Contacts of the helix formed by residues 226 - 238 (chain A) in PDB entry 3LDH
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 LYS 226 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 5.9 0.7 - - - -
221A GLU* 6.1 0.2 - - - -
223A ILE 3.5 10.3 + - - +
224A LYS 3.2 7.6 + - - +
225A LEU* 1.3 82.9 - - - +
227A GLY* 1.3 62.6 + - - +
228A TYR* 2.5 21.1 - - + +
229A THR* 2.5 37.6 + - - +
230A SER* 3.5 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 5.8 4.5 - - - -
203A TRP* 3.4 19.6 - - - -
220A TYR* 6.3 1.6 - - - -
221A GLU* 5.0 4.7 - - - +
224A LYS* 4.9 7.9 - - - +
225A LEU 3.6 3.2 - - - +
226A LYS* 1.3 74.7 - - - +
228A TYR* 1.3 65.5 + - - +
230A SER* 3.0 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TRP* 3.9 14.1 - + - -
221A GLU* 2.8 48.6 - - + +
222A VAL* 5.1 3.4 - - + +
223A ILE 6.0 0.4 - - - +
226A LYS* 4.1 17.3 - - + -
227A GLY* 1.3 80.6 - - - +
229A THR* 1.3 65.8 - - - +
231A TRP* 3.2 16.0 + + - +
232A ALA* 3.4 15.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LYS* 2.5 47.5 + - - +
228A TYR* 1.3 70.6 - - - +
230A SER* 1.3 71.5 + - - +
231A TRP 2.9 1.0 + - - -
232A ALA* 3.0 15.1 + - + +
233A ILE* 3.0 27.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PHE* 4.0 21.7 + - - -
175A LEU* 4.8 19.9 - - - +
176A MET* 5.6 6.6 + - - +
203A TRP* 5.4 0.4 - - - -
226A LYS 3.5 2.4 + - - -
227A GLY* 3.0 18.7 + - - -
229A THR* 1.3 82.7 - - - +
231A TRP* 1.3 63.2 + - - +
233A ILE* 3.6 11.6 - - - +
234A GLY* 3.8 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP* 4.1 12.6 - - + -
172A PHE* 3.7 19.8 - + + -
191A VAL* 2.7 29.2 - - + -
198A SER* 4.0 3.8 + - - +
199A VAL* 2.0 92.6 + - + +
200A PRO* 4.4 1.4 - - - +
201A SER* 3.8 21.1 + - - +
203A TRP* 4.2 10.8 - + + -
227A GLY 3.6 0.4 + - - -
228A TYR* 3.2 12.2 + + - +
229A THR 2.9 2.6 + - - -
230A SER* 1.3 76.9 - - - +
232A ALA* 1.3 56.1 - - + +
234A GLY* 2.4 24.2 + - - -
235A LEU* 2.0 48.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A TYR* 3.4 15.2 + - + +
229A THR* 3.0 15.1 + - + +
231A TRP* 1.3 78.6 - - + +
233A ILE* 1.3 52.1 + - + +
235A LEU* 2.8 19.4 + - - +
236A VAL* 2.3 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 4.9 11.4 - - + +
229A THR* 3.0 34.1 - - + +
230A SER* 3.6 7.4 - - - +
231A TRP 3.0 1.0 + - - -
232A ALA* 1.3 72.9 - - + +
234A GLY* 1.3 52.3 + - - +
236A VAL* 3.0 34.8 - - + -
237A VAL* 2.6 36.3 + - + +
240A PRO* 4.9 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP* 4.8 5.5 - - - +
171A ARG* 3.8 15.1 + - - -
172A PHE* 6.0 4.7 - - - -
175A LEU* 5.3 5.2 - - - -
230A SER 4.3 3.8 - - - -
231A TRP* 2.4 26.5 + - - -
233A ILE* 1.3 74.2 - - - +
235A LEU* 1.3 67.4 + - - +
237A VAL* 2.9 25.3 - - - +
238A SER 4.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG* 5.3 2.3 + - - -
168A ASP* 5.7 0.2 - - - -
196A GLY* 5.0 1.0 - - - -
197A ASP* 3.1 33.0 + - + +
198A SER 3.0 18.6 - - - +
199A VAL* 2.6 40.8 - - + -
231A TRP* 2.0 67.5 - - + +
232A ALA* 2.8 15.9 - - - +
234A GLY 1.3 82.0 - - - +
236A VAL* 1.3 60.8 + - + +
237A VAL 3.2 0.7 + - - -
238A SER* 3.5 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ASP* 5.3 1.8 - - + +
232A ALA* 2.3 33.1 + - + +
233A ILE* 3.0 35.0 - - + -
235A LEU* 1.3 67.7 - - + +
237A VAL* 1.3 68.0 + - - +
238A SER 2.6 2.3 + - - -
239A ASN* 2.6 24.9 + - + +
240A PRO* 3.0 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ARG* 2.8 64.4 - - + +
175A LEU* 5.0 5.6 - - + -
233A ILE* 2.6 36.9 + - + +
234A GLY* 2.9 19.3 - - - +
235A LEU 3.1 0.2 - - - -
236A VAL* 1.3 78.0 - - - +
238A SER* 1.3 71.2 + - - +
240A PRO* 3.3 12.5 - - - +
241A VAL* 3.7 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLN* 5.8 3.4 - - - -
109A ARG* 2.3 44.0 + - - -
171A ARG* 4.9 2.2 + - - +
234A GLY 4.3 0.2 + - - -
235A LEU 3.5 11.7 + - - -
236A VAL 2.6 3.2 + - - -
237A VAL* 1.3 86.7 - - - +
239A ASN* 1.3 66.1 + - - -
240A PRO 3.4 0.2 - - - -
241A VAL* 3.6 12.2 - - - +
242A ASP* 3.4 16.6 + - - +
333A PYR 4.2 9.1 + - - -
----------------------------------------------------------
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