Contacts of the helix formed by residues 150 - 167 (chain A) in PDB entry 2L6X
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 150 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A MET* 4.2 17.7 - - + -
147A ALA* 3.4 31.2 - - - +
149A TRP* 1.3 99.5 - - + +
151A ALA* 1.3 54.0 + - - -
152A PHE 3.0 3.4 - - - -
153A ILE* 2.7 42.0 + - + +
154A ILE* 3.2 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ALA 2.8 22.5 + - - +
148A ALA* 3.2 16.2 - - - +
149A TRP 3.1 0.4 - - - -
150A PRO* 1.3 77.5 - - - +
152A PHE* 1.3 55.6 + - - +
154A ILE* 3.5 11.0 - - - -
155A GLY* 2.9 25.8 + - - -
200A TYR* 5.2 7.0 - - + +
201A PRO* 5.8 2.5 - - + -
204A TYR* 5.4 3.4 - - + -
301A RET 3.0 34.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ALA 4.3 1.0 + - - +
149A TRP* 3.5 22.0 + + + +
150A PRO 2.9 0.6 + - - -
151A ALA* 1.3 79.4 - - - +
153A ILE* 1.3 67.3 + - + +
156A CYS* 2.9 48.9 + - + +
201A PRO* 4.8 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A TRP* 4.1 15.9 - - + +
150A PRO* 2.7 35.3 + - + +
152A PHE* 1.3 79.4 - - + +
154A ILE* 1.3 72.8 + - + +
156A CYS* 3.1 5.2 + - - +
157A LEU* 2.9 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A VAL* 3.3 43.3 - - + -
147A ALA* 4.7 5.4 - - + +
150A PRO* 3.4 14.1 - - + +
151A ALA* 3.3 20.0 - - + +
153A ILE* 1.3 81.4 - - + +
155A GLY* 1.3 71.1 + - - +
157A LEU* 3.6 5.3 + - - +
158A ALA* 3.0 25.1 + - - +
301A RET 3.6 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ALA 2.9 18.4 + - - -
154A ILE* 1.3 75.4 - - - +
156A CYS* 1.3 54.1 + - - +
158A ALA* 3.2 5.2 + - - +
159A TRP* 2.7 37.9 + - - +
301A RET 3.7 29.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PHE* 2.9 41.7 + - + +
153A ILE* 3.6 4.5 - - - +
155A GLY* 1.3 74.3 - - - +
157A LEU* 1.3 63.4 + - + +
159A TRP* 3.2 28.8 + - + +
160A VAL* 2.9 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ILE* 2.9 28.3 + - + +
154A ILE* 3.9 5.2 - - - +
156A CYS* 1.3 82.3 - - + +
158A ALA* 1.3 63.5 + - - +
160A VAL* 3.4 7.6 + - + +
161A TYR* 3.0 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A VAL* 4.2 15.9 - - + +
132A LEU* 6.2 2.7 - - + -
133A VAL* 4.6 13.0 - - + -
154A ILE 3.0 18.9 + - - +
155A GLY* 3.7 4.7 - - - +
157A LEU* 1.3 77.4 - - - +
159A TRP* 1.3 57.9 + - - +
161A TYR* 3.9 4.6 - - - +
162A MET* 2.9 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLY 2.7 21.5 + - - +
156A CYS* 3.5 32.8 - - + -
158A ALA* 1.3 70.7 - - - +
160A VAL* 1.3 84.0 + - + +
162A MET* 3.0 14.5 + - - -
163A ILE* 3.1 35.2 + - + +
194A ILE* 3.2 37.4 - - + +
197A TRP* 5.8 17.0 - + + -
198A ALA* 5.4 12.1 - - + -
301A RET 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A CYS* 2.9 34.8 + - - +
157A LEU* 3.8 8.7 - - + +
159A TRP* 1.3 100.1 - - + +
161A TYR* 1.3 54.9 + - + +
163A ILE* 3.5 3.1 + - - +
164A TYR* 2.8 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A VAL* 5.8 4.5 - - + -
157A LEU* 3.0 30.3 + - + +
158A ALA* 3.9 5.6 - - - +
160A VAL* 1.3 77.0 - - + +
162A MET* 1.3 67.4 + - - +
164A TYR* 3.3 21.4 - + + +
165A GLU* 3.1 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LYS* 4.1 4.2 - - + +
126A LYS* 3.5 58.1 + - + +
129A VAL* 3.2 54.3 - - + +
130A GLY 4.8 1.1 - - - +
158A ALA 2.9 14.7 + - - +
159A TRP* 3.0 8.9 + - - +
161A TYR* 1.3 77.8 - - - +
163A ILE* 1.3 66.7 + - + +
165A GLU* 3.6 1.6 + - - +
166A LEU* 2.9 33.9 + - - +
193A ILE* 5.7 3.8 - - - -
197A TRP* 4.3 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TRP* 3.1 40.9 + - + +
160A VAL* 4.1 2.9 - - - +
162A MET* 1.3 81.5 - - + +
164A TYR* 1.3 59.6 + - - +
166A LEU* 3.8 8.3 - - + -
167A TRP* 2.7 63.3 + - + +
190A MET* 3.2 20.2 - - + -
193A ILE* 5.7 5.4 - - + -
194A ILE* 3.3 34.1 - - + -
197A TRP* 6.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A VAL* 2.8 26.2 + - + +
161A TYR* 3.2 28.5 + + + +
163A ILE* 1.3 81.1 - - - +
165A GLU* 1.3 80.8 + - + +
167A TRP* 3.7 12.9 + - - +
168A ALA* 4.1 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LYS* 4.3 32.7 - - + -
161A TYR* 3.1 24.5 + - + +
162A MET 4.3 1.1 - - - +
164A TYR* 1.3 97.1 - - + +
166A LEU* 1.3 67.2 + - - +
168A ALA* 3.0 23.1 + - - +
169A GLY* 3.3 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TYR* 3.5 23.3 - - + +
122A SER* 4.3 12.1 - - - +
125A LYS* 5.6 7.7 - - + +
126A LYS* 3.6 25.6 - - - +
162A MET* 2.9 24.4 + - - +
163A ILE* 3.7 9.4 - - + +
165A GLU* 1.3 73.2 - - - +
167A TRP* 1.3 51.4 + - - +
168A ALA 2.9 5.2 - - - -
169A GLY* 2.7 28.2 + - - +
186A TYR* 2.6 36.3 + - + +
190A MET* 3.4 27.6 - - + -
193A ILE* 6.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ILE* 2.7 51.2 + - + +
164A TYR* 3.7 9.2 - - - +
165A GLU 3.2 0.2 - - - -
166A LEU* 1.3 72.5 - - - +
168A ALA* 1.3 57.1 + - + +
169A GLY 3.4 0.8 + - - -
186A TYR* 3.8 10.8 + + - -
190A MET* 3.7 16.9 - - + +
----------------------------------------------------------
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