Contacts of the helix formed by residues 259 - 266 (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 LEU 259 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218M VAL* 3.7 27.1 - - + -
221M ILE* 3.9 35.7 - - + -
222M LEU* 5.3 4.5 - - + -
230M LYS* 5.5 6.7 - - + +
234M PHE* 5.5 3.1 - - + -
250M LEU* 4.1 10.5 - - + -
255M GLN 4.0 6.9 + - - +
256M MET* 3.3 31.0 + - + +
258M LYS* 1.3 77.0 - - - +
260M GLN* 1.3 60.7 + - - +
261M LEU 3.2 0.7 - - - -
262M LEU* 3.1 42.9 + - + +
263M TYR* 3.4 10.2 + - - +
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Residues in contact with GLN 260 (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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208M ILE* 5.9 1.0 - - - +
213M LEU* 3.5 46.6 + - + +
214M GLN* 5.7 1.6 - - - +
216M ILE* 4.1 26.0 - - + +
218M VAL* 4.8 21.8 - - + +
256M MET* 3.6 13.9 + - - +
257M THR* 4.0 13.8 - - - +
258M LYS 3.3 0.6 - - - -
259M LEU* 1.3 78.3 - - - +
261M LEU* 1.3 59.3 + - + +
262M LEU 3.5 0.2 + - - -
263M TYR* 3.8 8.1 + - - +
264M TYR* 3.6 14.4 + - - +
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Residues in contact with LEU 261 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204M ILE* 4.2 35.9 - - + -
208M ILE* 4.9 16.2 - - + -
213M LEU* 6.0 2.9 - - + -
257M THR 4.8 3.6 - - - +
258M LYS* 3.2 36.4 + - + +
259M LEU 3.2 0.6 - - - -
260M GLN* 1.3 77.4 - - + +
262M LEU* 1.3 51.3 + - - +
263M TYR 3.4 0.4 - - - -
264M TYR* 3.1 11.3 + - + +
265M LEU* 2.6 35.4 + - + +
334M ALA 4.8 3.1 - - - +
335M ILE* 3.8 41.2 - - + +
338M HIS* 5.1 5.2 - - + -
339M LEU* 5.7 1.1 - - + -
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Residues in contact with LEU 262 (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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230M LYS* 5.6 1.8 - - + +
234M PHE* 3.6 33.8 - - + -
243M VAL* 4.4 12.2 - - + +
246M LYS 5.7 0.4 - - - -
247M LEU* 4.6 21.3 - - + -
250M LEU* 3.7 35.9 - - + -
258M LYS 3.4 3.6 + - - +
259M LEU* 3.1 25.5 + - + +
261M LEU* 1.3 74.8 - - - +
263M TYR* 1.3 62.0 + - - +
264M TYR 3.2 0.7 - - - -
265M LEU* 2.7 44.0 - - + +
266M SER* 3.0 10.4 + - - -
339M LEU* 6.1 0.7 - - + -
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Residues in contact with TYR 263 (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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216M ILE* 5.1 20.4 - - + -
234M PHE* 5.5 10.4 - + + -
235M PRO* 3.5 34.9 - - + +
259M LEU 3.4 7.6 + - - +
260M GLN* 4.0 9.9 - - - +
261M LEU 3.4 0.2 - - - -
262M LEU* 1.3 76.9 - - - +
264M TYR* 1.3 60.6 + - + +
266M SER* 3.0 27.3 + - - -
267M LEU* 3.2 27.3 + - + +
287M LEU* 5.1 0.7 - - - +
290M PRO* 3.4 25.3 - - - +
291M PRO* 4.7 2.4 + - + -
294M LEU* 3.7 41.6 - - + +
295M VAL* 5.5 2.3 - - - +
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Residues in contact with TYR 264 (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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207M ILE* 4.9 8.8 - - + +
208M ILE* 3.9 31.2 - - + -
260M GLN 3.6 4.7 + - - +
261M LEU* 3.1 20.9 + - + +
263M TYR* 1.3 78.2 - - + +
265M LEU* 1.3 53.8 + - - +
267M LEU* 3.0 13.3 + - + +
268M LEU* 2.5 37.5 + - + -
298M ILE* 3.7 33.1 - - + +
302M PHE* 6.1 1.0 - - - -
331M TYR* 3.2 62.2 - + + +
335M ILE* 4.1 17.5 - - + -
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Residues in contact with LEU 265 (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 6.0 0.4 - - - +
243M VAL* 3.8 35.5 - - + +
246M LYS* 6.5 0.2 - - + -
258M LYS 5.4 1.1 - - - +
261M LEU* 2.6 17.0 + - + +
262M LEU* 2.7 59.9 - - + +
264M TYR* 1.3 73.1 - - - +
266M SER* 1.3 55.1 + - - +
268M LEU* 3.0 38.9 + - + +
269M LEU* 3.8 10.6 - - - +
335M ILE* 3.8 32.5 - - + -
336M ILE* 6.1 2.5 - - + -
339M LEU* 5.2 11.0 - - + -
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Residues in contact with SER 266 (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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234M PHE* 4.4 15.4 - - - +
235M PRO* 4.4 5.4 - - - +
236M TYR* 3.3 51.3 + - - +
243M VAL* 4.7 8.5 - - - +
262M LEU 3.0 11.9 + - - -
263M TYR* 3.0 21.8 + - - -
265M LEU* 1.3 74.1 - - - +
267M LEU* 1.3 60.1 + - - +
269M LEU* 4.8 4.7 - - - -
270M GLY* 4.7 2.4 - - - -
287M LEU* 5.0 1.7 - - - +
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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