Contacts of the helix formed by residues 282 - 290 (chain B) in PDB entry 6UZA
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 282 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ALA* 3.2 28.0 + - - +
228B HIS* 5.5 0.2 - - - -
230B GLN* 3.5 12.6 - - - -
278B LYS 4.1 7.6 - - - -
279B GLY 3.5 14.1 + - - -
280B LEU 3.3 2.4 - - - -
281B ALA* 1.3 79.1 - - - +
283B PRO* 1.3 63.3 - - - +
284B ALA 3.8 1.4 + - - -
285B TYR* 3.5 14.7 + - - +
286B LEU* 2.9 30.7 + - - +
324B GLN* 3.9 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B GLN* 3.4 24.7 - - - +
232B TYR* 3.8 13.7 - - - +
281B ALA 4.4 2.5 - - - +
282B SER* 1.3 84.0 - - - +
284B ALA* 1.3 49.5 + - - +
286B LEU* 4.2 3.1 - - + -
287B SER* 2.3 41.0 + - - -
324B GLN* 4.9 13.0 - - + +
328B PHE* 4.0 22.9 - - + -
866B TYR* 3.7 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ALA* 4.9 2.0 - - - +
230B GLN* 3.8 32.1 + - - +
231B GLU 4.5 0.7 - - - +
232B TYR* 3.7 25.7 + - + -
235B VAL* 3.4 22.4 - - + +
282B SER* 3.3 5.7 - - - +
283B PRO* 1.3 79.2 - - - +
285B TYR* 1.3 58.7 + - - +
288B LEU* 3.3 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ILE* 4.3 14.8 - - + -
227B ALA* 4.2 6.5 - - + -
235B VAL* 4.6 7.6 - - + +
239B LEU* 4.1 16.4 - - + -
244B ARG* 3.7 16.1 - - - +
245B ILE* 3.1 45.6 + - + +
279B GLY 3.8 11.9 - - - +
280B LEU* 3.7 36.3 - - + +
282B SER* 3.3 16.7 + - - +
283B PRO 3.2 0.2 - - - -
284B ALA* 1.3 79.3 - - - +
286B LEU* 1.3 57.7 + - + +
287B SER 3.3 0.4 - - - -
289B SER* 2.7 64.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU 3.8 18.2 - - - +
281B ALA 4.5 3.4 - - - +
282B SER 2.9 24.4 + - - +
283B PRO* 4.2 5.2 - - + +
285B TYR* 1.3 80.1 - - + +
287B SER* 1.3 60.9 + - - +
289B SER* 4.4 3.4 - - - +
290B SER* 3.2 23.1 + - - +
293B PRO* 3.3 12.4 - - + +
296B THR* 4.0 27.8 - - + -
297B ALA* 4.1 24.9 - - + +
300B LEU* 4.2 9.0 - - + -
325B CYS* 4.4 19.3 - - - -
328B PHE* 4.2 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TYR* 3.8 16.3 - - - -
283B PRO 2.3 27.7 + - - -
284B ALA 4.0 1.6 + - - -
286B LEU* 1.3 78.7 - - - +
288B LEU* 1.3 63.1 + - - +
290B SER 4.5 4.8 - - - +
293B PRO* 4.5 3.6 - - - -
328B PHE* 4.0 20.0 - - - -
863B ILE* 3.4 39.8 - - - +
866B TYR* 4.3 11.4 - - - -
867B VAL* 4.4 5.1 - - - +
88C PHE* 4.3 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TYR* 3.6 36.8 - - + +
235B VAL* 3.8 10.5 - - + -
236B HIS* 4.2 18.8 - - + +
239B LEU* 3.8 15.2 - - + +
284B ALA 3.3 20.8 + - - +
285B TYR 3.6 1.4 + - - -
286B LEU 3.4 0.2 - - - -
287B SER* 1.3 83.3 + - - +
289B SER* 1.3 62.3 + - - +
290B SER 3.5 2.4 + - - -
863B ILE* 5.3 0.2 - - + -
867B VAL* 4.3 14.4 - - + -
87C MET* 3.6 6.9 - - - +
88C PHE* 3.4 55.6 + - + +
131C TYR* 6.3 0.2 - - + -
132C MET* 5.2 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LEU* 4.1 11.9 - - - -
244B ARG* 3.5 10.4 + - - +
285B TYR* 2.7 61.4 + - - -
286B LEU* 4.4 2.1 - - - +
288B LEU* 1.3 78.2 - - - +
290B SER* 1.3 66.4 + - - +
86C TYR* 3.1 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 3.2 19.1 + - - -
287B SER 4.5 8.7 - - - +
288B LEU 4.7 0.7 - - - -
289B SER* 1.3 84.3 + - - +
291B GLU* 1.3 63.2 - - - +
292B ASP 4.5 1.1 - - - -
293B PRO* 3.6 20.8 - - - +
296B THR* 4.0 24.7 + - - +
863B ILE* 4.9 2.9 - - - +
86C TYR* 3.3 18.1 - - - -
88C PHE* 6.0 0.2 - - - +
----------------------------------------------------------
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