Contacts of the helix formed by residues 229 - 238 (chain 9) in PDB entry 2J28
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 ALA 229 (chain 9).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089 LEU* 6.3 0.4 - - - -
2219 VAL* 4.2 28.0 - - + -
2259 THR* 3.2 18.5 - - + +
2269 GLY* 2.5 20.6 + - - +
2289 ASP* 1.3 71.8 - - - +
2309 ALA* 1.3 71.6 + - - +
2329 THR* 2.6 32.0 + - - -
2339 ALA* 4.5 3.8 - - + +
2479 LEU* 5.9 0.4 - - + -
2599 ALA* 5.4 4.7 - - - +
2639 ARG* 5.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 230 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2279 GLN 2.9 7.4 - - - +
2289 ASP 2.7 4.1 + - - +
2299 ALA* 1.3 85.3 - - - +
2319 ASN* 1.3 64.0 + - + +
2339 ALA* 2.9 9.4 + - - +
2349 LYS* 2.9 22.3 + - + -
2629 ILE* 1.7 49.3 - - + +
2639 ARG* 4.6 3.1 - - - +
2669 THR* 5.0 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 231 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1989 ASP* 5.2 5.7 + - - +
2289 ASP 4.2 7.0 - - - +
2299 ALA 2.8 1.7 + - - +
2309 ALA* 1.3 75.4 - - + +
2329 THR* 1.3 83.3 + - - +
2349 LYS* 2.6 32.1 + - - +
2359 ALA* 2.7 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 232 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089 LEU* 3.2 49.0 - - + +
1989 ASP* 3.3 24.5 + - + +
2019 MET* 5.0 6.3 - - + +
2199 PHE* 5.9 1.3 - - + -
2259 THR* 5.6 1.2 - - - +
2299 ALA* 2.6 24.8 + - - -
2319 ASN* 1.3 86.4 + - - +
2339 ALA* 1.3 55.6 + - + +
2359 ALA* 2.5 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2199 PHE* 5.0 5.2 - - + -
2299 ALA* 4.6 4.0 - - + +
2309 ALA* 2.9 11.9 + - - +
2329 THR* 1.3 79.0 - - + +
2349 LYS* 1.3 70.8 + - - +
2359 ALA 2.6 11.5 - - - +
2369 PHE* 2.9 17.1 - - - +
2379 ASN* 3.4 3.5 + - - -
2639 ARG* 5.7 5.2 - - + +
2669 THR* 6.4 0.2 - - + -
2689 LYS* 2.8 42.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 234 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2309 ALA* 2.9 8.6 + - + +
2319 ASN* 2.6 38.3 + - - +
2339 ALA* 1.3 68.9 - - - +
2359 ALA* 1.3 49.4 + - + +
2369 PHE 2.5 19.6 + - - -
2379 ASN* 2.5 35.5 + - + +
2389 GLU* 3.6 16.9 + - + +
2669 THR* 4.3 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 235 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1989 ASP* 6.5 1.1 - - + -
1999 GLU* 5.7 9.6 - - + -
2019 MET* 5.8 1.9 - - - +
2029 MET* 4.6 13.0 - - + +
2319 ASN* 2.7 21.8 + - - +
2329 THR* 2.5 23.7 - - - +
2349 LYS* 1.3 71.2 - - - +
2369 PHE* 1.3 68.0 + - - +
2389 GLU* 5.0 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 236 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2019 MET* 6.0 0.2 - - + -
2029 MET* 4.2 5.0 - - + -
2179 THR* 4.7 6.3 - - + -
2199 PHE* 2.5 65.3 - + + -
2339 ALA 2.9 11.7 - - - +
2349 LYS 2.5 3.2 + - - -
2359 ALA* 1.3 83.4 - - - +
2379 ASN* 1.3 56.5 + - - -
2389 GLU* 2.4 10.5 - - - +
2399 ALA* 2.4 41.8 + - + +
2409 LEU* 2.4 25.4 + - + -
2439 THR* 1.6 58.6 - - + -
2459 VAL* 4.2 3.6 - - + -
2689 LYS* 4.0 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 237 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2339 ALA 3.9 1.3 - - - +
2349 LYS* 2.5 27.4 + - + +
2369 PHE* 1.3 75.6 - - - +
2389 GLU* 1.3 58.3 + - + +
2419 PRO* 3.0 36.1 - - + +
2439 THR* 3.4 19.4 + - - +
2669 THR* 3.3 40.9 + - - +
2679 GLY 5.4 0.7 - - - -
2689 LYS* 3.6 33.0 + - - +
2699 PRO* 3.9 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 238 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2349 LYS* 4.5 20.0 - - + +
2359 ALA* 5.0 7.2 - - - +
2369 PHE 2.4 5.6 - - - +
2379 ASN* 1.3 81.5 - - + +
2399 ALA* 1.3 70.1 - - - +
2409 LEU* 3.2 1.5 + - - -
2419 PRO* 4.2 6.7 - - - +
----------------------------------------------------------
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