Contacts of the helix formed by residues 243 - 250 (chain M) in PDB entry 6RQT
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 VAL 243 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231M LEU* 4.6 15.0 - - + -
234M PHE* 5.6 1.6 - - + -
236M TYR* 5.8 1.3 - - + -
238M ASN* 3.4 26.5 - - - +
240M SER 5.6 0.2 - - - +
241M LYS 3.2 0.2 - - - -
242M TYR* 1.3 80.4 - - + +
244M ALA* 1.3 57.6 + - + +
245M LYS 3.2 5.7 + - - -
246M LYS* 4.1 7.1 + - - +
247M LEU* 4.7 2.6 + - + +
262M LEU* 4.4 17.1 - - + +
265M LEU* 3.8 58.1 - - + +
266M SER* 4.7 5.8 - - - +
268M LEU* 6.5 0.2 - - + -
269M LEU* 4.2 11.7 - - + -
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Residues in contact with ALA 244 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227M LYS* 4.7 10.7 + - + +
231M LEU* 3.7 29.6 - - + -
241M LYS* 3.2 26.1 + - + +
243M VAL* 1.3 75.1 - - - +
245M LYS* 1.3 61.9 + - - +
246M LYS 3.2 3.1 - - - -
247M LEU* 3.3 33.9 + - + +
248M ASP 4.7 0.9 + - - -
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Residues in contact with LYS 245 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241M LYS* 2.9 19.0 + - + +
242M TYR* 4.4 11.7 - - + +
243M VAL 3.2 2.8 + - - -
244M ALA* 1.3 76.6 - - - +
246M LYS* 1.3 92.1 + - + +
336M ILE* 5.8 3.3 - - + +
340M ASP* 5.6 0.6 + - - -
348M PRO* 4.7 21.3 + - - +
349M LEU* 5.6 4.6 - - - +
352M GLU* 4.8 15.3 - - - +
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Residues in contact with LYS 246 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242M TYR 6.2 0.2 - - - +
243M VAL 4.1 5.5 + - - +
244M ALA 3.2 0.2 - - - -
245M LYS* 1.3 117.1 + - + +
247M LEU* 1.3 50.5 + - - +
248M ASP 3.3 3.4 - - - -
249M SER* 3.1 18.9 + - - -
250M LEU* 2.6 29.8 - - - +
262M LEU* 5.7 0.9 - - - -
265M LEU* 6.5 0.4 - - + -
336M ILE* 3.7 52.5 - - + +
339M LEU* 3.8 41.1 - - + +
340M ASP* 4.1 17.5 + - + +
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Residues in contact with LEU 247 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227M LYS* 3.7 34.1 - - + -
230M LYS* 3.7 36.3 - - + +
231M LEU* 3.8 31.9 - - + -
243M VAL* 4.7 1.1 + - + +
244M ALA* 3.3 31.8 + - + +
246M LYS* 1.3 78.3 - - - +
248M ASP* 1.3 58.1 + - - +
250M LEU* 2.8 32.1 - - - +
251M THR* 3.9 2.4 + - - +
262M LEU* 4.6 22.7 - - + -
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Residues in contact with ASP 248 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227M LYS* 3.4 30.8 + - - +
244M ALA 4.7 0.4 + - - -
246M LYS 3.3 0.8 - - - -
247M LEU* 1.3 74.4 - - - +
249M SER* 1.3 59.5 + - - +
250M LEU 3.1 5.9 + - - -
251M THR* 3.6 16.6 + - - -
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Residues in contact with SER 249 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246M LYS* 3.1 27.2 + - - +
248M ASP* 1.3 78.1 - - - +
250M LEU* 1.3 58.7 + - - +
251M THR 4.2 0.2 - - - -
255M GLN* 2.9 17.0 + - - +
339M LEU* 3.7 19.3 + - - +
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Residues in contact with LEU 250 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222M LEU* 5.3 1.5 - - - +
230M LYS* 4.0 9.5 + - - +
246M LYS* 2.6 33.0 - - + +
247M LEU* 2.8 29.7 - - + +
249M SER* 1.3 81.4 - - - +
251M THR* 1.3 60.7 + - - +
252M GLN 4.8 1.1 - - - +
255M GLN* 3.3 29.2 - - + +
258M LYS* 4.5 9.6 - - + +
259M LEU* 4.1 31.2 - - + +
262M LEU* 3.7 24.9 - - + -
339M LEU* 5.5 11.7 - - + -
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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