Contacts of the helix formed by residues 283 - 293 (chain B) in PDB entry 6XWQ
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 283 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B MET* 4.9 1.3 - - - -
270B ALA* 4.7 2.9 + - - +
273B THR* 3.7 20.9 - - - +
274B ALA* 4.3 7.3 + - + -
277B THR* 4.8 4.7 - - - -
279B SER 3.7 11.7 - - - +
280B SER 3.2 14.8 + - - +
282B GLY* 1.3 78.4 - - - +
284B LEU* 1.3 63.9 + - - +
285B PRO* 3.4 5.8 - - - -
286B VAL* 3.3 21.5 + - - +
287B THR* 3.0 20.5 + - + +
406B VAL* 3.9 27.6 - - + -
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Residues in contact with LEU 284 (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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63B ILE* 3.5 30.7 - - + -
64B VAL* 6.2 0.2 - - - -
197B TYR* 4.4 11.4 - - + +
280B SER 4.5 2.5 - - - +
281B SER* 4.3 18.8 - - - +
282B GLY 3.6 1.2 - - - -
283B THR* 1.3 75.6 - - - +
285B PRO* 1.3 71.9 - - + +
287B THR* 3.3 13.5 - - + +
288B MET* 2.9 40.8 + - + +
306B LEU 4.0 12.3 - - - +
307B PRO* 4.4 20.0 - - + +
310B ALA* 3.5 30.3 - - + -
311B THR* 5.4 2.9 - - - +
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Residues in contact with PRO 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B TYR* 4.4 31.8 - - + +
200B VAL* 3.5 37.0 - - + -
201B GLY* 4.5 7.9 - - - +
204B MET* 5.8 1.6 - - + -
282B GLY 4.8 0.2 - - - +
283B THR* 3.5 2.9 - - - -
284B LEU* 1.3 92.7 - - + +
286B VAL* 1.3 63.4 + - + +
288B MET* 3.9 3.6 - - + +
289B ARG* 2.9 37.5 + - - +
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 5.9 8.5 - - + -
204B MET* 5.4 9.2 - - + -
269B ASP 3.8 14.6 - - - +
270B ALA* 3.7 23.8 - - + -
273B THR* 4.5 16.4 - - + +
283B THR* 3.3 18.5 + - - +
284B LEU 3.3 0.6 - - - -
285B PRO* 1.3 83.4 - - + +
287B THR* 1.3 60.0 + - - +
289B ARG* 3.1 18.1 - - + +
290B VAL* 2.9 31.1 + - + +
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Residues in contact with THR 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ALA* 4.2 4.0 - - - -
283B THR* 3.0 21.9 + - + +
284B LEU* 3.3 26.7 - - + +
286B VAL* 1.3 77.1 - - - +
288B MET* 1.3 62.5 + - + +
290B VAL* 3.1 10.3 - - - +
291B ALA* 2.9 28.8 + - - +
306B LEU* 3.9 12.4 - - + +
310B ALA* 5.6 2.7 - - + -
406B VAL* 4.1 18.8 - - + +
409B ASP* 5.6 0.3 - - - +
410B LEU* 3.2 26.3 - - - +
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Residues in contact with MET 288 (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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197B TYR* 3.2 46.7 - - + +
284B LEU* 2.9 28.2 + - + +
285B PRO* 4.0 2.7 - - + +
287B THR* 1.3 79.6 - - + +
289B ARG* 1.3 57.8 + - - +
291B ALA 3.3 0.7 + - - -
292B GLU* 2.9 25.6 + - - +
302B PHE* 3.4 50.8 - - + +
303B SER* 4.5 13.2 - - - +
306B LEU* 4.2 14.6 - - + -
307B PRO* 4.5 10.3 - - + -
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Residues in contact with ARG 289 (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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285B PRO* 2.9 19.8 + - - +
286B VAL* 3.1 30.0 - - + +
288B MET* 1.3 77.4 - - - +
290B VAL* 1.3 58.8 + - + +
292B GLU* 4.6 4.5 - - - -
293B GLU* 2.9 61.1 + - + +
302B PHE* 5.5 0.2 - - - -
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Residues in contact with VAL 290 (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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266B LYS 3.1 27.8 - - - +
267B ALA* 4.6 3.1 - - - -
269B ASP* 4.8 12.3 - - + -
270B ALA* 3.8 16.2 - - + +
286B VAL* 2.9 19.1 + - + +
287B THR* 3.1 21.3 - - - +
289B ARG* 1.3 76.3 - - + +
291B ALA* 1.3 60.3 + - - +
293B GLU* 4.6 4.7 - - - +
294B GLU* 3.4 18.9 - - + +
295B MET* 2.9 26.5 + - + +
410B LEU* 4.1 14.1 - - + -
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Residues in contact with ALA 291 (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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287B THR 2.9 17.5 + - - +
288B MET 3.3 3.8 + - - +
290B VAL* 1.3 79.4 - - - +
292B GLU* 1.3 57.8 + - - +
295B MET* 3.2 13.7 - - + +
296B GLY 2.7 23.9 + - - -
297B VAL* 3.2 25.0 + - + +
302B PHE* 4.0 2.9 - - + -
306B LEU* 3.7 21.3 - - + -
410B LEU* 4.2 9.0 - - + -
413B THR* 5.1 2.7 - - + -
414B VAL* 6.3 0.2 - - + -
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Residues in contact with GLU 292 (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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288B MET 2.9 17.2 + - - +
289B ARG* 4.1 4.3 - - - +
291B ALA* 1.3 76.1 - - - +
293B GLU* 1.3 69.1 + - + +
296B GLY* 3.4 19.6 + - - -
297B VAL 2.8 28.4 + - - +
298B ASP* 4.4 3.7 - - - +
299B LYS* 4.5 13.1 + - - +
302B PHE* 3.6 25.5 - - + -
427B LYS* 4.6 1.2 + - - -
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Residues in contact with GLU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ARG* 2.9 55.6 + - + +
290B VAL* 4.6 3.2 - - - +
292B GLU* 1.3 79.7 - - + +
294B GLU* 1.3 63.9 + - + +
427B LYS* 2.7 24.6 + - - -
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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