Contacts of the helix formed by residues 272 - 287 (chain U) 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 U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177U LYS* 4.5 2.9 - - - -
208U VAL* 3.4 17.2 + - - +
271U ASP* 1.3 82.8 + - - +
273U LEU* 1.3 66.4 + - - +
274U SER* 2.7 40.2 + - - -
275U LYS* 2.9 45.1 + - + +
276U GLN* 3.1 8.4 + - - +
328U VAL* 3.2 23.3 - - - +
329U ILE* 3.9 0.2 - - - -
330U GLU* 3.7 19.0 - - - +
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Residues in contact with LEU 273 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168U LEU* 5.3 0.2 - - + -
208U VAL* 6.3 0.9 - - + -
249U PRO* 5.0 1.6 - - + -
270U TYR* 3.6 34.1 - - + -
271U ASP* 4.2 2.0 - - - +
272U ASP* 1.3 72.4 + - - +
274U SER* 1.3 56.1 + - - +
276U GLN* 2.8 48.4 + - + +
277U ALA* 3.0 11.1 + - - +
304U HIS* 3.5 30.1 + - + +
307U LEU* 4.7 3.8 - - + -
308U LEU* 4.7 4.9 - - + -
327U PRO* 3.4 34.5 - - + -
328U VAL 3.0 17.3 + - - +
329U ILE* 4.9 5.4 - - + -
340U ILE* 5.8 1.1 - - + -
344U VAL* 4.4 13.0 - - + -
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Residues in contact with SER 274 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272U ASP* 2.7 16.3 + - - -
273U LEU* 1.3 74.5 - - - +
275U LYS* 1.3 61.3 + - - -
277U ALA* 3.4 8.2 + - - +
278U VAL* 3.2 27.3 + - - +
296U TYR* 4.6 1.6 + - - -
329U ILE* 2.9 18.6 - - - +
330U GLU* 2.9 38.9 + - - -
340U ILE* 5.0 7.0 - - - -
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Residues in contact with LYS 275 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208U VAL* 3.5 26.0 - - - +
209U GLY* 3.7 22.9 - - - +
210U GLN* 5.3 2.9 - - + +
245U GLN* 3.9 6.4 - - - +
272U ASP* 2.9 31.8 + - + +
274U SER* 1.3 75.3 - - - +
276U GLN* 1.3 63.2 + - - +
278U VAL* 3.6 10.3 + - + +
279U ALA* 3.3 20.3 + - - +
330U GLU* 3.5 22.4 + - - -
324X THR* 5.2 14.8 - - + +
327X ALA* 4.0 28.1 - - - +
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Residues in contact with GLN 276 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208U VAL* 4.0 15.2 - - + +
245U GLN 4.2 8.5 - - - +
246U TYR* 4.2 5.8 + - - -
249U PRO* 3.2 35.5 - - + +
250U PHE* 3.7 24.7 - - - -
272U ASP 3.1 6.2 + - - +
273U LEU* 2.8 24.7 + - - +
275U LYS* 1.3 76.2 - - - +
277U ALA* 1.3 61.3 + - - +
279U ALA* 3.1 7.4 + - - +
280U TYR* 3.1 20.8 + - - +
303U LEU* 4.5 12.7 + - + +
304U HIS* 2.8 34.4 + - - -
307U LEU* 4.0 5.7 - - - +
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Residues in contact with ALA 277 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273U LEU 3.0 9.5 + - - +
274U SER 3.6 9.0 - - - +
275U LYS 3.3 0.2 - - - -
276U GLN* 1.3 79.3 - - - +
278U VAL* 1.3 57.1 + - - +
280U TYR* 3.4 5.5 + - - +
281U ARG* 2.9 29.8 + - - +
296U TYR* 3.6 24.2 - - + -
300U VAL* 4.4 6.7 - - + +
303U LEU* 4.8 3.6 - - - -
304U HIS* 4.3 13.4 - - + -
340U ILE* 4.1 19.1 - - + -
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Residues in contact with VAL 278 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274U SER* 3.2 18.2 - - - +
275U LYS* 3.8 10.3 - - + +
276U GLN 3.3 0.4 - - - -
277U ALA* 1.3 77.1 - - - +
279U ALA* 1.3 62.1 + - - +
281U ARG* 3.4 30.3 + - - +
282U GLN* 3.2 21.7 + - - +
296U TYR* 3.9 17.7 - - + +
283X PRO 5.1 6.1 - - - +
285X LEU* 6.3 2.2 - - + -
286X ALA* 4.2 26.7 - - + +
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Residues in contact with ALA 279 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242U ALA* 3.9 15.4 - - + +
245U GLN* 3.7 37.0 - - + +
246U TYR 4.5 3.8 - - - +
275U LYS 3.3 8.4 + - - +
276U GLN 3.1 9.9 + - - +
278U VAL* 1.3 78.5 - - - +
280U TYR* 1.3 61.9 + - - +
282U GLN* 3.0 17.6 + - - +
283U LEU* 3.2 19.3 + - - +
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Residues in contact with TYR 280 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66U LEU* 5.6 6.1 - - + -
246U TYR* 3.5 46.4 - + + +
276U GLN 3.1 7.9 + - - +
277U ALA 4.0 2.9 - - - +
279U ALA* 1.3 78.8 - - - +
281U ARG* 1.3 62.3 - - - +
283U LEU* 3.4 18.1 + - + +
284U SER* 3.3 26.0 + - - -
289U ARG* 3.3 21.7 + - - -
297U PRO* 3.6 27.6 - - + -
299U ASP* 2.7 38.4 + - - -
300U VAL* 5.0 4.0 - - + -
303U LEU* 3.7 33.9 - - + -
306U ARG* 5.3 1.4 + - - -
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Residues in contact with ARG 281 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277U ALA 2.9 18.0 + - - +
278U VAL* 3.5 30.1 + - - +
280U TYR* 1.3 77.5 - - - +
282U GLN* 1.3 58.6 + - - +
284U SER* 3.6 1.6 + - - -
285U LEU* 3.1 40.3 + - + +
294U GLU 3.8 6.0 + - - -
295U ALA 3.6 16.8 - - - +
296U TYR* 3.7 54.5 + - + +
297U PRO* 3.8 14.1 - - + -
277X SER* 2.9 32.1 + - - -
278X ALA* 4.2 12.1 - - - +
282X GLN 5.4 2.2 + - - -
283X PRO* 5.0 7.9 + - - +
285X LEU* 5.9 3.6 - - - +
320X PRO* 6.0 4.6 - - - +
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Residues in contact with GLN 282 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38U ASP 5.5 1.6 + - - -
39U GLY* 6.4 0.2 - - - -
242U ALA* 3.6 21.1 - - + +
278U VAL* 3.2 11.9 + - - +
279U ALA* 3.0 12.0 + - - +
281U ARG* 1.3 76.2 - - - +
283U LEU* 1.3 65.7 + - + +
285U LEU* 4.0 0.4 - - - -
286U LEU* 3.1 41.0 + - + +
283X PRO* 3.4 21.4 - - - +
284X THR* 3.2 31.7 - - + +
285X LEU 4.4 0.3 + - - -
286X ALA* 5.2 1.2 + - - +
287X THR* 3.2 33.1 + - - +
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Residues in contact with LEU 283 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40U ILE* 5.5 0.9 - - - -
66U LEU* 4.1 18.6 - - + -
76U VAL* 3.9 35.2 - - + -
242U ALA* 3.6 25.4 - - + +
243U PRO* 3.8 21.3 - - + -
246U TYR* 4.5 16.6 - - + -
279U ALA 3.2 25.9 + - - +
280U TYR* 3.6 17.0 - - + +
282U GLN* 1.3 81.3 - - + +
284U SER* 1.3 58.4 + - - +
286U LEU* 3.3 4.4 + - - +
287U LEU* 2.9 38.8 + - + +
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Residues in contact with SER 284 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280U TYR* 3.3 16.5 + - - -
281U ARG 3.9 1.8 - - - -
283U LEU* 1.3 78.0 - - - +
285U LEU* 1.3 59.5 + - - +
287U LEU* 2.9 3.6 + - - -
288U ARG 2.8 26.2 + - - -
289U ARG* 2.9 44.5 + - - +
297U PRO* 3.3 36.9 - - - +
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Residues in contact with LEU 285 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281U ARG* 3.1 31.3 + - + +
282U GLN 4.1 2.7 - - - +
284U SER* 1.3 81.0 - - - +
286U LEU* 1.3 61.9 + - - +
288U ARG* 3.6 11.3 + - - +
289U ARG 4.9 2.7 - - - +
291U PRO* 3.7 35.7 - - + -
295U ALA* 4.0 9.2 - - + +
274X ARG* 5.4 0.3 - - - -
275X ILE* 4.0 48.8 + - + +
276X PRO 4.4 2.9 - - - +
277X SER* 3.8 33.9 - - - +
283X PRO* 4.2 15.9 - - + -
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Residues in contact with LEU 286 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38U ASP* 3.4 32.5 - - + +
40U ILE* 3.8 27.2 - - + +
282U GLN* 3.1 41.0 + - + +
283U LEU* 3.9 3.4 - - - +
285U LEU* 1.3 76.8 - - - +
287U LEU* 1.3 59.6 + - - +
288U ARG* 3.1 12.8 + - - +
274X ARG* 4.1 32.3 - - + +
283X PRO* 4.6 11.7 - - + -
284X THR* 3.8 14.4 - - + -
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Residues in contact with LEU 287 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40U ILE* 3.5 32.3 - - + -
66U LEU* 4.3 19.3 - - + -
67U ASN* 3.4 44.0 + - - +
69U GLU* 5.2 1.4 - - - +
74U GLY* 4.5 16.8 - - - -
76U VAL* 4.0 19.1 - - + -
283U LEU* 2.9 27.7 + - + +
284U SER* 2.9 4.7 + - - +
286U LEU* 1.3 75.3 - - - +
288U ARG* 1.3 70.5 + - - +
289U ARG* 3.4 12.4 + - + +
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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