Contacts of the helix formed by residues 210 - 220 (chain D) in PDB entry 4LQL
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 PRO 210 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ARG* 5.0 0.6 - - - -
280B GLN 4.7 4.7 - - - +
281B ASP* 3.6 40.4 - - + +
283B GLU* 4.9 3.8 - - + -
181D PHE* 4.5 0.9 - - - -
182D GLY 5.4 1.1 - - - +
208D TYR* 5.4 1.3 - - + -
209D TYR* 1.3 76.2 - - - +
211D THR* 1.3 67.7 + - - +
212D ASN 3.2 2.0 - - - +
213D GLU* 3.0 38.7 + - + +
214D LEU* 3.7 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D PHE* 4.0 22.5 + - - +
182D GLY* 5.0 0.4 - - - +
209D TYR 3.6 2.9 + - - -
210D PRO* 1.3 72.4 - - - +
212D ASN* 1.3 61.8 + - - +
214D LEU* 3.2 14.3 + - - +
215D VAL* 3.2 19.9 + - - +
281D ASP* 3.4 46.0 + - - -
282D LEU* 4.4 5.0 - - - -
283D GLU* 4.6 8.2 + - - -
285D LEU* 5.0 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B GLU* 3.4 36.3 - - + -
210D PRO* 3.2 1.0 - - - +
211D THR* 1.3 73.3 - - - +
213D GLU* 1.3 56.8 + - - +
214D LEU 2.8 11.3 + - - -
215D VAL* 3.1 23.5 + - + +
216D ALA* 3.7 7.3 + - - +
283D GLU 4.6 8.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ARG* 5.6 4.3 - - - +
280B GLN 5.2 7.2 - - - +
283B GLU* 4.9 1.6 - - - +
209D TYR* 4.8 2.9 - - + -
210D PRO* 3.0 36.4 + - + +
212D ASN* 1.3 76.3 - - - +
214D LEU* 1.3 57.0 + - - +
216D ALA* 4.2 7.9 - - - +
217D VAL* 3.5 17.7 - - - +
266D PHE* 3.7 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D PHE* 3.6 50.9 - - + -
210D PRO 3.7 5.1 + - - +
211D THR* 3.2 12.1 + - - +
212D ASN 2.9 0.8 - - - -
213D GLU* 1.3 77.3 - - - +
215D VAL* 1.3 68.4 + - - +
216D ALA 3.2 2.0 - - - -
217D VAL* 3.1 6.0 + - + +
218D VAL* 3.0 36.3 + - + +
262D GLY 4.3 2.5 - - - +
263D ILE* 4.3 20.4 - - + -
266D PHE* 4.0 21.3 - - + -
285D LEU* 3.9 24.2 - - + -
289D PRO* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D THR* 3.2 17.9 - - - +
212D ASN* 3.1 14.1 + - - +
214D LEU* 1.3 78.0 - - + +
216D ALA* 1.3 63.1 + - - +
218D VAL* 3.4 8.2 + - + +
219D ASN* 3.1 44.0 + - - +
282D LEU 6.0 0.2 - - - -
283D GLU 4.0 3.8 - - - +
284D GLY* 3.0 47.6 - - - +
285D LEU* 4.7 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D ASN 3.7 5.8 + - - +
213D GLU* 4.2 11.2 - - - +
215D VAL* 1.3 79.8 - - - +
217D VAL* 1.3 60.8 + - + +
219D ASN* 4.1 2.2 - - - +
220D GLY* 3.0 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 217 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D GLU 3.5 20.2 - - - +
214D LEU 3.1 5.1 + - - +
216D ALA* 1.3 78.3 - - + +
218D VAL* 1.3 61.8 + - - +
220D GLY 3.5 7.4 - - - +
221D ILE* 3.3 22.5 - - + +
262D GLY* 3.8 19.9 - - - +
265D LYS* 4.2 10.8 - - + -
266D PHE* 3.6 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D LEU* 3.0 40.9 + - + +
215D VAL* 3.7 7.2 - - - +
216D ALA 3.3 0.2 - - - -
217D VAL* 1.3 74.0 - - - +
219D ASN* 1.3 68.6 + - - +
221D ILE* 3.5 9.7 - - - +
258D ARG* 3.2 52.6 + - + +
259D GLU* 4.1 10.3 - - + +
262D GLY* 4.0 18.4 - - - -
263D ILE 4.8 1.1 - - - +
285D LEU* 4.3 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D VAL* 3.1 33.3 + - - +
216D ALA* 4.1 2.4 - - - +
218D VAL* 1.3 78.0 - - - +
220D GLY* 1.3 52.4 + - - +
221D ILE 2.4 18.6 + - - +
258D ARG* 2.4 45.1 + - - +
284D GLY 4.8 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D ALA 3.0 16.1 + - - -
217D VAL* 3.5 6.3 - - - +
218D VAL 3.5 0.2 - - - -
219D ASN* 1.3 73.9 - - - +
221D ILE* 1.3 70.5 + - - +
----------------------------------------------------------
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