Contacts of the helix formed by residues 284 - 294 (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 THR 284 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38J ASP* 5.4 5.8 - - + +
282J GLN* 3.8 20.4 - - - +
286J LEU* 3.9 19.1 - - + -
274M ARG* 3.2 31.8 + - - +
282M GLN* 3.0 3.1 - - - +
283M PRO* 1.3 79.3 - - + +
285M LEU* 1.3 54.7 + - - +
286M ALA 3.2 3.3 + - - -
287M THR* 3.2 10.5 + - - +
288M ASP* 2.7 63.7 + - - +
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Residues in contact with LEU 285 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281J ARG* 6.2 3.8 - - - +
262M THR* 3.6 19.3 - - + +
281M TYR* 3.4 40.2 - - + -
282M GLN* 3.0 31.5 + - - +
283M PRO 3.4 1.4 - - - -
284M THR* 1.3 76.3 - - - +
286M ALA* 1.3 68.8 + - + +
288M ASP* 3.9 1.9 - - - +
289M MET* 3.3 25.6 + - + +
320M PRO* 4.0 11.9 - - + +
321M ALA* 4.0 15.9 - - - +
324M THR* 3.6 28.9 - - + +
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Residues in contact with ALA 286 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238J ALA* 4.6 5.7 - - - +
245J GLN* 6.1 0.9 - - - +
278J VAL* 3.9 27.8 - - + -
279J ALA* 6.0 1.3 - - - +
282J GLN* 5.1 3.8 - - + +
283M PRO 4.9 2.3 + - - +
284M THR 3.2 0.6 - - - -
285M LEU* 1.3 90.6 - - + +
287M THR* 1.3 65.3 + - + +
289M MET* 3.8 2.4 + - - +
290M GLY* 3.3 15.2 + - - -
324M THR* 4.6 15.4 - - + +
328M HIS* 5.3 1.2 + - - -
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Residues in contact with THR 287 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238J ALA 4.2 7.6 - - - +
239J SER 6.0 0.2 - - - -
240J GLU 4.4 11.2 - - - +
241J ALA* 5.3 0.4 - - - -
242J ALA* 4.3 21.1 - - + +
245J GLN* 4.6 11.0 - - - +
279J ALA* 6.3 1.1 - - - -
282J GLN* 3.2 36.6 + - - +
284M THR* 3.2 8.2 + - - +
286M ALA* 1.3 77.7 - - + +
288M ASP* 1.3 73.2 + - - +
290M GLY* 2.9 2.6 + - - +
291M LEU* 2.9 34.3 + - - +
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Residues in contact with ASP 288 (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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261M PHE* 4.0 18.8 - - + -
262M THR* 6.4 0.2 - - + -
265M GLY* 5.7 1.6 - - - -
274M ARG* 4.6 3.5 + - - -
282M GLN* 4.0 15.1 + - - +
284M THR* 2.7 54.3 + - - +
285M LEU* 3.9 5.2 - - - +
287M THR* 1.3 76.2 + - - +
289M MET* 1.3 61.3 + - - +
290M GLY 3.3 0.2 + - - -
291M LEU* 3.4 18.2 + - - +
292M LEU* 3.5 11.8 + - - +
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Residues in contact with MET 289 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258M ILE* 4.2 16.4 - - + -
259M PHE* 5.9 2.2 - - + -
261M PHE* 4.1 12.7 - - + -
262M THR* 3.1 31.2 - - + +
285M LEU* 3.3 16.3 + - + +
286M ALA 4.2 2.9 - - - +
288M ASP* 1.3 79.3 - - - +
290M GLY* 1.3 56.9 + - - +
291M LEU 3.4 0.2 - - - -
292M LEU* 3.7 1.3 - - + -
293M GLN* 2.8 48.7 + - + +
321M ALA* 4.1 9.4 - - + +
324M THR* 4.4 9.4 - - + -
325M THR* 3.5 44.9 - - - +
328M HIS* 4.4 11.2 - - + +
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Residues in contact with GLY 290 (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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238J ALA* 3.4 24.2 - - - -
239J SER* 4.0 1.7 - - - -
286M ALA 3.3 10.1 + - - -
287M THR 2.9 7.8 + - - -
289M MET* 1.3 74.4 - - - +
291M LEU* 1.3 57.4 + - - +
292M LEU 3.0 9.4 + - - -
294M GLU* 3.2 30.7 + - - +
328M HIS* 4.2 13.0 - - - -
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Residues in contact with LEU 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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239J SER* 3.5 32.8 - - - +
120M ASP* 5.0 7.4 - - - +
121M PRO* 4.8 12.1 - - + +
234M LEU* 5.2 2.0 - - - +
287M THR* 2.9 24.4 + - - +
288M ASP* 3.4 11.2 + - - +
290M GLY* 1.3 74.9 - - - +
292M LEU* 1.3 57.0 + - - +
294M GLU* 4.7 0.9 - - - -
295M ARG* 3.3 27.0 - - - +
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Residues in contact with LEU 292 (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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233M ALA* 4.4 11.2 - - + +
234M LEU* 3.4 36.3 - - + +
237M LEU* 3.5 24.5 - - + -
258M ILE* 5.0 13.2 - - + -
261M PHE* 3.4 44.4 - - + -
288M ASP 3.5 9.6 + - - +
289M MET* 3.4 7.4 + - - +
290M GLY 3.0 0.8 - - - -
291M LEU* 1.3 79.7 - - - +
293M GLN* 1.3 69.7 + - - +
294M GLU 3.3 0.9 - - - -
295M ARG* 3.0 19.7 + - - +
296M ILE* 3.5 16.1 - - + +
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Residues in contact with GLN 293 (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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152M LYS* 2.9 36.0 + - - +
258M ILE* 3.2 28.3 - - - +
289M MET* 2.8 38.6 + - + +
292M LEU* 1.3 76.4 - - + +
294M GLU* 1.3 58.4 + - - +
296M ILE* 2.9 27.4 + - - +
297M THR* 5.2 0.2 - - - -
308M GLN* 3.0 37.8 + - - +
325M THR* 5.0 3.7 - - - +
328M HIS* 3.2 35.3 - - + +
329M LEU* 5.2 0.7 - - - +
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Residues in contact with GLU 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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210J GLN 4.1 0.3 - - - +
211J LYS* 3.4 21.2 - - + +
212J ARG* 3.0 51.0 + - - +
213J SER* 4.8 2.4 + - - -
237J THR* 3.7 11.8 + - - -
238J ALA 4.7 1.6 - - - -
239J SER* 3.4 26.0 + - - +
121M PRO* 3.7 12.2 - - + +
122M PRO* 3.6 14.6 - - - +
127M GLN* 4.9 4.4 + - - -
290M GLY* 3.2 20.4 + - - +
291M LEU 5.1 0.2 - - - -
293M GLN* 1.3 78.8 - - - +
295M ARG* 1.3 60.5 + - - +
296M ILE 3.3 0.7 - - - -
297M THR* 3.6 14.5 - - - +
328M HIS* 4.9 4.0 - - + -
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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