Contacts of the helix formed by residues 291 - 307 (chain B) in PDB entry 4K93
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 SER 291 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B GLY 4.0 0.4 + - - -
290B ARG* 1.3 77.7 - - - +
292B LEU* 1.3 59.9 + - - +
293B GLU* 3.7 8.3 + - - +
294B ASP* 3.0 31.3 + - - +
295B CYS* 2.8 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ILE* 3.9 23.3 - - + -
251B ILE* 3.9 22.0 - - + +
253B LYS* 3.9 33.9 - - + -
256B GLU* 4.4 1.8 - - - +
258B TYR* 3.8 35.4 - - + -
282B PHE* 4.0 20.2 - - + -
286B TYR* 4.3 13.2 - - + -
290B ARG 3.8 1.7 + - - +
291B SER* 1.3 72.8 - - - +
293B GLU* 1.3 62.9 + - - +
295B CYS* 3.2 6.2 + - - +
296B GLY* 2.9 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B TYR* 4.4 30.1 - - + +
259B TYR 4.3 11.1 - - - +
260B VAL* 3.7 14.8 - - + +
291B SER* 3.2 7.7 + - - +
292B LEU* 1.3 77.4 - - - +
294B ASP* 1.3 60.6 + - - +
296B GLY* 3.1 3.5 + - - -
297B LYS* 2.8 55.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ARG* 3.0 44.8 + - + +
291B SER* 3.0 23.7 + - - +
293B GLU* 1.3 75.0 - - - +
295B CYS* 1.3 60.6 + - - +
297B LYS* 3.6 25.6 + - - +
298B LEU* 2.9 35.3 + - + +
327B LEU* 5.3 4.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PHE* 3.4 40.9 - - + +
285B GLY 3.5 6.3 - - - -
286B TYR* 3.2 44.9 - - - -
290B ARG* 3.7 9.6 - - - -
291B SER 2.8 23.6 + - - -
292B LEU* 3.4 10.1 - - - +
294B ASP* 1.3 75.5 - - - +
296B GLY* 1.3 55.6 + - - +
298B LEU* 3.3 7.7 + - - +
299B GLY* 2.9 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ALA* 5.8 0.2 - - - -
251B ILE* 4.2 17.9 - - - -
260B VAL* 3.9 16.4 - - - -
278B PHE* 3.8 5.6 - - - -
282B PHE* 3.8 3.7 - - - -
292B LEU 2.9 14.6 + - - -
293B GLU 3.1 4.2 + - - -
295B CYS* 1.3 76.4 - - - +
297B LYS* 1.3 55.4 + - - +
299B GLY* 3.3 1.6 + - - -
300B CYS* 2.9 34.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B VAL* 3.7 21.8 - - + +
263B ILE* 5.4 0.9 - - - +
293B GLU* 2.8 45.8 + - - +
294B ASP* 3.2 24.1 + - - +
296B GLY* 1.3 72.9 - - - +
298B LEU* 1.3 57.0 + - - +
300B CYS* 3.3 2.9 + - - +
301B LEU* 3.0 28.6 + - - +
327B LEU* 3.8 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 4.7 7.2 - - + +
281B GLY* 3.4 23.3 - - - +
284B TYR* 4.1 17.0 - - + -
285B GLY* 3.7 28.9 - - - -
290B ARG* 4.4 18.4 - - + +
294B ASP 2.9 22.4 + - - +
295B CYS 3.3 1.3 + - - +
297B LYS* 1.3 72.1 - - - +
299B GLY* 1.3 63.9 + - - +
301B LEU* 3.4 4.5 + - + +
302B ALA* 3.1 19.8 + - - +
322B ALA* 4.1 19.5 - - + -
327B LEU* 3.9 29.8 - - + -
328B ILE* 4.1 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PHE* 3.3 49.1 - - - -
281B GLY* 3.7 2.8 - - - -
282B PHE 3.8 4.3 - - - -
295B CYS 2.9 12.2 + - - -
296B GLY 3.3 2.4 + - - -
298B LEU* 1.3 76.4 - - - +
300B CYS* 1.3 56.0 + - - +
302B ALA* 3.4 1.4 + - - -
303B ALA* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B GLY* 4.3 12.8 - - - -
249B ALA* 4.2 13.2 - - - -
260B VAL* 3.9 10.8 - - + -
261B ASN 3.7 25.4 - - - +
262B ALA* 4.6 4.7 - - - -
263B ILE* 3.8 12.8 + - + +
278B PHE* 3.9 15.7 - - - -
296B GLY 2.9 19.0 + - - +
297B LYS* 3.8 4.0 - - - +
299B GLY* 1.3 72.1 - - - +
301B LEU* 1.3 66.4 + - - +
303B ALA* 4.0 3.9 - - - +
304B GLY* 2.9 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 6.0 1.6 - - + -
263B ILE* 3.9 24.9 - - + +
297B LYS 3.0 16.7 + - - +
298B LEU* 3.7 7.2 - - + +
299B GLY 3.3 0.2 - - - -
300B CYS* 1.3 77.2 - - - +
302B ALA* 1.3 64.0 + - - +
304B GLY* 3.2 2.6 + - - -
305B ILE* 3.0 47.6 + - + +
318B LEU* 4.8 2.2 - - + +
321B ALA* 3.9 9.2 - - + +
322B ALA* 3.6 39.5 - - + +
325B ALA* 4.1 11.4 - - + -
327B LEU* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 4.8 4.0 - - + -
277B LEU* 3.3 37.3 - - + +
281B GLY* 4.4 6.7 - - - +
298B LEU 3.1 14.6 + - - +
301B LEU* 1.3 79.6 - - + +
303B ALA* 1.3 62.3 + - - +
305B ILE* 3.4 3.5 + - - +
306B VAL* 3.1 18.5 + - - +
314B PRO* 4.8 0.2 - - - +
318B LEU* 4.2 30.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ALA* 3.4 31.4 - - + +
277B LEU* 4.1 2.6 - - - +
278B PHE* 4.0 8.5 - - + +
299B GLY 3.0 18.1 + - - +
300B CYS* 4.0 5.4 - - - +
302B ALA* 1.3 76.7 - - - +
304B GLY* 1.3 63.2 + - - +
306B VAL* 3.3 7.0 + - - +
307B ILE* 3.3 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ILE* 3.7 16.8 - - - -
265B ILE* 3.8 4.5 - - - +
300B CYS 2.9 18.3 + - - -
301B LEU 3.7 1.1 - - - -
303B ALA* 1.3 76.0 - - - +
305B ILE* 1.3 60.9 + - - +
307B ILE* 3.5 14.9 - - - +
308B GLN* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ILE* 4.7 4.3 - - + -
301B LEU* 3.0 31.0 + - + +
302B ALA 3.6 7.2 - - - +
304B GLY* 1.3 76.4 - - - +
306B VAL* 1.3 65.5 + - - +
308B GLN* 3.2 23.2 + - - +
309B GLN* 4.1 7.7 + - - +
314B PRO* 4.4 8.7 - - + -
316B THR* 3.9 21.8 - - - +
318B LEU* 3.7 23.6 - - + -
321B ALA* 3.5 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B THR 4.1 2.2 - - - +
273B GLY 3.7 28.3 - - - +
274B ALA* 3.8 6.5 - - - +
277B LEU* 4.0 4.9 - - + -
302B ALA 3.1 15.0 + - - +
303B ALA 3.4 11.0 - - - +
305B ILE* 1.3 80.8 - - - +
307B ILE* 1.3 61.6 + - + +
308B GLN 3.2 0.2 - - - -
309B GLN* 3.2 18.0 - - - +
311B GLY 3.9 6.7 - - - +
312B PRO 3.4 33.4 - - - +
314B PRO* 3.8 22.7 - - + -
408B K 2.8 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ILE* 4.0 24.5 - - + -
268B VAL* 3.8 15.1 - - + -
269B VAL 3.0 23.4 + - - -
270B ASP 3.1 19.3 + - - +
271B THR* 3.9 19.3 - - + +
274B ALA* 3.5 28.0 - - + -
303B ALA 3.3 15.0 + - - +
304B GLY* 3.5 21.8 - - - +
306B VAL* 1.3 78.9 - - + +
308B GLN* 1.3 59.8 + - + +
309B GLN 3.3 1.6 - - - -
----------------------------------------------------------
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