - + -
550A GLU* 2.5 37.1 + - + +
554A GLN* 3.1 41.9 + - - +
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Residues in contact with LYS 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 TRP 3.4 8.2 + - - +
250A LYS* 2.9 40.3 + - + +
252A LYS* 1.3 80.1 - - - +
254A ASP* 1.3 51.6 + - - +
256A VAL* 2.9 12.8 + - - +
257A ALA* 2.8 30.5 + - + -
284A THR* 3.9 43.5 - - + +
286A LEU* 6.2 0.9 - - + -
306A THR* 4.8 14.2 + - - +
322A TYR* 4.7 12.6 + - - +
349A TYR* 3.9 12.8 + - + +
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Residues in contact with ASP 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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250A LYS* 3.3 40.8 + - - +
251A LEU* 3.1 17.3 + - + +
253A LYS* 1.3 77.1 - - - +
255A ARG* 1.3 54.1 + - - +
256A VAL 2.5 18.5 + - - -
257A ALA* 2.8 23.7 + - - +
258A GLN* 2.8 21.7 + - + +
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Residues in contact with ARG 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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202A ARG* 5.4 5.7 - - - +
213A TYR* 6.1 1.6 - - - -
251A LEU* 3.0 52.1 + - + +
252A LYS* 3.7 29.2 - - - +
253A LYS 3.3 0.2 - - - -
254A ASP* 1.3 73.1 - - - +
256A VAL* 1.3 59.1 + - - +
258A GLN* 4.7 10.6 - - - +
259A LEU* 3.7 16.4 - - - +
549A PHE* 5.5 6.1 - - - -
550A GLU* 3.9 21.2 + - - +
551A ALA 4.8 2.0 + - - -
552A MET* 4.5 1.2 - - - +
553A GLY* 2.7 42.0 - - - +
554A GLN* 4.2 12.1 + - - +
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Residues in contact with VAL 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 LYS* 4.2 8.7 - - - +
253A LYS* 2.9 9.3 + - - +
254A ASP 2.5 5.5 + - - -
255A ARG* 1.3 78.0 - - - +
257A ALA* 1.3 59.4 + - - +
258A GLN 3.1 1.6 - - - -
259A LEU* 2.7 27.3 + - + +
260A TYR* 2.8 15.2 + - + +
283A ALA 3.8 22.9 - - - +
284A THR* 4.7 3.4 - - + -
349A TYR* 4.8 14.6 - - + -
351A CYS* 3.8 12.6 - - - -
353A MET* 3.9 24.7 - - + -
554A GLN* 3.6 24.7 - - + +
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Residues in contact with ALA 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 LYS* 2.8 16.7 + - + +
254A ASP* 3.7 19.1 - - - +
256A VAL* 1.3 78.6 - - - +
258A GLN* 1.3 56.5 + - - +
259A LEU 3.1 4.0 + - - -
260A TYR* 3.7 5.3 + - - +
261A LYS* 3.2 23.2 + - - +
280A GLU* 3.9 10.2 - - - +
284A THR* 4.1 23.3 - - + -
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Residues in contact with GLN 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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254A ASP* 2.8 23.5 + - + +
255A ARG* 4.7 8.1 - - - +
257A ALA* 1.3 76.0 - - - +
259A LEU* 1.3 58.7 + - - +
261A LYS* 3.7 21.8 - - - +
262A THR* 3.1 26.5 + - - +
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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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255A ARG 3.7 11.2 - - - +
256A VAL* 2.7 24.5 + - + +
258A GLN* 1.3 83.2 - - - +
260A TYR* 1.3 55.3 + - - +
261A LYS 3.3 0.4 - - - -
262A THR* 3.9 8.3 - - + +
263A LEU* 2.6 59.2 - - + +
353A MET* 3.7 29.4 - - + -
554A GLN* 5.7 4.5 - - + +
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Residues in contact with TYR 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 VAL 2.8 11.9 + - - +
257A ALA* 3.7 5.1 + - - +
259A LEU* 1.3 77.1 - - - +
261A LYS* 1.3 57.7 + - - +
263A LEU* 3.7 6.3 - - + +
264A LYS* 3.0 35.8 + - + +
279A HIS* 3.5 45.5 + + + +
280A GLU* 2.9 34.5 - - - +
283A ALA* 3.6 29.4 - - + +
284A THR* 6.2 1.1 - - + -
351A CYS* 4.5 14.6 - - + -
353A MET* 6.1 1.7 - - - +
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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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257A ALA* 3.2 15.4 + - - +
258A GLN* 3.7 24.9 - - - +
260A TYR* 1.3 78.2 - - - +
262A THR* 1.3 76.5 + - - +
263A LEU 2.8 11.1 + - - -
264A LYS* 2.8 33.7 + - + +
265A ALA* 3.7 4.5 + - - +
280A GLU* 3.9 17.2 + - - +
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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