Contacts of the helix formed by residues 253 - 270 (chain E) in PDB entry 4K4I
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 253 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E ASN* 2.7 15.6 + - - +
252E HIS* 1.3 76.2 - - - +
254E LEU* 1.3 57.7 - - - +
255E HIS* 3.2 9.4 - - - -
256E ILE* 3.0 24.2 + - + +
257E THR* 2.8 27.1 + - - +
286E LEU* 3.2 33.9 + - + +
289E PHE* 4.2 7.3 + - - +
291E LYS 3.2 20.2 + - - -
292E PRO* 3.3 4.2 - - - +
293E VAL* 2.7 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 254 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E ASN* 3.2 32.2 + - + +
252E HIS 3.7 1.6 - - - -
253E ASN* 1.3 76.6 - - - +
255E HIS* 1.3 64.0 + - - +
257E THR* 3.2 8.5 - - - +
258E GLU* 3.0 54.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 255 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252E HIS 4.3 7.4 + - - -
253E ASN* 4.0 15.6 - - - -
254E LEU* 1.3 78.6 + - - +
256E ILE* 1.3 84.8 + - + +
258E GLU* 3.5 14.7 - - - +
259E LYS* 3.3 34.3 + - - +
292E PRO* 5.2 7.2 - - + -
293E VAL 5.4 0.7 - - - -
316E ILE* 4.1 13.1 - - + +
317E LEU* 3.7 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 256 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253E ASN* 3.0 33.0 + - + +
255E HIS* 1.3 100.1 - - + +
257E THR* 1.3 65.2 + - - +
258E GLU 3.3 0.2 - - - -
259E LYS* 3.1 7.8 + - - +
260E LEU* 3.0 32.4 + - + +
286E LEU* 3.7 24.5 - - + -
293E VAL* 4.6 6.3 - - + +
313E ILE* 3.8 32.8 - - + -
316E ILE* 4.2 20.8 - - + +
317E LEU* 4.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 257 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E ASN* 3.3 10.9 + - - +
253E ASN 2.8 25.4 + - - +
254E LEU* 3.2 16.3 - - - +
256E ILE* 1.3 73.3 - - - +
258E GLU* 1.3 59.4 + - - +
260E LEU* 3.9 6.0 - - - +
261E GLU* 3.0 30.6 + - - +
283E ILE* 3.8 25.1 - - + +
286E LEU* 3.6 34.1 - - + -
287E LYS* 4.3 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 258 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254E LEU* 3.0 35.6 + - + +
255E HIS* 3.5 25.0 + - - +
257E THR* 1.3 78.3 + - - +
259E LYS* 1.3 76.0 + - + +
261E GLU* 3.6 10.2 + - - +
262E VAL* 3.6 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 259 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255E HIS* 3.3 26.1 + - - +
256E ILE 3.1 6.4 + - - +
258E GLU* 1.3 87.7 + - + +
260E LEU* 1.3 66.0 + - - +
261E GLU 3.1 1.3 - - - -
262E VAL* 3.1 20.4 + - - +
263E LEU* 3.5 3.6 + - - +
316E ILE* 4.0 31.0 - - + +
320E GLY* 3.4 26.0 + - - +
321E HIS* 4.3 5.4 - - - +
322E LEU* 4.6 11.4 - - + +
325E LEU* 3.8 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256E ILE* 3.0 26.1 + - + +
257E THR* 4.0 1.1 - - - +
259E LYS* 1.3 76.7 - - - +
261E GLU* 1.3 57.7 + - - +
263E LEU* 3.0 8.4 + - + +
264E ALA* 2.8 27.9 + - - +
279E TYR* 4.0 10.7 - - + -
282E ALA* 5.3 0.2 - - + -
283E ILE* 3.9 23.6 - - + +
286E LEU* 3.7 30.1 - - + -
309E MET* 4.3 28.7 - - + -
312E LYS* 4.3 15.9 - - + -
313E ILE* 4.5 5.6 - - + -
316E ILE* 4.6 4.3 - - + -
322E LEU* 4.3 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 261 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257E THR* 3.0 18.8 + - - +
258E GLU* 3.9 9.7 - - - +
259E LYS 3.1 0.4 - - - -
260E LEU* 1.3 74.2 - - - +
262E VAL* 1.3 65.3 + - - +
264E ALA* 3.7 3.3 - - + +
265E LYS* 2.9 26.1 + - - +
283E ILE* 3.5 30.6 - - + +
287E LYS* 3.0 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258E GLU 3.6 15.3 - - - +
259E LYS* 3.1 10.7 + - - +
261E GLU* 1.3 77.6 - - + +
263E LEU* 1.3 56.4 + - - +
265E LYS* 3.3 6.7 + - - +
266E ALA* 3.0 26.1 + - + +
325E LEU* 3.7 22.2 - - + -
328E ILE* 5.2 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E LYS 3.5 1.6 + - - +
260E LEU* 3.0 11.8 + - + +
262E VAL* 1.3 77.9 - - - +
264E ALA* 1.3 65.3 + - - +
266E ALA* 3.2 5.1 + - + +
267E TYR* 3.1 46.4 + - + +
279E TYR* 3.6 26.0 - - + +
312E LYS* 4.7 6.3 - - + +
322E LEU* 3.9 26.2 - - + -
324E LYS* 3.9 29.4 - - + -
325E LEU* 4.0 11.2 - - + +
328E ILE* 3.5 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E LEU 2.8 13.6 + - - +
261E GLU* 3.7 8.7 - - + +
263E LEU* 1.3 73.5 - - - +
265E LYS* 1.3 57.8 + - - +
267E TYR* 4.0 2.4 - - - +
268E SER* 2.9 29.0 + - - -
276E ALA* 3.8 14.2 - - + +
279E TYR* 3.5 33.2 - - + -
280E ALA* 4.8 2.2 - - + +
283E ILE* 4.0 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 265 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E GLU 2.9 17.7 + - - +
262E VAL* 3.6 7.4 - - - +
263E LEU 3.1 0.2 - - - -
264E ALA* 1.3 77.8 - - - +
266E ALA* 1.3 59.1 + - - +
268E SER* 4.2 9.4 + - - -
269E VAL* 2.9 50.7 + - + +
332E VAL* 6.1 1.8 - - + -
336E GLU* 3.6 35.9 - - - +
339E SER* 5.1 3.6 + - - -
340E ASN* 4.9 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 266 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262E VAL* 3.0 17.3 + - + +
263E LEU* 3.2 5.6 + - + +
265E LYS* 1.3 78.0 - - - +
267E TYR* 1.3 61.3 + - + +
269E VAL* 3.5 2.4 - - - +
270E GLN* 3.0 35.1 + - - +
328E ILE* 3.9 39.3 - - + -
332E VAL* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 267 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263E LEU* 3.1 33.9 + - + +
264E ALA* 4.0 3.6 - - - +
266E ALA* 1.3 74.3 - - + +
268E SER* 1.3 66.0 + - - +
270E GLN* 3.4 15.2 + - - +
271E GLY 3.4 3.1 + - - -
272E ASP* 2.9 48.2 + - + +
275E ARG* 3.6 37.4 + - + -
276E ALA 4.5 6.3 - - - +
279E TYR* 3.7 31.5 + + - -
324E LYS* 4.2 20.2 + - - +
1H G 2.9 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 268 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264E ALA 2.9 19.4 + - - -
265E LYS* 3.5 15.1 + - - -
266E ALA 3.3 0.2 - - - -
267E TYR* 1.3 76.3 - - - +
269E VAL* 1.3 58.9 + - - +
271E GLY* 2.8 21.5 + - - -
272E ASP 4.8 2.0 - - - +
273E LYS* 5.4 2.3 - - - +
276E ALA* 3.9 15.6 - - - +
346E THR* 3.3 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 269 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E LYS* 2.9 46.9 + - + +
266E ALA* 3.5 15.5 - - - +
268E SER* 1.3 73.6 - - - +
270E GLN* 1.3 58.0 + - - +
271E GLY 3.2 1.1 + - - -
332E VAL* 4.1 20.0 - - + +
335E LEU* 3.9 34.4 - - + +
336E GLU* 3.9 19.3 - - + -
339E SER* 3.9 10.8 - - - +
346E THR* 3.3 26.5 - - - +
349E ALA* 5.6 0.5 - - - +
350E GLN* 4.3 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 270 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E ALA* 3.0 29.5 + - - +
267E TYR* 3.8 18.5 - - - +
268E SER 3.0 1.0 + - - -
269E VAL* 1.3 74.6 - - - +
271E GLY* 1.3 59.7 + - - +
272E ASP* 3.3 5.7 + - + +
328E ILE* 5.6 1.0 - - - +
329E SER* 3.7 23.0 + - - +
331E SER* 4.6 1.6 + - - +
332E VAL* 3.7 18.6 - - + +
335E LEU* 4.2 13.9 - - + -
350E GLN* 3.1 25.2 + - - +
----------------------------------------------------------
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