Contacts of the helix formed by residues 274 - 293 (chain K) in PDB entry 3E20
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 ASN 274 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275K VAL* 1.3 70.3 + - - +
276K LYS 3.1 3.1 - - - -
277K TYR* 2.8 34.0 + - + +
278K VAL* 2.7 47.2 + - + +
281K LYS* 5.8 6.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 275 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274K ASN* 1.3 76.4 - - - +
276K LYS* 1.3 81.2 + - + +
278K VAL* 3.0 22.8 - - - +
279K GLN* 4.2 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 276 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K ARG* 5.6 5.5 - - - +
137K LEU 4.6 18.4 + - - -
274K ASN 2.9 1.0 + - - -
275K VAL* 1.3 100.5 - - + +
277K TYR* 1.3 82.5 + - + +
279K GLN* 4.1 4.0 + - - +
280K GLU* 3.6 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 277 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274K ASN* 2.8 37.3 + - + +
276K LYS* 1.3 94.6 - - + +
278K VAL* 1.3 67.8 + - - +
279K GLN 3.2 0.7 - - - -
280K GLU* 3.2 16.5 + - - +
281K LYS* 2.9 31.4 + - + +
392K SER* 5.4 2.0 - - - -
394K ARG* 3.6 40.3 - - + +
395K SER* 4.8 10.8 - - - -
----------------------------------------------------------
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 ASN* 2.7 37.7 + - + +
275K VAL* 3.0 27.4 - - + +
277K TYR* 1.3 72.4 - - - +
279K GLN* 1.3 63.3 + - + +
281K LYS* 3.8 8.5 - - + +
282K LYS* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 279 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K ALA* 4.9 10.4 + - - +
275K VAL 4.7 4.3 - - - +
276K LYS* 4.1 6.6 + - - +
277K TYR 3.2 0.2 - - - -
278K VAL* 1.3 88.0 - - + +
280K GLU* 1.3 60.1 + - - +
282K LYS* 3.9 17.0 - - + +
283K LEU* 2.7 40.0 + - + +
389K GLU* 4.2 15.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 280 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276K LYS 3.6 14.5 + - - +
277K TYR* 3.2 19.6 + - - +
279K GLN* 1.3 78.4 - - - +
281K LYS* 1.3 61.1 + - - +
283K LEU* 4.1 3.0 - - - +
284K ILE* 3.2 30.5 + - + +
390K PHE 4.6 2.2 - - - +
391K VAL* 3.3 23.6 - - + +
392K SER* 2.4 55.9 + - - +
394K ARG 4.0 0.2 + - - -
395K SER* 2.8 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 281 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274K ASN* 5.8 6.2 - - - +
277K TYR* 2.9 22.4 + - + +
278K VAL* 3.8 6.5 - - + +
280K GLU* 1.3 72.9 - - - +
282K LYS* 1.3 69.3 + - - +
284K ILE* 2.8 15.1 + - - +
285K GLN* 2.9 13.9 + - + +
395K SER* 3.3 30.7 - - - -
396K GLN* 5.1 3.3 - - - +
397K GLU* 3.1 43.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 282 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278K VAL 2.9 24.4 + - - +
279K GLN* 3.5 19.0 - - + +
281K LYS* 1.3 73.0 - - - +
283K LEU* 1.3 62.6 + - - +
285K GLN* 3.3 16.5 + - - +
286K ARG* 3.3 10.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
279K GLN* 2.7 21.7 + - + +
280K GLU* 4.1 3.4 - - - +
282K LYS* 1.3 71.9 - - - +
284K ILE* 1.3 61.8 + - - +
286K ARG* 3.0 61.0 - - - +
287K PHE* 3.2 6.4 + - - +
316K THR* 3.8 13.7 - - + -
318K LEU* 3.3 22.2 - - + +
389K GLU* 3.3 48.5 - - + +
391K VAL* 5.1 6.5 - - + -
411K VAL* 6.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 284 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280K GLU* 3.2 17.4 + - + +
281K LYS 2.8 11.4 + - - +
283K LEU* 1.3 73.1 - - + +
285K GLN* 1.3 52.1 + - - +
287K PHE* 3.1 7.5 + - + +
288K PHE* 2.7 61.4 + - + -
318K LEU* 3.9 20.2 - - + -
391K VAL* 4.3 15.5 - - + -
397K GLU* 3.8 8.7 - - + +
398K GLY* 3.8 23.3 - - - +
401K PHE* 3.6 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 285 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570J PRO 4.9 2.0 + - - -
571J SER* 3.9 32.5 + - - +
572J ILE 5.1 1.9 + - - +
281K LYS 2.9 8.9 + - - +
282K LYS* 3.4 13.7 - - - +
284K ILE* 1.3 73.3 - - - +
286K ARG* 1.3 60.7 + - - +
288K PHE* 3.2 25.0 + - - +
289K ASP* 2.9 46.8 + - - +
397K GLU* 3.7 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 286 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282K LYS 3.3 6.6 + - - +
283K LEU* 3.0 40.4 + - - +
285K GLN* 1.3 80.1 - - - +
287K PHE* 1.3 58.1 + - - +
289K ASP* 3.5 16.7 + - - +
290K GLU* 3.6 17.0 + - + +
315K GLU* 2.7 27.2 + - - -
316K THR* 3.6 9.3 + - - +
411K VAL* 3.8 31.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 287 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283K LEU 3.2 2.5 + - - +
284K ILE* 3.1 10.0 + - + +
286K ARG* 1.3 78.3 - - - +
288K PHE* 1.3 76.3 + + - +
290K GLU* 3.1 18.4 + - - +
291K ILE* 3.7 32.2 - - + +
298K TYR* 4.1 20.0 - + + -
299K CYS 4.1 14.8 - - - -
300K PHE* 4.1 20.4 - - + -
318K LEU* 3.9 23.8 - - + -
401K PHE* 4.1 20.6 - + - -
405K PHE* 4.0 19.3 - + - -
410K ALA 4.1 12.1 - - - -
411K VAL* 3.5 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 288 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571J SER* 5.6 0.4 - - - +
572J ILE* 3.4 27.7 - - + +
574J THR* 4.4 2.0 - - - -
284K ILE* 2.7 38.9 + - + +
285K GLN* 3.2 32.7 + - - +
287K PHE* 1.3 85.7 - + - +
289K ASP* 1.3 55.8 + - - +
291K ILE* 2.7 33.2 + - + +
292K SER* 2.8 14.5 + - - -
397K GLU* 4.0 13.9 - - + -
400K GLN* 3.7 41.3 - - + -
401K PHE* 4.5 1.8 - - - -
405K PHE* 3.4 28.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 289 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571J SER* 4.5 9.7 + - - -
285K GLN* 2.9 35.8 + - - +
286K ARG* 3.7 11.6 - - - +
287K PHE 3.3 0.2 - - - -
288K PHE* 1.3 75.2 - - - +
290K GLU* 1.3 63.9 + - - +
291K ILE 3.0 0.2 - - - -
292K SER* 3.6 8.0 - - - -
293K LEU* 2.8 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 290 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286K ARG* 3.6 15.6 - - + +
287K PHE* 3.1 10.2 + - - +
288K PHE 3.0 1.2 - - - -
289K ASP* 1.3 81.6 - - - +
291K ILE* 1.3 60.1 + - - +
293K LEU* 5.8 3.7 - - - +
294K ASP* 4.3 4.4 - - - +
295K SER* 2.3 45.3 + - - +
297K LYS* 2.8 40.1 - - + +
298K TYR* 3.5 23.0 - - + -
411K VAL* 4.6 12.6 - - + -
412K MET 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 291 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572J ILE* 4.0 8.7 - - + -
611J MET* 5.0 9.2 - - + -
612J PHE* 3.3 38.9 - - + -
287K PHE* 3.7 31.4 - - + +
288K PHE* 2.7 17.7 + - + +
290K GLU* 1.3 77.4 - - - +
292K SER* 1.3 65.9 + - - +
293K LEU 3.4 1.1 - - - -
294K ASP* 3.4 12.9 + - - +
298K TYR* 3.2 43.7 - - + +
405K PHE* 3.7 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 292 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571J SER* 3.0 25.4 + - - -
572J ILE* 3.5 18.4 - - - +
612J PHE* 4.0 18.5 - - - -
614J THR* 5.7 1.4 + - - -
288K PHE 2.8 12.1 + - - -
289K ASP* 3.8 11.2 - - - -
291K ILE* 1.3 80.8 - - - +
293K LEU* 1.3 64.3 + - - +
294K ASP* 4.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289K ASP* 2.8 22.4 + - + +
290K GLU* 5.3 4.3 - - - +
292K SER* 1.3 76.7 - - - +
294K ASP* 1.3 73.9 + - - +
295K SER* 4.8 9.2 - - - +
----------------------------------------------------------
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