Contacts of the helix formed by residues 185 - 201 (chain A) in PDB entry 4XWX
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 185 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A PRO 3.3 0.6 + - - -
184A GLU* 1.3 79.7 - - - +
186A LEU* 1.4 64.0 + - - +
187A ALA* 3.4 3.2 + - - +
188A GLN* 4.1 9.8 + - - +
189A ASP* 4.4 6.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
52A TYR* 4.3 24.0 - - + -
53A LEU* 4.4 8.1 - - + +
54A VAL* 5.3 0.4 - - + -
182A CYS* 4.3 6.7 - - + -
183A PRO* 3.0 39.0 + - + +
184A GLU 4.3 5.4 - - - +
185A GLY* 1.4 76.1 - - - +
187A ALA* 1.3 65.7 + - - +
188A GLN 3.3 1.3 - - - -
189A ASP* 3.1 21.3 + - + +
190A VAL* 2.8 29.8 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
161A ALA 3.4 25.6 - - - +
162A GLU* 3.8 22.2 - - - +
163A TYR 4.2 3.6 - - - +
164A VAL* 3.7 9.1 - - + +
182A CYS* 3.9 15.5 - - - +
183A PRO 4.2 1.0 + - - +
185A GLY 3.4 1.8 - - - +
186A LEU* 1.3 77.3 - - - +
188A GLN* 1.3 62.8 + - + +
190A VAL* 3.2 3.8 + - - +
191A ILE* 3.0 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 5.1 1.1 - - - -
155A GLY* 4.8 5.4 - - - -
161A ALA* 4.7 9.1 - - - +
185A GLY 4.1 6.7 + - - +
186A LEU 3.3 0.2 - - - -
187A ALA* 1.3 77.9 - - + +
189A ASP* 1.3 59.7 + - - +
191A ILE* 3.8 27.5 - - - +
192A SER* 2.9 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.0 20.9 - - + +
40A HIS* 2.9 27.0 + - - -
52A TYR* 2.6 37.1 + - + -
185A GLY 4.4 3.6 + - - +
186A LEU* 3.1 26.1 + - + +
188A GLN* 1.3 78.1 - - - +
190A VAL* 1.3 62.0 + - - +
192A SER* 3.6 0.9 - - - -
193A THR* 2.8 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR* 3.7 40.6 - - + -
54A VAL* 4.8 0.9 - - + -
124A LEU* 3.8 24.0 - - + -
126A VAL* 5.0 0.8 - - + +
164A VAL* 4.1 17.7 - - + -
180A LEU* 4.6 2.2 - - + -
182A CYS* 4.4 11.4 - - - -
186A LEU* 2.8 24.1 + - + +
187A ALA 3.5 7.4 - - - +
189A ASP* 1.3 71.7 - - - +
191A ILE* 1.3 57.7 + - - +
193A THR* 3.2 1.4 + - - -
194A ILE* 2.8 45.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ALA* 5.0 9.2 - - + +
154A SER* 3.8 18.4 - - - +
155A GLY* 3.4 33.0 - - - +
163A TYR 4.3 1.3 - - - +
164A VAL* 3.8 24.0 - - + -
187A ALA* 3.0 24.6 + - + +
188A GLN* 3.8 27.8 - - - +
189A ASP 3.3 0.2 - - - -
190A VAL* 1.3 76.4 - - - +
192A SER* 1.3 63.3 + - - +
194A ILE* 3.5 8.6 + - - +
195A GLY* 3.3 16.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
37A GLY 4.1 3.1 + - - -
38A TRP* 3.8 24.0 + - - -
39A LEU* 3.3 28.5 + - - +
188A GLN 2.9 19.4 + - - -
189A ASP 3.6 0.2 - - - -
191A ILE* 1.3 77.1 - - - +
193A THR* 1.3 58.6 + - - +
195A GLY* 3.2 4.0 + - - -
196A GLN* 3.0 25.9 + - - +
301A EDO 4.5 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.6 2.6 + - - +
40A HIS* 3.2 21.6 - - + -
45A VAL* 4.0 20.6 - - + -
50A VAL* 4.1 8.3 - - + -
52A TYR* 2.9 24.9 + - - +
126A VAL* 3.6 16.3 - - + +
189A ASP* 2.8 20.4 + - - -
190A VAL 3.9 2.0 - - - -
192A SER* 1.3 74.3 - - - +
194A ILE* 1.3 62.1 + - - +
196A GLN* 3.6 7.8 + - - +
197A ALA* 2.9 28.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
124A LEU* 5.5 0.9 - - + -
126A VAL* 3.9 13.9 - - + -
131A LEU* 4.0 39.3 - - + -
147A MET* 4.1 5.6 - - - +
150A ILE* 4.7 12.8 - - + -
153A ALA* 4.2 23.1 - - + -
164A VAL* 4.2 16.2 - - + -
166A TYR* 4.5 8.5 - - + -
180A LEU* 5.5 1.6 - - + -
190A VAL* 2.8 36.8 + - + +
191A ILE* 3.7 6.5 - - - +
193A THR* 1.3 77.6 - - - +
195A GLY* 1.3 57.5 + - - +
197A ALA* 3.4 2.1 + - - +
198A PHE* 3.0 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE 3.3 7.4 + - - -
192A SER 3.2 8.0 + - - -
194A ILE* 1.3 80.7 - - - +
196A GLN* 1.3 56.7 + - - +
198A PHE* 3.3 4.3 + - - +
199A GLU* 3.0 20.3 + - - +
301A EDO 2.8 39.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TRP* 3.4 50.2 - - + +
39A LEU 4.2 1.9 + - - -
40A HIS* 2.9 33.5 + - - +
42A ASN* 2.9 29.5 + - - +
45A VAL* 3.6 18.9 - - + +
192A SER 3.0 9.9 + - - +
193A THR* 3.6 14.7 + - - +
195A GLY* 1.3 75.3 - - - +
197A ALA* 1.3 57.3 + - - +
199A GLU* 3.3 1.6 + - - +
200A LEU* 3.0 43.8 + - + +
301A EDO 3.8 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 3.6 15.2 - - + +
126A VAL* 3.9 10.5 - - + -
127A SER 3.4 31.0 - - - +
128A THR* 3.5 10.1 - - - +
147A MET* 3.9 7.1 - - + +
193A THR 2.9 17.2 + - - +
194A ILE 3.7 4.3 - - - +
196A GLN* 1.3 73.8 - - - +
198A PHE* 1.3 65.6 + - - +
201A ARG* 3.2 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A MET* 3.7 33.8 - - - -
148A GLN* 4.9 4.7 - - - -
150A ILE* 3.6 26.5 - - + -
194A ILE* 3.0 15.8 + - + +
195A GLY* 3.3 11.4 + - - +
197A ALA* 1.3 75.0 - - - +
199A GLU* 1.3 63.7 + - - +
201A ARG* 2.5 74.9 + - - +
301A EDO 4.4 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TRP* 4.0 23.6 - - + -
195A GLY 3.0 16.5 + - - +
196A GLN 3.8 3.6 - - - +
197A ALA 3.2 0.2 - - - -
198A PHE* 1.3 87.6 - - - +
200A LEU* 1.3 62.6 + - + +
201A ARG* 3.4 12.4 + - - +
301A EDO 3.8 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TRP* 4.2 13.9 - - + -
42A ASN* 3.6 46.7 - - + +
45A VAL* 4.4 5.2 - - + -
46A MET* 3.9 21.7 - - + +
128A THR* 3.6 17.8 - - + +
196A GLN* 3.0 41.0 + - + +
198A PHE 3.4 0.2 - - - -
199A GLU* 1.3 75.6 - - + +
201A ARG* 1.3 65.8 + - - +
303A EDO 4.6 5.4 - - - +
306A EDO 4.1 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR* 3.8 26.7 - - - +
147A MET* 4.1 10.5 - - + -
148A GLN* 4.7 15.4 - - - +
197A ALA 3.2 11.8 + - - +
198A PHE* 2.5 83.9 + - - +
199A GLU* 3.2 18.6 + - - +
200A LEU* 1.3 82.2 - - - +
----------------------------------------------------------
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