Contacts of the helix formed by residues 247 - 258 (chain A) in PDB entry 3BNF
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 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A ILE* 1.3 83.7 - - - +
248A THR* 1.3 65.8 + - - +
249A GLU* 3.3 13.7 + - - +
250A GLN* 3.0 41.2 + - - +
251A MET* 3.0 22.7 + - - +
285A THR* 5.8 3.8 - - - -
409A GLU* 5.7 2.5 - - - -
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Residues in contact with THR 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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246A ILE 3.8 1.2 + - - -
247A SER* 1.3 71.9 - - - +
249A GLU* 1.3 64.3 + - - +
251A MET* 3.4 2.0 + - - +
252A GLU* 2.8 24.8 + - - +
282A LEU* 4.6 3.3 - - - +
391A TRP* 3.0 34.0 + - + +
392A ARG* 4.1 17.7 - - + -
395A MET* 3.5 29.6 - - + +
409A GLU* 4.6 3.3 + - - -
413A LEU* 3.4 44.2 - - + +
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Residues in contact with GLU 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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247A SER* 3.2 12.6 + - - +
248A THR* 1.3 84.8 + - + +
250A GLN* 1.3 61.2 + - + +
252A GLU* 3.4 16.6 + - - +
253A ALA* 3.0 27.0 + - - +
392A ARG* 4.9 16.6 - - - +
409A GLU* 4.3 2.1 - - - +
412A ARG* 2.7 39.7 + - - -
413A LEU* 3.5 10.2 - - - +
416A SER* 5.0 1.6 + - - -
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Residues in contact with GLN 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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244A LYS* 3.3 34.0 - - + +
245A GLY* 3.3 10.9 - - - +
246A ILE 3.2 11.7 - - - +
247A SER* 3.0 41.3 + - - +
249A GLU* 1.3 75.8 - - + +
251A MET* 1.3 59.1 + - - +
253A ALA* 3.3 8.1 + - - +
254A TYR* 3.0 25.5 + - - +
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Residues in contact with MET 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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217A GLU* 3.9 10.8 - - - -
241A PRO* 3.5 31.6 - - + +
242A TRP* 3.4 21.3 - - + +
245A GLY 4.0 5.2 - - - +
246A ILE 3.7 12.1 - - - +
247A SER 3.0 18.9 + - - +
248A THR 3.8 3.8 - - - +
250A GLN* 1.3 74.4 - - - +
252A GLU* 1.3 64.9 + - - +
254A TYR* 3.0 23.6 - - - +
255A TYR* 3.0 14.4 + - - -
281A GLU* 3.4 39.5 - - + +
391A TRP* 3.8 11.4 - - + -
395A MET* 3.9 19.3 - - + -
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Residues in contact with GLU 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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248A THR 2.8 17.4 + - - +
249A GLU* 3.5 14.1 - - - +
250A GLN 3.2 0.2 - - - -
251A MET* 1.3 78.3 - - - +
253A ALA* 1.3 56.8 + - - +
255A TYR* 3.3 4.9 + - - +
256A ASP* 3.0 37.8 + - - +
273A LEU* 5.0 3.4 - - + -
388A HIS* 3.4 40.1 + - + +
391A TRP* 3.3 29.3 - - + +
392A ARG* 2.9 43.0 + - - +
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Residues in contact with ALA 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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244A LYS* 3.7 16.2 - - + -
249A GLU 3.0 13.4 + - - +
250A GLN* 3.5 10.8 - - - +
252A GLU* 1.3 72.9 - - - +
254A TYR* 1.3 65.8 + - - +
256A ASP* 3.8 7.4 - - - +
257A GLU* 2.9 27.5 + - - +
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Residues in contact with TYR 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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219A TYR* 2.9 48.7 + + - -
221A LYS* 5.5 0.9 + - - +
239A THR* 3.7 10.2 - - - +
240A LEU 4.2 1.9 + - - -
241A PRO* 3.6 34.5 - - + +
242A TRP 4.0 0.4 - - - -
243A SER* 3.0 34.9 - - - -
244A LYS* 3.5 16.0 - - + +
250A GLN 3.0 13.7 + - - +
251A MET* 3.0 15.5 - - - +
253A ALA* 1.3 77.8 - - - +
255A TYR* 1.3 69.8 + + - +
257A GLU* 3.4 9.6 + - - +
258A ILE* 3.4 26.9 + - + +
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Residues in contact with TYR 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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217A GLU* 2.6 29.8 + - - -
218A TYR 3.6 0.5 + - - -
219A TYR* 3.1 44.5 - + + +
241A PRO* 3.3 25.2 - - + +
251A MET* 3.0 20.9 + - + +
252A GLU 3.8 1.6 - - - +
254A TYR* 1.3 83.9 - + - +
256A ASP* 1.3 61.3 + - - +
258A ILE* 3.4 4.0 - - + +
259A ASN 3.1 6.2 + - - -
260A PHE* 2.9 56.0 + + + -
262A ASP* 5.4 0.9 - - - -
273A LEU* 3.6 36.6 - - + -
387A ARG* 3.5 2.4 + - - -
391A TRP* 3.6 17.7 - + - -
513A CA 3.8 1.7 - - - -
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Residues in contact with ASP 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 GLU* 3.0 20.4 + - - +
253A ALA* 3.9 7.5 - - - +
255A TYR* 1.3 76.2 - - - +
257A GLU* 1.3 63.7 + - - +
259A ASN* 3.1 21.1 + - - +
273A LEU* 4.7 1.0 - - - +
387A ARG* 2.8 34.6 + - - +
388A HIS* 2.8 32.2 + - - -
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Residues in contact with GLU 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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244A LYS* 2.5 36.6 + - - -
253A ALA 2.9 19.6 + - - +
254A TYR 3.6 4.8 - - - +
255A TYR 3.3 0.2 - - - -
256A ASP* 1.3 77.6 - - - +
258A ILE* 1.3 69.2 + - + +
259A ASN* 3.3 9.5 + - - -
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Residues in contact with ILE 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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219A TYR* 3.8 17.7 - - + +
254A TYR* 3.4 43.7 - - + +
255A TYR* 3.4 8.7 - - + +
257A GLU* 1.3 89.1 - - + +
259A ASN* 1.3 74.9 + - - +
260A PHE* 3.2 25.5 + - + -
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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