Contacts of the helix formed by residues 272 - 287 (chain L) 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 ASP 272 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177L LYS* 4.1 4.7 + - - -
208L VAL* 3.2 18.5 + - - +
210L GLN* 5.7 0.2 - - + -
270L TYR 3.9 0.4 - - - -
271L ASP* 1.3 81.6 + - - +
273L LEU* 1.3 60.6 + - - +
274L SER* 2.8 40.3 + - - -
275L LYS* 2.9 51.2 + - + +
276L GLN 3.4 6.8 + - - -
328L VAL* 3.4 26.3 - - - +
330L GLU* 3.6 18.1 + - - +
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Residues in contact with LEU 273 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208L VAL* 6.2 0.7 - - + -
249L PRO* 4.4 5.6 - - + -
270L TYR* 3.5 26.7 + - + +
272L ASP* 1.3 69.5 - - - +
274L SER* 1.3 60.5 + - - +
275L LYS 3.3 0.2 - - - -
276L GLN* 3.1 32.0 + - + +
277L ALA* 3.4 12.1 + - - +
304L HIS* 3.4 40.4 + - + +
307L LEU* 3.9 17.5 - - + -
308L LEU* 4.7 8.3 - - + -
327L PRO* 3.5 29.2 - - + -
328L VAL 3.0 16.8 + - - +
329L ILE* 5.2 6.5 - - + -
344L VAL* 4.8 7.9 - - + -
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Residues in contact with SER 274 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272L ASP* 2.8 13.4 + - - -
273L LEU* 1.3 80.3 - - - +
275L LYS* 1.3 61.6 + - - +
276L GLN 3.4 0.9 + - - -
277L ALA* 3.6 6.1 + - - +
278L VAL* 3.2 26.0 + - - +
296L TYR* 4.9 0.9 + - - -
328L VAL 4.2 0.4 + - - -
329L ILE* 2.9 19.3 - - - +
330L GLU* 2.9 39.8 + - - -
340L ILE* 5.6 5.4 - - - +
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Residues in contact with LYS 275 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208L VAL* 3.5 25.1 - - - +
209L GLY* 3.5 26.0 - - - +
210L GLN* 4.7 5.9 - - - +
245L GLN* 3.8 12.3 - - - +
271L ASP* 5.0 1.0 + - - -
272L ASP* 2.9 31.3 + - + +
274L SER* 1.3 76.7 - - - +
276L GLN* 1.3 63.4 + - - +
278L VAL* 3.8 10.8 - - - +
279L ALA 3.4 14.0 + - - -
330L GLU* 3.8 22.2 + - - +
327O ALA* 3.9 26.9 - - - +
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Residues in contact with GLN 276 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208L VAL* 4.0 14.5 - - + +
245L GLN 3.8 9.2 - - - +
246L TYR* 3.6 18.8 + - + -
249L PRO* 3.3 36.3 - - + +
250L PHE* 3.8 7.1 - - - -
272L ASP 3.4 3.6 + - - -
273L LEU* 3.1 21.0 - - - +
274L SER 3.2 0.4 - - - -
275L LYS* 1.3 75.5 - - - +
277L ALA* 1.3 59.1 + - - +
278L VAL 3.0 1.8 - - - -
279L ALA* 2.9 7.0 + - - +
280L TYR* 2.8 26.6 + - - +
303L LEU* 3.7 26.5 - - + +
304L HIS* 3.1 27.9 + - - -
307L LEU* 4.4 2.3 - - - +
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Residues in contact with ALA 277 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273L LEU 3.4 4.5 + - - +
274L SER 4.0 7.2 - - - +
276L GLN* 1.3 78.3 - - - +
278L VAL* 1.3 56.4 + - - +
280L TYR* 3.6 3.3 + - - +
281L ARG* 3.0 20.8 + - - +
296L TYR* 3.4 31.3 - - + -
300L VAL* 4.3 9.9 - - + -
303L LEU* 3.9 12.9 - - - +
304L HIS* 3.9 23.3 - - + -
340L ILE* 4.6 9.4 - - + -
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Residues in contact with VAL 278 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274L SER 3.2 18.2 - - - +
275L LYS* 3.8 12.6 - - - +
276L GLN 3.0 0.2 - - - -
277L ALA* 1.3 76.2 - - - +
279L ALA* 1.3 64.9 + - - +
281L ARG* 3.0 31.8 + - - +
282L GLN* 3.0 20.1 + - - +
296L TYR* 3.9 18.6 - - - +
283O PRO 5.5 0.2 - - - +
286O ALA* 4.5 21.5 - - + +
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Residues in contact with ALA 279 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242L ALA* 3.7 13.7 - - + +
245L GLN* 3.3 42.8 - - + +
246L TYR* 4.6 3.4 - - - +
275L LYS 3.4 3.8 + - - +
276L GLN* 2.9 8.6 + - - +
278L VAL* 1.3 80.1 - - - +
280L TYR* 1.3 62.6 + - - +
282L GLN* 3.0 20.2 + - - +
283L LEU* 3.1 22.0 + - - +
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Residues in contact with TYR 280 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246L TYR* 3.6 45.5 - + + +
276L GLN 2.8 14.6 + - - +
277L ALA 3.8 4.5 - - - +
279L ALA* 1.3 77.1 - - - +
281L ARG* 1.3 62.0 + - - +
283L LEU* 3.5 11.3 + - + +
284L SER* 3.5 24.4 + - - -
289L ARG* 4.7 11.3 + - - -
297L PRO* 3.3 44.1 - - + +
299L ASP* 2.8 31.2 + - - -
300L VAL* 4.4 11.9 - - + -
303L LEU* 3.8 32.8 - - + -
306L ARG* 5.2 4.9 + - - -
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Residues in contact with ARG 281 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277L ALA 3.0 14.2 + - - +
278L VAL* 3.0 35.0 + - - +
280L TYR* 1.3 77.5 - - - +
282L GLN* 1.3 62.9 + - - +
284L SER* 3.6 1.0 + - - -
285L LEU* 3.1 39.6 + - + +
294L GLU* 3.5 7.7 + - - +
295L ALA* 3.5 40.2 - - - +
296L TYR* 3.4 36.3 + - + +
297L PRO* 3.9 14.4 - - + -
277O SER* 3.3 18.9 + - - +
278O ALA* 3.7 17.9 - - - +
283O PRO 5.9 0.8 + - - -
320O PRO* 5.9 3.8 - - - +
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Residues in contact with GLN 282 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242L ALA* 3.4 19.6 - - + +
278L VAL* 3.0 11.6 + - - +
279L ALA* 3.0 14.5 + - - +
281L ARG* 1.3 78.9 - - - +
283L LEU* 1.3 59.9 + - - +
285L LEU* 3.8 1.2 + - - +
286L LEU* 3.1 45.5 + - + +
283O PRO* 3.2 32.3 - - - +
284O THR* 3.6 17.9 - - - +
286O ALA* 4.3 8.0 - - - +
287O THR* 3.2 43.6 + - - +
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Residues in contact with LEU 283 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L ILE* 5.5 0.7 - - - -
66L LEU* 4.1 23.6 - - + -
76L VAL* 4.3 9.6 - - + -
242L ALA* 3.5 26.7 - - + +
243L PRO* 3.6 27.8 - - + -
246L TYR* 4.1 27.4 - - + -
279L ALA 3.1 27.8 + - - +
280L TYR* 3.8 13.9 - - + +
281L ARG 3.2 0.4 - - - -
282L GLN* 1.3 73.6 - - - +
284L SER* 1.3 61.7 + - - +
285L LEU 3.1 2.0 - - - -
286L LEU* 2.9 7.6 + - - +
287L LEU* 2.8 39.8 + - + +
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Residues in contact with SER 284 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280L TYR* 3.5 13.5 + - - -
281L ARG 4.3 1.8 - - - -
283L LEU* 1.3 79.3 - - - +
285L LEU* 1.3 59.3 + - - +
287L LEU* 3.6 3.7 + - - -
288L ARG 3.3 1.7 + - - -
289L ARG* 2.6 73.1 + - - +
290L PRO 5.8 0.9 - - - -
297L PRO* 3.7 34.1 - - - +
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Residues in contact with LEU 285 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281L ARG* 3.1 34.9 + - + +
282L GLN 4.2 0.2 - - - +
283L LEU 3.1 0.8 - - - -
284L SER* 1.3 80.4 - - - +
286L LEU* 1.3 61.8 + - - +
288L ARG* 3.4 15.1 + - - +
289L ARG 3.8 10.5 - - - +
291L PRO* 3.4 31.6 - - + -
295L ALA* 3.9 12.1 - - + +
297L PRO* 6.3 0.4 - - + -
274O ARG* 5.4 0.9 - - - -
275O ILE* 3.6 45.4 + - + +
276O PRO 4.0 2.9 - - - +
277O SER* 3.9 23.3 - - - +
283O PRO* 4.1 14.6 - - + -
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Residues in contact with LEU 286 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L ASP* 3.3 34.3 - - + +
40L ILE* 3.5 34.2 - - + +
282L GLN* 3.1 30.0 + - + +
283L LEU* 2.9 2.5 + - - +
285L LEU* 1.3 74.9 - - - +
287L LEU* 1.3 58.7 + - - +
288L ARG* 3.1 13.3 + - - +
274O ARG* 4.5 18.6 - - + -
283O PRO* 4.3 13.2 - - + -
284O THR* 3.8 29.4 - - + -
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Residues in contact with LEU 287 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L ILE* 3.9 23.1 - - + -
66L LEU* 3.8 31.4 - - + -
67L ASN* 3.6 42.4 + - - +
69L GLU* 5.5 1.0 - - - +
74L GLY* 4.5 17.3 - - - -
76L VAL* 4.0 17.9 - - + -
283L LEU* 2.8 21.9 + - + +
284L SER* 4.1 4.9 - - - +
285L LEU 3.3 0.2 - - - -
286L LEU* 1.3 76.4 - - - +
288L ARG* 1.3 69.7 + - - +
289L ARG* 3.1 15.1 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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