Contacts of the helix formed by residues 252 - 261 (chain D) in PDB entry 3L49
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 252 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D HIS* 6.2 0.4 - - - -
44D ASP* 4.3 18.2 - - - -
45D TRP* 5.9 0.7 - - - -
226D ASP* 2.9 30.3 + - - -
227D VAL* 4.7 7.3 - - - +
230D ILE* 4.0 11.0 - - - +
250D ASP* 3.6 5.5 - - - +
251D GLY* 1.3 76.3 - - - +
253D PRO* 1.4 76.8 - - - +
254D GLU* 3.2 1.6 - - - -
255D PHE* 3.0 23.4 + - - +
256D VAL 3.1 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ASP* 3.8 25.4 - - + +
48D LYS* 5.3 6.1 - - - +
251D GLY 3.5 5.8 - - - +
252D SER* 1.4 85.1 - - - +
254D GLU* 1.3 62.0 + - - +
256D VAL* 3.5 6.4 + - + +
257D GLU* 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D ILE* 4.6 6.9 - - - +
230D ILE* 3.6 43.3 - - + +
234D GLN* 3.8 9.9 - - - +
252D SER* 3.2 1.7 - - - +
253D PRO* 1.3 80.7 - - - +
255D PHE* 1.3 60.9 + - - +
257D GLU* 3.4 12.0 + - - +
258D MET* 3.2 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D ASP* 3.7 32.1 - - + +
229D MET* 3.6 17.7 - - + -
230D ILE* 3.9 17.7 - - + -
233D THR* 3.5 22.2 - - - -
246D THR* 3.6 24.2 - - - -
247D TYR 4.6 0.2 - - - -
248D GLY 4.2 7.0 - - - -
252D SER* 3.0 9.0 + - - +
254D GLU* 1.3 77.6 - - - +
256D VAL* 1.3 60.2 + - - +
258D MET* 3.3 18.7 + - - +
259D VAL* 3.0 35.3 + - + +
266D ALA* 3.7 12.6 - - + -
268D ALA 3.7 20.0 - - - -
269D VAL* 3.7 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D GLY* 3.4 38.1 - - - +
252D SER 3.1 5.0 + - - +
253D PRO* 3.8 9.9 - - + +
255D PHE* 1.3 72.1 - - - +
257D GLU* 1.3 60.3 + - - +
259D VAL* 3.8 2.0 - - - +
260D ALA* 3.0 30.6 + - + +
269D VAL* 3.9 20.2 - - + -
271D ALA* 5.3 3.6 - - + -
305D ILE* 5.1 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D PRO* 3.1 15.9 + - - +
254D GLU* 3.4 15.4 - - - +
256D VAL* 1.3 77.8 - - - +
258D MET* 1.3 56.3 + - + +
260D ALA* 3.6 5.3 + - - +
261D ASP* 3.0 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D ILE* 3.9 35.4 - - + +
233D THR* 4.0 18.6 - - + -
234D GLN* 4.1 17.5 - - + +
237D GLN* 5.5 4.0 - - - +
254D GLU* 3.2 21.7 + - + +
255D PHE* 3.4 28.5 - - - +
256D VAL 3.2 0.4 - - - -
257D GLU* 1.3 75.9 - - + +
259D VAL* 1.3 65.5 + - - +
261D ASP* 3.1 14.2 + - - +
264D SER* 2.4 32.9 + - - +
266D ALA* 3.6 12.1 - - + -
307D LYS* 3.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D PHE* 3.0 45.2 + - + +
256D VAL* 3.8 7.2 - - - +
258D MET* 1.3 74.1 - - - +
260D ALA* 1.3 59.8 + - - +
266D ALA* 3.8 14.6 - - + -
267D GLY 4.1 5.8 - - - +
268D ALA 3.9 15.7 - - - +
269D VAL* 4.1 5.6 - - + +
305D ILE* 3.6 29.6 - - + +
306D THR 3.7 19.1 - - - +
307D LYS* 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D VAL* 3.0 19.6 + - + +
257D GLU* 3.9 5.8 - - - +
259D VAL* 1.3 77.9 - - - +
261D ASP* 1.3 61.9 + - - +
262D PRO* 3.4 9.7 - - - +
305D ILE* 5.8 4.2 - - + +
306D THR 5.4 1.3 - - - -
307D LYS* 4.7 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D GLN* 4.7 2.3 - - - +
257D GLU* 3.0 19.3 + - + +
258D MET* 3.1 9.4 + - - +
260D ALA* 1.3 73.4 - - - +
262D PRO* 1.3 66.9 - - - +
263D GLU* 3.1 21.9 + - - +
264D SER* 3.3 21.7 + - - +
307D LYS* 2.6 27.5 + - - -
----------------------------------------------------------
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