Contacts of the helix formed by residues 247 - 258 (chain B) in PDB entry 4TVJ
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 ASN 247 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243B LYS 3.5 12.6 + - - +
244B LEU* 3.5 18.2 - - + +
245B ILE 3.4 2.9 - - - +
246B CYS* 1.3 71.0 - - - +
248B VAL* 1.3 62.0 + - - +
249B GLN* 3.1 16.7 + - - +
250B ALA* 2.8 38.5 + - + +
251B MET* 3.3 22.3 + - - +
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Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B CYS 3.1 14.9 + - - +
247B ASN* 1.3 69.4 + - - +
249B GLN* 1.3 61.2 + - - +
251B MET* 3.0 19.3 + - + +
252B GLU* 2.9 43.9 + - + +
267B LEU* 5.8 2.0 - - + -
343B ALA 5.7 0.2 - - - -
344B ILE* 4.5 29.8 - - + +
347B VAL* 4.2 21.5 - - + -
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Residues in contact with GLN 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B ASN* 3.1 13.2 + - - +
248B VAL* 1.3 75.7 - - - +
250B ALA* 1.3 63.3 + - - +
252B GLU* 3.2 29.2 + - - +
253B GLU* 3.1 43.9 + - - +
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Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B LEU* 5.4 3.4 - - + +
247B ASN* 2.8 33.7 + - + +
248B VAL 3.3 0.4 - - - -
249B GLN* 1.3 73.2 - - - +
251B MET* 1.3 62.9 + - - +
253B GLU* 3.4 14.2 + - - +
254B MET* 2.9 41.9 + - + +
480B LYS* 5.2 8.6 - - - +
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Residues in contact with MET 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B ILE 3.5 25.4 - - - +
246B CYS* 4.5 8.7 - - - +
247B ASN 3.3 11.5 + - - +
248B VAL* 3.0 25.1 + - + +
250B ALA* 1.3 76.8 - - - +
252B GLU* 1.3 56.9 + - - +
254B MET* 3.1 11.7 + - + +
255B MET* 2.9 33.8 + - - +
267B LEU* 4.3 4.0 - - + -
340B ILE* 3.9 37.2 - - + +
343B ALA* 3.3 33.7 - - + -
344B ILE* 5.2 0.7 - - - -
347B VAL* 6.1 0.2 - - + -
433B SER* 4.1 23.3 - - - +
436B VAL* 4.7 3.1 - - + -
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Residues in contact with GLU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B VAL* 2.9 29.5 + - - +
249B GLN* 3.2 31.2 + - - +
251B MET* 1.3 75.2 - - - +
253B GLU* 1.3 58.7 + - + +
255B MET* 3.2 3.6 + - - +
256B MET* 2.9 37.4 + - + +
262B THR* 3.9 13.8 - - + +
267B LEU* 3.8 26.1 - - + +
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Residues in contact with GLU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B GLN* 3.1 37.0 + - - +
250B ALA* 3.7 11.9 - - - +
252B GLU* 1.3 73.3 - - + +
254B MET* 1.3 66.4 + - - +
256B MET* 3.4 13.6 + - - +
257B GLU* 3.0 23.6 + - - +
480B LYS* 3.7 32.7 + - - -
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Residues in contact with MET 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B ASN 5.5 0.2 - - - +
250B ALA* 2.9 46.2 + - + +
251B MET* 3.1 8.9 + - + +
253B GLU* 1.3 76.1 - - + +
255B MET* 1.3 74.8 + - + +
257B GLU* 3.2 10.9 + - - +
258B MET* 3.1 25.5 + - - +
431B ARG* 4.9 6.3 - - - +
432B MET* 3.6 24.7 - - + +
433B SER* 3.3 43.5 - - - +
480B LYS* 5.5 11.0 - - + -
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Residues in contact with MET 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B MET 2.9 13.1 + - - +
252B GLU 3.2 4.0 + - - +
254B MET* 1.3 87.6 - - + +
256B MET* 1.3 62.7 + - - +
258B MET* 3.1 33.5 + - - +
259B LYS 3.2 0.2 + - - -
260B TYR* 3.0 40.5 + - + +
262B THR* 4.3 4.9 - - + -
267B LEU* 4.2 12.8 - - + -
333B LEU* 3.9 15.5 - - - -
336B ALA* 3.7 18.2 - - + -
337B LEU* 3.9 18.4 - - + -
340B ILE* 3.3 33.2 - - + -
431B ARG* 5.6 0.2 - - - -
433B SER* 4.2 4.7 - - - +
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Residues in contact with MET 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B GLU* 2.9 25.2 + - - +
253B GLU* 3.6 13.5 - - - +
254B MET 3.3 0.2 - - - -
255B MET* 1.3 76.5 - - - +
257B GLU* 1.3 53.4 + - - +
259B LYS* 2.8 27.2 + - - +
260B TYR 3.8 11.4 + - - +
262B THR* 3.6 23.8 - - + +
263B LYS* 3.8 26.5 - - + +
312B ASP* 5.6 4.9 - - - +
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Residues in contact with GLU 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B GLU 3.0 14.3 + - - +
254B MET* 3.3 12.4 - - - +
256B MET* 1.3 76.6 - - - +
258B MET* 1.3 62.7 + - - +
259B LYS* 3.3 13.9 + - - +
431B ARG* 4.2 17.5 + - - -
475B PHE* 5.6 3.1 - - - +
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Residues in contact with MET 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B MET* 3.3 11.7 - - + +
255B MET* 3.1 37.3 + - - +
257B GLU* 1.3 81.2 - - - +
259B LYS* 1.3 70.2 + - - +
260B TYR 3.3 4.8 + - - -
329B GLU* 4.5 3.8 - - + +
330B LYS* 4.3 6.8 + - - -
332B GLN* 4.2 5.2 - - + +
333B LEU* 3.8 52.9 - - + +
336B ALA* 4.6 0.9 - - - -
431B ARG* 3.6 50.5 - - - +
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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