Contacts of the helix formed by residues 282 - 299 (chain B) in PDB entry 4ZPK
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 HIS 282 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A PHE* 3.8 29.8 - + - -
377A ASP* 4.5 8.2 + - - -
280B PHE 3.5 1.8 + - - -
281B TYR* 1.3 79.0 - - - +
283B ALA* 1.3 75.9 + - - +
284B LEU* 3.2 31.3 + - + -
285B ASP* 3.6 11.4 + - - +
286B SER* 3.4 15.9 + - - -
308B ARG* 3.0 53.3 + - + +
310B LEU* 4.2 9.3 - - + +
316B TYR* 4.1 24.3 - + - -
349B LYS* 6.1 0.2 + - - -
354B PHE* 3.9 15.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ILE* 3.8 26.2 - - + -
366A ARG* 3.7 18.9 - - + +
375A PHE* 3.3 32.1 - - + -
458A ILE* 6.2 1.3 - - + -
282B HIS* 1.3 72.8 + - - +
284B LEU* 1.3 55.9 + - - +
285B ASP 2.7 17.4 + - - -
286B SER* 3.1 21.1 + - - +
287B GLU* 4.3 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ILE* 3.6 28.0 - - + -
377A ASP* 4.8 6.3 - - - +
282B HIS* 3.2 23.4 + - + +
283B ALA* 1.3 76.9 - - - +
285B ASP* 1.3 60.8 - - - +
287B GLU* 5.2 3.1 - - - +
288B ASN* 4.1 9.5 + - - -
308B ARG* 3.7 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B TYR* 5.8 0.9 - - + -
282B HIS* 3.8 12.8 - - - +
283B ALA 2.7 6.5 + - - -
284B LEU* 1.3 83.0 - - - +
286B SER* 1.3 50.6 + - - +
287B GLU 2.7 5.5 + - - -
288B ASN* 2.6 41.8 + - - +
289B MET* 2.9 14.9 + - + -
306B GLN 5.1 1.4 - - - +
307B TYR* 3.9 27.4 - - + -
308B ARG* 3.2 52.7 + - - +
318B TRP* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ARG* 5.1 3.6 + - - -
456A TYR* 3.8 23.2 + - - -
458A ILE* 4.4 14.8 - - - +
278B TYR* 4.0 5.4 - - - -
281B TYR* 4.3 10.3 - - - -
282B HIS 3.4 12.4 + - - -
283B ALA* 3.1 18.3 + - - +
285B ASP* 1.3 76.7 - - - +
287B GLU* 1.3 50.9 + - - +
289B MET* 3.6 14.0 - - - +
290B THR* 2.3 37.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A PHE* 6.4 1.6 - - + -
458A ILE* 6.5 0.4 - - - -
283B ALA 4.3 2.5 + - - +
284B LEU 5.6 3.1 - - - +
285B ASP 2.7 6.0 + - - -
286B SER* 1.3 75.2 + - - +
288B ASN* 1.3 81.1 + - - +
290B THR* 3.1 10.8 + - - -
291B LYS* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LEU 4.1 14.1 + - - -
285B ASP* 2.6 22.0 + - - +
287B GLU* 1.3 92.9 - - - +
289B MET* 1.3 66.2 + - + +
291B LYS* 3.2 16.7 + - + +
292B SER* 2.9 28.4 + - - -
305B GLY* 6.2 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B TYR* 3.7 4.3 + - + -
281B TYR* 3.8 40.1 - - + -
285B ASP* 2.9 19.2 + - + +
286B SER* 3.7 14.4 - - - +
288B ASN* 1.3 89.3 - - + +
290B THR* 1.3 59.8 + - - +
292B SER* 3.3 5.6 + - - +
293B HIS* 2.9 30.0 + - - +
304B SER* 3.9 20.6 - - - -
305B GLY* 4.2 9.4 - - - +
307B TYR* 3.4 49.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A PHE* 3.4 35.7 - - + -
449A PRO* 3.7 15.4 - - + +
278B TYR* 3.6 8.7 + - - -
286B SER 2.3 27.8 + - - -
287B GLU* 3.2 11.6 + - - -
289B MET* 1.3 74.5 - - - +
291B LYS* 1.3 64.8 + - - +
293B HIS* 3.2 1.4 + - - +
294B GLN* 2.9 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE* 4.2 12.1 - - - -
287B GLU* 3.0 13.4 + - - +
288B ASN* 3.2 19.5 - - + +
290B THR* 1.3 76.1 - - - +
292B SER* 1.3 82.0 + - - +
294B GLN* 3.2 20.7 - - - +
295B ASN* 2.9 55.4 + - - +
302B VAL* 4.4 0.6 - - - +
303B VAL 4.1 14.5 + - - -
304B SER* 4.9 1.4 - - - +
305B GLY 5.2 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ASN 2.9 13.9 + - - -
289B MET* 3.5 13.4 - - - +
291B LYS* 1.3 96.3 + - - +
293B HIS* 1.3 56.8 + - - +
295B ASN* 3.4 0.8 - - - +
296B LEU* 2.9 23.3 + - - +
302B VAL* 3.1 27.7 - - - +
304B SER* 3.5 28.7 - - - -
305B GLY 4.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A ASN* 3.6 26.5 - - - -
449A PRO* 3.5 14.8 - - + +
450A TYR* 4.1 7.9 - - + -
250B MET 3.2 24.0 + - - -
251B ASP* 4.1 0.2 - - - -
252B MET* 3.4 39.6 - - + +
278B TYR* 3.2 28.2 + - + +
289B MET 2.9 9.4 + - - +
290B THR 3.2 2.0 + - - +
292B SER* 1.3 75.6 - - - +
294B GLN* 1.3 60.9 + - - +
296B LEU* 2.9 17.7 + - + +
297B CYS* 2.9 38.3 + - - -
337B ILE* 4.5 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A PRO* 4.2 18.3 - - + +
290B THR* 2.9 29.9 + - - +
291B LYS* 3.2 26.6 + - - +
293B HIS* 1.3 72.7 - - - +
295B ASN* 1.3 58.9 + - - +
297B CYS* 3.5 6.0 + - - +
298B THR* 2.6 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B GLU* 4.8 7.6 + - - +
168B PHE* 6.1 0.2 - - - +
169B PHE* 3.8 26.8 - - + +
291B LYS* 2.9 39.8 + - - +
292B SER* 3.4 6.7 - - - +
294B GLN* 1.3 82.0 + - - +
296B LEU* 1.3 55.5 + - - +
298B THR* 3.2 7.0 + - - -
299B LYS* 2.6 57.7 + - + +
302B VAL* 3.7 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B MET* 4.7 5.4 - - - -
292B SER 2.9 14.8 + - - +
293B HIS* 2.9 20.8 + - + +
295B ASN* 1.3 75.9 - - - +
297B CYS* 1.3 57.7 - - - +
299B LYS 2.9 17.2 - - - +
300B GLY 3.3 24.7 - - - +
301B GLN* 3.6 6.3 - - - -
302B VAL* 3.2 11.2 - - + +
323B GLY* 3.5 28.7 - - - +
325B VAL* 3.5 23.1 - - + +
337B ILE* 3.8 36.3 - - + -
339B CYS* 5.6 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A PRO* 5.1 1.6 - - - +
450A TYR* 3.7 39.9 - - + -
250B MET* 4.6 11.0 - - - -
293B HIS* 2.9 38.7 + - - +
294B GLN* 3.9 7.6 - - - +
295B ASN 3.1 0.2 - - - -
296B LEU* 1.3 80.0 - - - +
298B THR* 1.3 63.6 + - + +
299B LYS 3.2 6.9 - - - +
327B TYR* 5.7 0.2 + - - -
337B ILE* 5.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ARG* 3.5 25.0 + - - -
294B GLN* 2.6 27.5 + - + +
295B ASN* 3.0 18.4 + - - -
297B CYS* 1.3 78.6 - - + +
299B LYS* 1.3 65.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B CYS 5.3 0.8 + - - -
139B ASP* 3.8 23.1 + - - +
142B GLU* 3.1 32.6 + - - -
169B PHE* 3.5 43.5 + - + +
170B MET* 4.4 1.8 - - - +
171B ARG* 4.2 25.6 - - + +
192B VAL* 4.5 8.3 - - + -
295B ASN* 2.6 34.2 + - + +
296B LEU 2.9 16.6 - - - +
297B CYS 3.2 8.1 - - - +
298B THR* 1.3 81.0 + - - +
300B GLY* 1.3 61.5 + - - +
301B GLN 4.4 8.3 - - - +
325B VAL* 5.0 0.3 - - - +
327B TYR* 4.5 6.3 + - - -
----------------------------------------------------------
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