Contacts of the helix formed by residues 185 - 199 (chain A) in PDB entry 1DGD
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 TYR 185 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A PRO* 4.1 9.2 - - + -
172A THR* 4.8 4.5 - - + -
183A TYR* 3.7 44.3 - + + +
184A ASP* 1.3 71.7 + - - +
186A LEU* 1.3 92.1 + - + +
188A GLU* 3.5 8.7 + - - +
189A LEU* 3.2 18.7 + - - +
222A PRO* 3.5 33.0 - - + +
223A ASP* 2.5 42.0 + - - -
225A TYR* 4.0 14.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ASP* 3.2 7.2 + - - +
185A TYR* 1.3 102.3 - - + +
187A ALA* 1.3 67.1 + - - +
189A LEU* 3.0 9.9 - - + +
190A ASP* 3.0 26.0 + - - +
223A ASP 5.4 1.3 - - - +
224A GLY* 3.8 26.0 - - - +
225A TYR* 4.1 7.2 - - + -
228A ALA* 3.8 20.0 - - + -
231A ARG* 6.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PHE* 3.8 14.5 - - + -
179A ARG* 3.9 23.7 - - + +
184A ASP* 2.9 36.7 + - + +
186A LEU* 1.3 77.3 - - - +
188A GLU* 1.3 56.6 + - - +
190A ASP* 3.2 13.1 + - - +
191A TYR* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PRO* 4.4 29.8 - - + +
169A ALA 5.3 2.1 - - - +
170A PRO* 4.3 7.6 - - - +
176A ARG* 4.7 12.0 + - - +
177A PHE* 3.6 43.2 + - + +
183A TYR* 2.7 29.7 + - - -
184A ASP 3.1 13.2 + - - +
185A TYR* 3.6 9.6 - - - +
186A LEU 3.1 0.2 - - - -
187A ALA* 1.3 75.7 - - - +
189A LEU* 1.3 53.4 - - - +
191A TYR* 3.0 4.9 + - + +
192A ALA* 2.8 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 4.3 8.3 - - + -
185A TYR 3.2 9.6 + - - +
186A LEU* 3.0 13.0 + - + +
188A GLU* 1.3 78.2 - - - +
190A ASP* 1.3 63.4 + - - +
192A ALA* 3.4 3.5 + - - +
193A PHE* 3.0 50.1 + - + +
225A TYR* 3.8 32.5 - - + +
228A ALA* 3.6 33.4 - - + -
229A LEU* 3.9 16.6 - - + +
232A LYS* 4.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 5.3 7.3 + - - -
186A LEU* 3.0 15.8 + - - +
187A ALA* 3.2 13.1 + - - +
189A LEU* 1.3 77.1 - - - +
191A TYR* 1.3 62.0 + - - +
193A PHE* 4.0 1.2 - - - +
194A ASP* 3.2 24.3 + - - +
232A LYS* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PHE* 3.5 35.7 - + + -
187A ALA 2.9 12.5 + - - +
188A GLU* 3.3 9.2 - - + +
190A ASP* 1.3 78.2 - - - +
192A ALA* 1.3 65.6 + - + +
194A ASP* 3.4 14.6 + - + +
195A LEU* 3.4 20.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 3.9 33.0 - - + +
168A PRO* 4.1 14.1 - - + +
188A GLU* 2.8 18.7 + - + +
189A LEU* 3.7 7.9 - - - +
191A TYR* 1.3 77.5 - - + +
193A PHE* 1.3 61.6 + - - +
195A LEU* 3.2 10.8 + - - +
196A ILE* 3.2 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL* 5.1 3.6 - - + -
167A ILE* 4.7 6.7 - - + -
189A LEU* 3.0 40.7 + - + +
190A ASP 4.2 2.7 - - - +
192A ALA* 1.3 72.0 - - - +
194A ASP* 1.3 60.7 + - - +
196A ILE* 3.1 21.1 + - + +
197A ASP* 2.8 34.9 + - - +
207A PHE* 4.0 26.9 - + - -
229A LEU* 4.1 11.4 - - + -
232A LYS* 3.9 33.2 - - + +
233A CYS* 5.2 1.6 - - - -
236A ARG* 3.6 47.1 - - - +
238A MET* 4.2 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ASP 3.2 17.7 + - - +
191A TYR* 3.7 8.2 - - + +
192A ALA 3.3 0.4 - - - -
193A PHE* 1.3 76.0 - - - +
195A LEU* 1.3 65.4 + - - +
197A ASP* 3.3 10.0 + - - +
198A ARG* 3.1 61.7 + - - +
236A ARG* 5.1 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A TYR* 3.4 17.7 + - + +
192A ALA* 3.2 11.8 + - - +
193A PHE 3.1 0.2 - - - -
194A ASP* 1.3 81.0 + - - +
196A ILE* 1.3 67.0 + - + +
198A ARG* 2.8 21.7 + - + -
199A GLN* 3.1 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL* 4.3 9.6 - - + -
165A PHE* 3.5 36.2 - - + -
166A ALA 4.6 4.7 - - - +
167A ILE* 4.0 24.9 - - + -
192A ALA 3.4 13.5 - - - +
193A PHE* 3.3 20.6 - - + +
195A LEU* 1.3 76.3 - - + +
197A ASP* 1.3 57.4 + - - +
199A GLN* 2.9 12.1 + - - +
200A SER* 2.8 31.4 + - - -
204A LEU* 3.9 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A PHE* 2.8 14.9 + - - +
194A ASP* 3.5 10.3 - - - +
196A ILE* 1.3 78.9 - - - +
198A ARG* 1.3 62.0 + - + +
200A SER* 3.8 15.3 + - - +
204A LEU* 3.9 9.4 - - - +
236A ARG* 2.5 53.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ASP* 3.1 47.0 + - - +
195A LEU* 2.8 16.1 + - + +
197A ASP* 1.3 81.5 - - + +
199A GLN* 1.3 63.5 + - + +
200A SER 4.2 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 4.6 0.2 - - - +
165A PHE* 4.0 28.5 - - + -
195A LEU* 3.2 45.5 + - + +
196A ILE* 2.9 15.9 + - - +
198A ARG* 1.3 78.1 - - + +
200A SER* 1.3 70.5 + - - +
201A SER* 3.6 1.7 + - - -
----------------------------------------------------------
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