Contacts of the helix formed by residues 246 - 262 (chain B) in PDB entry 4WVD
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 THR 246 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245B LEU* 1.3 77.3 - - - +
247B PRO* 1.3 77.3 - - + +
248B ASP* 3.4 16.0 + - - +
249B GLN* 3.0 34.5 + - - +
250B GLN* 2.9 21.8 + - - +
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Residues in contact with PRO 247 (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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306A PRO* 3.6 33.0 - - + +
307A GLY* 3.8 17.3 - - - +
310A THR* 5.3 8.5 - - + +
407A LEU* 4.3 10.1 - - + -
245B LEU 3.9 0.6 - - - +
246B THR* 1.3 90.2 - - - +
248B ASP* 1.3 60.0 + - - +
250B GLN* 2.9 10.3 + - + +
251B THR* 2.7 39.2 + - - -
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Residues in contact with ASP 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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248A ASP* 5.8 9.9 - - + +
251A THR* 5.3 1.2 - - - +
306A PRO* 5.2 0.9 - - - +
246B THR* 3.4 14.5 + - - +
247B PRO* 1.3 90.2 - - - +
249B GLN* 1.3 56.9 + - - +
251B THR* 3.6 8.6 + - - -
252B LEU* 3.1 27.2 + - - +
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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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245B LEU* 3.6 23.2 - - + +
246B THR* 3.0 40.8 + - - +
248B ASP* 1.3 80.3 + - - +
250B GLN* 1.3 57.1 + - - +
252B LEU* 3.3 10.1 - - + +
253B LEU* 3.2 23.0 + - - +
410B PRO* 5.4 0.9 - - + +
413B ASP* 3.8 33.7 + - + +
414B VAL* 3.8 25.2 - - + +
417B LYS* 5.1 3.4 - - - +
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Residues in contact with GLN 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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310A THR* 6.0 3.4 - - - +
245B LEU* 3.7 33.4 - - + +
246B THR 2.9 11.1 + - - +
247B PRO* 2.9 11.9 + - + +
249B GLN* 1.3 74.9 - - - +
251B THR* 1.3 60.0 + - - +
252B LEU 3.1 1.1 - - - -
253B LEU* 3.2 8.6 + - + +
254B HIS* 2.9 31.4 + - + +
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Residues in contact with THR 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A THR* 3.5 24.9 - - + +
252A LEU* 4.1 7.9 - - - +
255A PHE* 3.7 40.4 - - + -
306A PRO* 3.4 25.1 - - + +
247B PRO 2.7 22.2 + - - -
248B ASP* 3.8 8.6 - - - -
250B GLN* 1.3 72.3 - - - +
252B LEU* 1.3 62.3 + - - +
254B HIS* 4.1 0.5 - - - +
255B PHE* 3.0 27.3 + - + +
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Residues in contact with LEU 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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251A THR* 4.0 10.9 - - + +
248B ASP 3.1 14.6 + - - +
249B GLN* 3.3 12.3 - - + +
251B THR* 1.3 77.2 - - - +
253B LEU* 1.3 57.7 + - - +
255B PHE* 3.3 2.6 - - - +
256B ILE* 2.9 46.9 + - + +
306B PRO* 3.7 31.0 - - + -
384B LEU* 5.9 0.2 - - + -
410B PRO* 3.9 23.3 - - + +
411B LEU* 3.8 20.2 - - + -
414B VAL* 3.9 22.4 - - + -
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Residues in contact with LEU 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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245B LEU* 4.1 13.9 - - + -
249B GLN 3.2 11.5 + - - +
250B GLN* 3.2 11.2 + - + +
252B LEU* 1.3 76.7 - - - +
254B HIS* 1.3 66.6 + - - +
255B PHE 3.1 1.3 - - - -
256B ILE* 3.2 6.0 + - + -
257B MET* 3.0 39.4 + - + +
380B GLU* 4.4 21.8 - - + +
384B LEU* 4.6 17.5 - - + -
414B VAL* 4.3 9.4 - - + -
418B LEU* 4.0 35.7 - - + -
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Residues in contact with HIS 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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255A PHE* 3.6 36.4 - + + -
258A ASP* 4.6 11.2 + - - -
250B GLN* 2.9 20.2 + - + +
251B THR 4.2 0.2 - - - +
253B LEU* 1.3 73.9 - - - +
255B PHE* 1.3 67.8 + - - +
257B MET* 3.2 5.6 + - + +
258B ASP* 3.0 39.1 + - + +
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Residues in contact with PHE 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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250A GLN* 4.8 8.5 - - - -
251A THR* 4.1 26.5 - - + -
254A HIS* 3.4 48.9 - + + -
255A PHE* 5.2 4.3 - + + -
251B THR* 3.0 20.4 + - + +
252B LEU 3.3 5.4 - - - +
254B HIS* 1.3 85.0 - - - +
256B ILE* 1.3 60.2 + - - +
258B ASP* 3.6 3.4 + - - +
259B SER* 2.5 40.4 + - - -
304B LYS* 3.4 46.2 - - + -
306B PRO* 4.1 21.8 - - + -
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Residues in contact with ILE 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 LEU* 2.9 36.9 + - + +
253B LEU* 3.2 6.9 + - + +
255B PHE* 1.3 78.6 - - + +
257B MET* 1.3 59.7 + - + +
259B SER* 3.4 5.9 + - - -
260B TYR* 2.9 27.6 + - - +
301B PHE* 3.8 24.6 - - + -
304B LYS 5.8 0.2 - - - -
305B LEU* 3.3 28.7 - - + -
306B PRO* 4.0 5.8 - - + -
383B ALA* 4.5 12.3 - - + +
384B LEU* 4.7 9.2 - - + -
387B ALA* 4.4 11.0 - - + -
411B LEU* 3.7 22.0 - - + -
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Residues in contact with MET 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 LEU* 3.0 35.8 + - + +
254B HIS* 3.7 6.7 - - - +
255B PHE 3.2 0.2 - - - -
256B ILE* 1.3 74.9 - - + +
258B ASP* 1.3 54.9 + - - +
260B TYR* 2.9 9.1 + - + +
261B ASN* 2.7 61.7 + - - +
379B GLN* 4.0 18.2 - - + +
380B GLU* 3.5 39.7 - - + +
383B ALA* 3.5 28.3 - - - -
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Residues in contact with ASP 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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254A HIS* 4.7 12.8 + - - -
258A ASP* 4.7 11.6 - - - +
254B HIS* 3.0 35.9 + - + +
255B PHE* 3.9 4.1 - - - +
257B MET* 1.3 74.4 - - - +
259B SER* 1.3 64.4 + - - +
261B ASN* 3.5 7.9 + - - +
262B LYS* 3.3 23.0 + - - +
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Residues in contact with SER 259 (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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255B PHE* 2.5 40.3 + - - -
256B ILE* 3.7 5.6 - - - -
258B ASP* 1.3 82.3 + - - +
260B TYR* 1.3 58.8 + - - +
262B LYS* 4.2 11.8 + - - +
263B GLN* 5.2 1.4 + - - +
300B GLU* 5.0 4.3 - - - +
301B PHE* 3.3 27.8 - - - +
304B LYS* 4.1 25.6 - - - +
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Residues in contact with TYR 260 (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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256B ILE 2.9 16.9 + - - +
257B MET* 2.9 10.5 + - + +
259B SER* 1.3 76.0 - - - +
261B ASN* 1.3 64.5 + - - +
262B LYS 3.4 1.1 - - - -
263B GLN* 4.0 8.2 + - - +
301B PHE* 3.7 23.3 - + + -
330B LEU 5.6 0.3 + - - -
331B ARG* 3.0 55.7 + - - +
334B GLU* 2.6 36.5 + - - +
379B GLN* 3.7 20.6 - - - -
382B TYR* 3.6 8.0 - - - +
383B ALA* 3.5 40.6 - - + -
386B THR* 4.3 13.2 + - + -
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Residues in contact with ASN 261 (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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257B MET* 2.7 39.8 + - - +
258B ASP* 3.8 8.6 + - - +
260B TYR* 1.3 77.1 + - - +
262B LYS* 1.3 56.7 + - - +
263B GLN 3.0 19.0 + - - +
379B GLN* 4.6 14.1 - - - +
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Residues in contact with LYS 262 (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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258B ASP 3.3 13.6 + - - +
259B SER* 4.2 11.4 - - - +
260B TYR 3.4 0.4 - - - -
261B ASN* 1.3 77.5 - - - +
263B GLN* 1.3 56.1 + - - +
264B ARG* 4.4 2.4 + - - +
300B GLU* 4.9 12.4 - - - +
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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