Contacts of the helix formed by residues 258 - 270 (chain M) in PDB entry 3FKS
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 ILE 258 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187M VAL* 5.3 0.9 - - - -
233M ALA* 6.2 1.1 - - + -
255M ILE* 4.1 23.2 + - + +
256M ASP* 4.2 2.2 - - - +
257M ASN* 1.3 75.8 + - - +
259M PHE* 1.3 64.8 + - - +
261M PHE* 3.2 27.8 - - + +
262M THR* 4.1 1.6 + - - -
289M MET* 4.2 22.2 - - + -
292M LEU* 5.0 9.2 - - + -
293M GLN* 3.2 30.5 - - - +
296M ILE* 6.0 0.4 - - + -
308M GLN* 3.7 17.0 - - + +
309M ALA 3.3 16.2 + - - +
310M VAL* 3.7 25.4 - - + -
325M THR* 4.9 3.6 - - + +
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Residues in contact with PHE 259 (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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257M ASN* 2.9 14.3 + - - +
258M ILE* 1.3 79.3 - - + +
260M ARG* 1.3 71.5 + - - +
261M PHE 2.8 11.7 + - - -
262M THR* 2.9 17.4 + - - +
263M GLN* 3.1 48.4 + - + -
281M TYR* 3.7 11.0 - + - -
289M MET* 5.9 2.0 - - + -
310M VAL* 5.0 2.7 - - + -
311M TYR* 3.3 52.3 - + + +
313M PRO* 3.5 22.7 - - + -
321M ALA* 3.5 33.7 - - + -
322M PRO* 4.9 1.3 - - + -
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Residues in contact with ARG 260 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301L PHE* 3.2 35.6 - - - -
343L ASN* 5.5 1.0 + - - -
346L SER* 3.4 31.9 + - - -
187M VAL* 3.2 24.9 - - + +
188M GLY* 3.0 35.0 + - - +
189M GLU* 5.3 4.9 + - - -
222M MET* 4.3 9.5 - - - +
229M ARG* 4.1 10.7 + - + +
257M ASN* 3.3 14.7 + - + +
259M PHE* 1.3 90.3 - - - +
261M PHE* 1.3 56.9 + - - +
262M THR 3.5 0.2 - - - -
263M GLN* 3.5 26.1 + - - +
264M ALA* 3.1 27.7 + - - +
311M TYR* 4.2 17.3 - - - -
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Residues in contact with PHE 261 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187M VAL* 4.3 3.5 - - + +
229M ARG 4.4 7.0 - - - -
230M ALA* 3.1 31.0 - - + +
231M ARG* 4.2 12.3 - - - -
233M ALA* 4.3 16.4 - - + -
234M LEU* 4.9 7.4 - - + -
257M ASN 4.3 0.8 + - - -
258M ILE* 3.2 21.6 + - + +
259M PHE 2.8 1.2 + - - -
260M ARG* 1.3 77.4 - - - +
262M THR* 1.3 76.4 + - - +
264M ALA* 3.7 4.8 + - - +
265M GLY* 3.5 13.7 + - - -
288M ASP* 4.0 21.5 - - + -
289M MET* 4.1 22.0 - - - -
292M LEU* 3.4 36.3 - - + -
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Residues in contact with THR 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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258M ILE 4.6 1.0 + - - -
259M PHE* 2.9 9.2 + - - -
261M PHE* 1.3 86.0 - - - +
263M GLN* 1.3 61.9 + - - +
265M GLY 3.0 13.9 + - - -
266M SER* 3.1 10.2 + - - -
281M TYR* 4.2 9.6 - - + -
282M GLN* 3.3 25.4 + - - +
285M LEU* 3.6 31.9 - - + +
288M ASP* 6.4 0.2 - - + -
289M MET* 3.1 30.0 - - + +
321M ALA* 4.5 9.0 - - + -
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Residues in contact with GLN 263 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298L GLY 5.6 1.8 - - - +
301L PHE* 3.2 55.7 - - + +
339L TYR* 5.1 5.9 + - - -
343L ASN* 4.4 8.7 + - - +
229M ARG* 4.4 3.7 + - - -
259M PHE* 3.1 41.3 + - + +
260M ARG* 3.5 21.5 + - - +
262M THR* 1.3 73.7 - - - +
264M ALA* 1.3 57.7 + - - +
265M GLY 2.9 4.5 - - - -
266M SER* 2.7 34.5 + - - +
267M GLU* 3.0 15.9 + - + +
281M TYR* 5.3 2.9 - - + -
311M TYR* 6.0 0.4 - - - -
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Residues in contact with ALA 264 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226M PRO* 3.5 28.9 - - - +
229M ARG* 4.1 7.6 - - + +
230M ALA* 3.7 20.1 - - + +
260M ARG 3.1 18.2 + - - +
261M PHE 3.8 4.9 - - - +
263M GLN* 1.3 79.2 - - - +
265M GLY* 1.3 59.8 + - - +
266M SER 3.7 0.2 + - - -
267M GLU* 3.7 20.1 + - - +
268M VAL* 3.5 18.5 + - - +
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Residues in contact with GLY 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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230M ALA* 5.5 2.7 - - - -
261M PHE 3.5 7.5 + - - -
262M THR 3.0 9.9 + - - -
263M GLN 2.9 1.2 - - - -
264M ALA* 1.3 80.3 - - - +
266M SER* 1.3 56.7 + - - +
268M VAL* 3.7 6.6 + - - +
269M SER* 3.0 28.9 + - - -
272M LEU* 5.6 0.2 - - - +
274M ARG* 4.9 2.9 + - - -
282M GLN* 3.4 17.0 - - - +
288M ASP* 5.7 0.9 - - - -
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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
----------------------------------------------------------
298L GLY* 4.5 12.2 + - - -
262M THR 3.1 3.7 + - - -
263M GLN* 2.7 30.1 + - - +
265M GLY* 1.3 74.6 - - - +
267M GLU* 1.3 66.3 + - - +
269M SER* 3.5 14.5 + - - -
270M ALA* 4.2 5.0 + - - +
280M GLY 3.8 22.6 - - - +
281M TYR* 4.1 15.0 - - - -
282M GLN* 3.1 17.3 + - - +
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Residues in contact with GLU 267 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298L GLY* 3.4 32.2 + - - +
299L ASP* 3.4 17.3 + - + +
301L PHE* 4.4 2.6 - - + +
302L TYR* 3.3 24.8 + - - +
226M PRO* 3.2 31.3 - - + +
229M ARG* 2.8 34.2 + - - -
263M GLN* 3.0 20.5 + - + +
264M ALA* 3.7 12.0 - - - +
265M GLY 3.3 0.4 - - - -
266M SER* 1.3 80.8 + - - +
268M VAL* 1.3 59.7 + - - +
270M ALA* 4.4 7.6 + - - +
271M LEU* 5.0 6.6 + - - +
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Residues in contact with VAL 268 (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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19M ALA* 4.3 8.7 - - + -
20M ILE* 4.0 25.6 - - + -
62M ILE* 4.4 18.4 - - + -
226M PRO* 3.6 31.2 - - + -
227M GLY 4.9 0.4 - - - +
264M ALA 3.5 13.7 - - - +
265M GLY* 3.8 6.7 - - - +
267M GLU* 1.3 75.9 - - - +
269M SER* 1.3 67.1 + - - +
270M ALA 3.1 4.4 + - - -
271M LEU* 3.2 8.4 + - + +
272M LEU* 3.1 36.5 + - + +
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Residues in contact with SER 269 (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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265M GLY 3.0 21.4 + - - -
266M SER* 3.8 9.6 - - - -
267M GLU 3.4 0.8 - - - -
268M VAL* 1.3 78.0 - - - +
270M ALA* 1.3 60.9 + - - +
272M LEU* 3.6 7.7 + - - -
274M ARG* 3.2 47.1 + - - +
276M PRO* 6.1 0.9 - - - +
281M TYR 4.8 1.2 + - - -
282M GLN* 3.1 32.8 - - - +
283M PRO* 3.9 0.7 - - - +
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Residues in contact with ALA 270 (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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290L PRO* 3.8 46.4 - - + +
291L PRO 5.5 2.9 - - - +
298L GLY* 6.1 3.6 - - - +
266M SER 4.2 4.9 + - - +
267M GLU 4.7 7.6 - - - +
268M VAL 3.1 0.8 - - - -
269M SER* 1.3 76.0 - - - +
271M LEU* 1.3 60.1 + - + +
272M LEU 3.1 4.7 - - - -
273M GLY* 3.1 19.6 + - - -
274M ARG 4.1 7.6 + - - +
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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