Contacts of the helix formed by residues 272 - 287 (chain K) 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 K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177K LYS* 3.8 4.2 - - - -
208K VAL* 3.3 20.8 + - - +
210K GLN* 4.7 0.6 - - + +
271K ASP* 1.3 81.4 + - - +
273K LEU* 1.3 63.4 + - - +
274K SER* 2.6 40.7 + - - -
275K LYS* 3.1 38.2 + - + +
276K GLN 3.3 6.8 + - - -
328K VAL* 2.6 34.0 - - - +
330K GLU* 3.7 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208K VAL* 6.3 0.2 - - + -
249K PRO* 4.6 5.6 - - + -
270K TYR* 3.8 20.2 - - + -
271K ASP* 4.3 2.6 - - - +
272K ASP* 1.3 71.2 + - - +
274K SER* 1.3 67.2 + - - +
276K GLN* 2.9 46.0 + - + +
277K ALA* 3.3 4.9 + - - +
304K HIS* 3.8 25.2 + - + +
307K LEU* 3.9 14.6 - - + -
308K LEU* 4.0 17.3 - - + -
327K PRO* 3.5 29.2 - - + -
328K VAL 3.1 6.5 + - - +
329K ILE* 3.6 15.0 - - + -
344K VAL* 4.6 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 274 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272K ASP* 2.6 17.8 + - - -
273K LEU* 1.3 74.9 - - - +
275K LYS* 1.3 61.1 + - - -
276K GLN 3.3 0.5 + - - -
277K ALA* 3.4 11.8 + - - +
278K VAL* 3.5 16.9 + - - +
296K TYR* 5.0 1.0 + - - -
329K ILE* 3.1 21.6 - - - +
330K GLU* 2.9 38.8 + - - -
340K ILE* 4.4 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 275 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208K VAL* 3.8 22.7 - - - +
209K GLY* 3.9 23.8 - - - +
210K GLN* 4.6 5.3 - - + +
245K GLN* 4.2 6.6 + - - +
272K ASP* 3.1 29.3 + - + +
274K SER* 1.3 76.2 - - - +
276K GLN* 1.3 62.7 + - - +
278K VAL* 3.8 11.8 + - + +
279K ALA* 3.4 18.4 + - - +
330K GLU* 2.9 29.9 + - - +
327N ALA* 4.9 17.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 276 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208K VAL* 4.0 15.2 - - + +
245K GLN 4.3 1.3 - - - +
246K TYR* 2.9 37.0 + - - -
249K PRO* 3.3 24.2 - - + +
250K PHE* 3.7 18.4 - - - -
272K ASP 3.3 4.9 + - - +
273K LEU* 2.9 34.7 + - + +
275K LYS* 1.3 76.7 - - - +
277K ALA* 1.3 60.2 + - - +
279K ALA* 3.0 8.1 + - - +
280K TYR* 2.9 26.3 + - - +
303K LEU* 4.3 13.0 - - + +
304K HIS* 3.3 15.8 + - - -
307K LEU* 4.2 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273K LEU 3.3 3.3 + - - +
274K SER 3.4 10.1 + - - +
276K GLN* 1.3 79.0 - - - +
278K VAL* 1.3 53.8 + - - +
280K TYR* 3.1 8.1 + - - +
281K ARG* 2.7 35.7 + - - +
296K TYR* 3.4 25.1 - - + -
300K VAL* 4.3 2.9 - - + +
303K LEU* 4.6 4.9 - - - -
304K HIS* 4.2 14.5 + - + -
340K ILE* 3.6 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 278 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274K SER 3.5 16.4 - - - +
275K LYS* 3.9 11.9 - - + +
276K GLN 3.3 0.6 - - - -
277K ALA* 1.3 75.2 - - - +
279K ALA* 1.3 60.1 + - - +
281K ARG* 3.4 29.7 + - - +
282K GLN* 3.3 19.2 + - - +
296K TYR* 3.8 18.1 - - - +
283N PRO 4.8 6.0 - - - +
285N LEU* 6.1 2.7 - - + -
286N ALA* 4.3 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 279 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242K ALA* 3.8 30.3 - - - +
245K GLN* 4.1 22.4 - - + +
246K TYR* 4.4 3.8 - - - +
275K LYS 3.4 11.4 + - - +
276K GLN* 3.0 10.8 + - - +
278K VAL* 1.3 75.6 - - - +
280K TYR* 1.3 59.9 + - - +
281K ARG 3.1 1.6 - - - -
282K GLN* 2.9 30.5 + - - +
283K LEU* 3.3 5.5 + - - +
286N ALA* 6.2 2.0 - - - -
287N THR* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 280 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246K TYR* 3.6 47.2 - + + +
276K GLN 2.9 11.6 + - - +
277K ALA* 3.6 5.6 - - - +
279K ALA* 1.3 72.6 - - - +
281K ARG* 1.3 62.0 + - - +
283K LEU* 3.3 14.7 + - + +
284K SER* 3.2 22.5 + - - -
289K ARG* 4.7 7.8 + - - -
297K PRO* 3.7 16.6 - - + -
299K ASP* 2.9 47.1 + - - -
300K VAL* 4.9 5.8 - - + -
303K LEU* 3.4 35.9 - - + -
306K ARG* 5.5 2.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 281 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277K ALA 2.7 21.3 + - - +
278K VAL* 3.4 29.2 + - - +
279K ALA 3.1 0.2 - - - -
280K TYR* 1.3 74.7 - - - +
282K GLN* 1.3 60.3 + - - +
284K SER* 2.9 19.6 + - - -
285K LEU* 3.2 33.2 + - + +
294K GLU* 3.2 18.8 + - - +
295K ALA 3.8 14.4 - - - +
296K TYR* 3.1 51.2 + - + -
297K PRO* 4.4 4.5 - - + -
277N SER* 2.9 24.1 + - - -
278N ALA* 3.9 14.8 - - - +
283N PRO 5.7 2.6 + - - -
285N LEU* 6.0 6.3 - - - +
320N PRO* 6.0 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 282 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242K ALA* 3.8 18.4 - - + +
278K VAL 3.3 8.2 + - - +
279K ALA* 2.9 16.1 + - - +
281K ARG* 1.3 77.0 - - - +
283K LEU* 1.3 66.4 + - - +
285K LEU* 4.1 1.4 - - - +
286K LEU* 3.3 35.4 + - + +
283N PRO* 3.7 18.9 + - - +
284N THR* 3.3 41.7 - - + +
285N LEU 4.9 0.3 + - - -
286N ALA* 5.0 3.1 + - - +
287N THR* 3.3 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 283 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K GLY* 5.6 5.8 - - - +
40K ILE* 5.7 4.5 - - + -
66K LEU* 6.5 0.7 - - + -
76K VAL* 3.7 33.4 - - + -
242K ALA* 4.6 5.8 - - + -
243K PRO* 3.9 20.4 - - + -
246K TYR* 3.8 38.1 - - + -
279K ALA 3.3 6.3 + - - +
280K TYR* 3.3 18.6 + - + +
282K GLN* 1.3 79.1 - - - +
284K SER* 1.3 65.4 + - - +
286K LEU* 3.0 12.4 + - + +
287K LEU* 2.9 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 284 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280K TYR* 3.2 13.8 + - - -
281K ARG 2.9 11.8 + - - -
283K LEU* 1.3 77.3 - - - +
285K LEU* 1.3 63.7 + - - +
287K LEU* 2.7 24.8 + - - -
288K ARG 2.9 10.0 + - - -
289K ARG* 3.0 41.4 + - - +
297K PRO* 3.5 30.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 285 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281K ARG* 3.2 29.4 + - + +
282K GLN 4.1 0.2 - - - +
284K SER* 1.3 83.0 + - - +
286K LEU* 1.3 59.1 + - - +
288K ARG 3.6 2.0 + - - -
289K ARG 4.4 10.3 - - - +
291K PRO* 4.2 14.8 - - + -
295K ALA 4.2 14.1 - - - +
275N ILE* 3.2 61.2 + - + +
276N PRO 4.4 2.9 - - - +
277N SER* 3.3 39.7 - - - +
283N PRO* 4.0 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 286 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K ASP* 3.5 48.4 - - + +
39K GLY* 4.6 3.4 - - - +
40K ILE* 4.4 13.5 - - + +
282K GLN* 3.3 33.4 + - + +
283K LEU* 3.0 12.8 + - + +
285K LEU* 1.3 74.3 - - - +
287K LEU* 1.3 59.6 + - + +
288K ARG* 3.1 14.9 + - - +
274N ARG* 3.7 40.8 - - + +
275N ILE* 5.3 1.3 - - - +
283N PRO* 4.3 10.5 - - + -
284N THR* 4.3 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 287 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40K ILE* 3.9 35.7 - - + -
66K LEU* 3.5 32.1 - - + -
67K ASN* 4.7 11.4 - - - +
76K VAL* 4.9 3.1 - - + -
283K LEU* 2.9 26.5 + - + +
284K SER* 2.7 9.9 + - - +
286K LEU* 1.3 76.4 - - - +
288K ARG* 1.3 66.3 + - - +
289K ARG* 3.1 38.2 + - + +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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