Contacts of the helix formed by residues 182 - 203 (chain A) in PDB entry 2X9D
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 GLY 182 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 3.5 6.3 - - - -
144A ALA* 5.7 1.7 - - - +
148A GLN* 5.1 6.7 - - - -
177A MET 4.7 4.3 + - - -
180A ASP* 3.0 14.7 + - - -
181A ASP* 1.3 74.8 - - - +
183A GLU* 1.3 57.9 + - - +
184A GLN 3.5 1.1 - - - -
185A ALA* 3.6 9.0 + - - +
186A PHE* 3.0 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A MET* 5.6 3.5 - - - +
87A ARG* 3.2 34.5 + - - +
180A ASP* 2.7 7.7 + - - +
181A ASP* 3.3 16.1 - - - +
182A GLY* 1.3 74.9 - - - +
184A GLN* 1.3 67.4 + - + +
186A PHE* 3.2 2.0 + - - +
187A LEU* 2.9 54.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ILE* 5.0 10.2 + - - +
179A SER* 4.2 14.1 + - - -
180A ASP* 2.8 40.0 + - + +
183A GLU* 1.3 72.9 - - + +
185A ALA* 1.3 62.5 + - - +
187A LEU* 3.9 4.2 - - - +
188A HIS* 3.0 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PHE* 4.4 3.0 - - - -
177A MET* 3.7 30.3 - - + -
180A ASP* 5.2 1.3 + - - +
182A GLY* 3.6 11.9 + - - +
183A GLU 3.4 0.2 - - - -
184A GLN* 1.3 78.5 - - - +
186A PHE* 1.3 62.4 + - - +
188A HIS* 3.8 5.0 + - - +
189A GLY* 3.2 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA* 3.9 22.9 - - + -
84A MET* 4.5 5.2 - - - -
87A ARG* 3.2 39.5 - - + +
140A PHE* 3.1 49.5 - + - -
141A THR* 3.5 33.0 - - + -
144A ALA* 4.1 20.9 - - + -
182A GLY 3.0 21.1 + - - +
183A GLU 3.6 1.6 - - - +
185A ALA* 1.3 78.9 - - - +
187A LEU* 1.3 81.7 + - + +
190A LEU* 2.9 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A MET* 3.8 34.8 - - + -
183A GLU* 2.9 47.6 + - - +
184A GLN* 4.0 3.6 - - - +
186A PHE* 1.3 91.7 - - + +
188A HIS* 1.3 64.9 + - - +
190A LEU* 3.4 2.4 + - + -
191A GLU* 3.2 11.7 + - - +
1213A CL 2.7 38.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A GLN 3.0 17.3 + - - +
185A ALA* 3.9 5.6 - - - +
187A LEU* 1.3 75.5 - - - +
189A GLY* 1.3 63.0 + - - +
191A GLU* 3.2 10.1 + - - +
192A SER* 3.2 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PHE* 3.8 17.6 - - - -
185A ALA 3.2 13.4 + - - -
186A PHE 3.8 1.1 - - - -
188A HIS* 1.3 77.4 - - - +
190A LEU* 1.3 63.2 + - - +
192A SER* 3.5 11.8 + - - -
193A LEU* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU 4.7 2.0 - - - +
80A ARG* 4.0 15.0 - - + +
83A ALA* 3.7 34.8 - - + -
84A MET* 4.4 1.6 - - + -
137A VAL* 4.8 12.3 - - + -
140A PHE* 3.6 14.5 - - + -
186A PHE* 2.9 24.8 + - + +
187A LEU* 3.4 21.3 - - + +
188A HIS 3.3 0.4 - - - -
189A GLY* 1.3 75.1 - - - +
191A GLU* 1.3 58.4 + - - +
193A LEU* 3.2 7.7 + - + +
194A ILE* 3.0 46.8 + - + +
1213A CL 3.7 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 2.9 38.3 + - - -
187A LEU 3.2 4.2 + - - +
188A HIS* 3.2 10.6 + - - +
190A LEU* 1.3 75.3 - - - +
192A SER* 1.3 64.3 + - - +
194A ILE* 4.1 11.2 - - - +
195A ARG* 3.2 25.5 + - - +
1213A CL 2.8 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A HIS* 3.2 21.4 + - - -
189A GLY* 3.7 13.6 - - - -
190A LEU 3.4 0.2 - - - -
191A GLU* 1.3 76.2 - - - +
193A LEU* 1.3 56.6 + - - +
195A ARG* 4.0 3.0 - - - +
196A GLY* 3.0 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA* 3.8 28.9 - - + +
137A VAL* 3.9 15.3 - - + -
140A PHE* 3.8 28.7 - - + -
189A GLY 3.2 9.2 + - - +
190A LEU* 3.4 11.9 - - + +
192A SER* 1.3 78.5 - - - +
194A ILE* 1.3 56.9 + - + +
196A GLY* 3.2 2.8 + - - -
197A PHE* 2.9 68.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TRP* 3.6 4.6 - - + -
76A GLN* 3.8 49.8 - - + +
79A LEU* 4.4 15.7 - - + -
80A ARG* 4.0 20.4 - - + +
137A VAL* 5.3 1.1 - - + -
190A LEU* 3.0 41.4 + - + +
191A GLU* 3.6 15.9 + - - +
193A LEU* 1.3 76.5 - - + +
195A ARG* 1.3 58.4 + - - +
197A PHE* 3.3 13.2 + - + +
198A GLU* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLU 3.2 16.6 + - - +
192A SER* 4.0 3.6 - - - +
194A ILE* 1.3 76.2 - - - +
196A GLY* 1.3 58.7 + - - +
198A GLU* 3.1 25.7 + - - +
199A VAL* 2.8 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A SER 3.0 16.7 + - - -
193A LEU 3.6 4.5 - - - -
195A ARG* 1.3 77.0 - - - +
197A PHE* 1.3 61.9 + - - +
199A VAL* 3.3 8.2 + - - +
200A GLN* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TRP* 3.9 11.7 - - + -
79A LEU* 3.8 15.0 - - + -
125A PHE* 4.5 7.1 - - + -
132A TYR 5.2 0.4 - - - -
133A ALA* 3.1 56.5 - - + -
136A ALA* 3.4 9.6 - - + -
137A VAL* 3.8 15.0 - - + -
193A LEU* 2.9 51.2 + - + -
194A ILE* 3.4 12.3 - - - +
196A GLY* 1.3 75.9 - - - +
198A GLU* 1.3 57.7 + - - +
200A GLN* 3.2 8.9 + - - +
201A LEU* 2.8 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TRP* 3.7 16.6 - - + -
76A GLN* 3.0 32.5 + - - +
194A ILE* 2.9 14.7 + - - +
195A ARG* 3.1 30.2 + - - +
197A PHE* 1.3 75.8 - - - +
199A VAL* 1.3 52.2 + - + +
201A LEU* 4.2 2.7 - - + -
202A THR* 2.6 57.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ARG* 2.8 41.3 + - + +
196A GLY* 3.6 7.6 - - - +
198A GLU* 1.3 74.0 - - + +
200A GLN* 1.3 63.0 + - - +
202A THR* 3.1 15.8 + - - +
203A ALA* 3.5 12.6 + - - +
208A VAL* 3.8 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PHE* 6.3 1.8 - - + -
129A ASP* 4.9 19.8 - - + +
196A GLY 3.1 13.1 + - - +
197A PHE* 3.3 11.4 - - - +
199A VAL* 1.3 78.2 - - - +
201A LEU* 1.3 68.3 + - - +
203A ALA* 3.5 10.7 + - - +
204A LEU 4.1 7.6 + - - +
208A VAL* 4.3 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TRP* 3.5 32.3 - - + +
123A ASN 3.6 12.6 - - - +
124A GLY* 3.0 38.4 - - - +
125A PHE* 3.7 25.6 - - + +
197A PHE 2.8 20.3 + - - +
198A GLU* 3.3 6.0 + - + +
200A GLN* 1.3 76.1 - - - +
202A THR* 1.3 70.3 + - + +
203A ALA 3.2 0.5 + - - -
204A LEU* 3.3 21.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLU* 2.6 47.7 + - + +
199A VAL* 3.1 16.1 + - - +
201A LEU* 1.3 79.8 - - + +
203A ALA* 1.3 60.3 + - - +
204A LEU* 3.3 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A VAL 3.5 14.2 + - - +
200A GLN 4.0 5.4 - - - +
201A LEU 3.2 1.6 + - - -
202A THR* 1.3 78.7 + - - +
204A LEU* 1.3 70.7 + - - +
205A LEU 3.0 0.5 + - - -
206A GLN* 2.9 36.8 + - + +
208A VAL* 3.8 31.4 - - + -
----------------------------------------------------------
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