Contacts of the helix formed by residues 290 - 301 (chain M) in PDB entry 6FF7
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 ARG 290 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289M VAL* 1.3 77.6 - - - +
291M ASP* 1.3 57.7 - - - +
292M PHE* 3.5 2.8 - - - +
293M THR* 3.7 19.4 - - - +
294M GLN* 3.2 22.2 + - - +
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Residues in contact with ASP 291 (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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259M TRP* 6.5 0.4 - - + -
282M ALA 5.5 1.6 - - - +
283M ILE* 5.8 1.6 - - - -
286M VAL* 3.9 28.0 - - + -
287M MET 5.4 0.9 - - - +
288M THR 3.8 10.1 + - - +
289M VAL 3.3 4.4 + - - -
290M ARG* 1.3 74.5 - - - +
292M PHE* 1.3 58.0 + - - +
293M THR 3.1 4.0 - - - -
294M GLN* 3.1 8.8 + - - +
295M VAL* 2.9 27.1 + - - +
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Residues in contact with PHE 292 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283M ILE* 6.6 0.2 - - - -
288M THR 5.3 0.2 + - - -
289M VAL* 5.7 0.6 - - - +
290M ARG* 3.5 2.1 - - - +
291M ASP* 1.3 78.0 - - - +
293M THR* 1.3 57.3 + - - +
295M VAL* 3.9 8.3 - - - +
296M PHE* 2.9 26.4 + - - +
317M LEU* 4.3 11.7 - - + +
320M GLU* 3.8 29.6 - - + -
330M ARG* 5.1 0.9 - - - +
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Residues in contact with THR 293 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290M ARG* 3.6 23.2 + - - +
291M ASP 3.1 0.6 - - - -
292M PHE* 1.3 77.1 - - - +
294M GLN* 1.3 59.4 + - - +
296M PHE* 3.2 7.4 - - - +
297M ASP* 2.9 30.1 + - - +
329M LEU* 4.1 22.4 - - - -
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Residues in contact with GLN 294 (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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263M ALA* 5.4 16.2 - - + -
266M TYR* 5.9 6.2 - - + +
290M ARG 3.2 13.6 + - - +
291M ASP* 3.1 10.7 + - - +
293M THR* 1.3 77.3 - - - +
295M VAL* 1.3 57.9 + - - +
297M ASP* 3.6 3.6 + - - +
298M SER* 2.9 28.5 + - - -
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Residues in contact with VAL 295 (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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266M TYR* 6.3 1.3 - - - -
279M TYR* 4.0 28.9 - - + +
283M ILE* 6.2 1.6 - - + -
291M ASP 2.9 15.1 + - - +
292M PHE* 4.1 8.3 - - - +
294M GLN* 1.3 73.9 - - - +
296M PHE* 1.3 60.8 + - - +
298M SER* 3.4 9.3 - - - -
299M TYR* 2.9 27.5 + - - +
313M THR* 5.6 0.3 - - - +
317M LEU* 5.2 5.2 - - + -
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Residues in contact with PHE 296 (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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292M PHE 2.9 21.8 + - - +
293M THR* 3.2 12.5 + - - +
295M VAL* 1.3 75.6 - - - +
297M ASP* 1.3 54.3 + - - +
299M TYR* 2.7 27.3 + - - +
300M ALA* 2.9 11.1 + - - +
314M ALA* 6.3 0.7 - - - +
317M LEU* 4.4 9.2 - - + +
329M LEU* 4.5 4.3 - - + +
330M ARG* 3.9 32.3 - - + +
333M ARG* 4.6 7.9 - - + +
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Residues in contact with ASP 297 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293M THR 2.9 17.8 + - - +
294M GLN* 4.2 4.0 - - - +
296M PHE* 1.3 72.4 - - - +
298M SER* 1.3 58.0 + - - +
300M ALA* 2.8 27.5 + - + +
301M GLN* 2.9 14.9 + - - +
333M ARG* 4.9 4.6 - - + +
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Residues in contact with SER 298 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266M TYR* 5.4 16.2 - - - -
267M ILE* 6.4 0.4 - - - -
271M HIS* 5.4 2.4 - - - -
275M ALA* 5.7 10.4 - - - +
279M TYR* 5.8 4.0 - - - -
294M GLN 2.9 20.5 + - - -
295M VAL* 3.4 11.7 - - - -
296M PHE 3.1 0.2 - - - -
297M ASP* 1.3 75.7 - - - +
299M TYR* 1.3 57.1 + - - +
301M GLN* 3.9 5.9 + - - +
302M PHE* 3.2 23.4 + - - +
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Residues in contact with TYR 299 (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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295M VAL 2.9 11.2 + - - +
296M PHE* 2.7 16.3 + - - +
298M SER* 1.3 71.4 - - - +
300M ALA* 1.3 58.5 + - - +
302M PHE* 3.2 12.7 + - + -
303M GLU* 3.1 24.1 + - - -
311M MET* 4.8 6.8 - - + +
313M THR* 4.3 32.5 - - - +
314M ALA* 4.5 11.1 - - + +
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Residues in contact with ALA 300 (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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296M PHE 2.9 5.8 + - - +
297M ASP* 2.8 22.5 + - + +
299M TYR* 1.3 75.6 - - - +
301M GLN* 1.3 62.0 + - - +
303M GLU* 3.3 20.8 + - - +
333M ARG* 4.3 24.2 - - + +
334M PHE* 6.4 0.2 - - - +
336M GLN 6.2 0.4 - - - -
337M LEU* 5.5 9.5 - - - +
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Residues in contact with GLN 301 (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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271M HIS* 3.6 16.9 - - + +
297M ASP 2.9 13.7 + - - +
298M SER* 4.2 6.3 - - - +
300M ALA* 1.3 75.3 - - - +
302M PHE* 1.3 56.2 + - - +
303M GLU* 3.3 3.1 + - - -
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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