Contacts of the helix formed by residues 158 - 174 (chain A) in PDB entry 2X8Y
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 ASP 158 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A TYR* 4.7 7.4 + - - -
156A SER* 3.1 10.8 + - - +
157A ARG* 1.3 75.3 - - - +
159A HIS* 1.3 66.3 + - - +
160A GLU* 3.1 11.8 + - - +
161A GLU* 2.9 32.1 + - + +
162A LEU* 3.0 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ARG 3.6 3.8 + - - -
158A ASP* 1.3 74.8 + - - +
160A GLU* 1.3 88.5 + - + +
162A LEU* 3.6 10.5 + - - -
163A ALA* 3.0 23.0 + - - +
243A TYR* 4.0 16.6 - + + -
247A VAL* 4.0 32.7 - - + +
257A HIS* 3.2 17.6 + - - +
258A LEU* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A TYR* 4.0 15.9 + - - +
158A ASP* 3.1 8.0 + - - +
159A HIS* 1.3 98.2 - - + +
161A GLU* 1.3 64.6 + - - +
163A ALA* 3.8 6.3 - - + +
164A TYR* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A TYR* 3.6 30.2 + - + +
136A LYS* 3.0 29.8 + - - -
152A VAL* 3.8 19.8 - - + +
156A SER* 2.6 26.3 + - - +
158A ASP* 2.9 25.7 + - - +
160A GLU* 1.3 76.2 - - - +
162A LEU* 1.3 63.4 + - - +
164A TYR* 3.2 10.9 + - - +
165A TYR* 3.2 37.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A VAL* 3.7 25.1 - - + +
153A ILE* 3.7 32.7 - - + +
156A SER* 3.5 25.4 - - - +
158A ASP 3.0 18.9 + - - +
159A HIS* 3.7 13.5 - - - +
161A GLU* 1.3 77.1 - - - +
163A ALA* 1.3 55.5 + - - +
165A TYR* 3.3 5.4 + - - +
166A TRP* 3.0 28.9 + - - +
243A TYR* 3.9 17.3 - - - +
257A HIS* 3.5 32.3 - - + +
258A LEU* 4.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A HIS 3.0 18.5 + - - +
160A GLU* 3.8 7.6 - - - +
162A LEU* 1.3 73.2 - - - +
164A TYR* 1.3 66.9 + - - +
166A TRP* 3.7 5.8 - - - +
167A ARG* 3.1 25.5 + - - +
257A HIS* 3.4 16.3 - - + +
482A PRO* 4.1 15.3 - - + +
483A VAL* 5.0 10.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
133A CYS* 2.6 43.1 + - - +
134A ASP 4.0 2.5 + - - -
135A TYR* 3.4 48.7 - + + -
160A GLU 3.0 14.6 + - - +
161A GLU 3.2 8.5 + - - +
163A ALA* 1.3 77.8 - - - +
165A TYR* 1.3 73.7 + + - +
167A ARG* 3.3 4.2 + - - +
168A GLU* 3.0 61.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL* 4.0 20.3 - - + +
133A CYS 4.0 1.6 - - - -
134A ASP* 3.6 9.9 + - - -
135A TYR* 2.9 41.3 + - + +
143A LEU* 3.6 24.9 - - + +
149A ILE* 4.0 25.0 - - + +
152A VAL* 3.6 36.1 - - + +
153A ILE* 4.2 8.7 - - + -
161A GLU* 3.2 28.7 + - + -
162A LEU 3.9 4.9 - - - +
164A TYR* 1.3 91.7 - + - +
166A TRP* 1.3 64.3 + - - +
168A GLU* 4.0 2.5 - - - +
169A PHE* 3.0 27.4 + - - +
262A MET* 4.1 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ILE* 4.5 3.2 - - + +
162A LEU 3.0 17.7 + - - +
163A ALA 3.7 4.9 - - - +
164A TYR 3.3 0.2 - - - -
165A TYR* 1.3 77.5 - - - +
167A ARG* 1.3 69.6 + - + +
169A PHE* 3.9 0.2 - - - -
170A TYR* 3.0 67.8 + + + -
256A MET* 3.4 23.9 - - + +
257A HIS* 4.3 11.9 - - + -
261A ASN 5.9 0.4 - - - -
262A MET* 4.0 21.3 - - - -
470A TRP* 3.7 28.0 - + - -
481A PRO* 3.7 15.9 - - + -
482A PRO* 3.4 36.8 - - + -
483A VAL* 4.3 4.3 - - + -
485A ARG* 3.7 40.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ALA 3.1 17.4 + - - +
164A TYR* 3.8 4.7 - - - +
166A TRP* 1.3 88.6 - - + +
168A GLU* 1.3 71.3 + - - +
170A TYR* 4.0 0.3 - - - +
171A ASP* 3.0 45.4 + - - +
483A VAL* 3.4 42.9 - - + +
484A VAL 5.0 5.5 + - - -
485A ARG* 4.0 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL* 3.8 22.0 - - + +
133A CYS* 5.3 2.8 + - - +
164A TYR* 3.0 56.1 + - + +
165A TYR* 4.0 4.9 - - - +
167A ARG* 1.3 85.8 - - - +
169A PHE* 1.3 63.0 + - - +
171A ASP* 3.9 6.3 - - - +
172A LYS* 3.3 49.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE* 3.8 14.1 - + - -
130A VAL* 3.8 28.5 - - + -
132A VAL* 4.3 5.1 - - - +
145A LEU* 3.7 41.5 - - + -
149A ILE* 4.1 13.0 - - + -
165A TYR 3.0 20.0 + - - +
166A TRP 4.0 1.1 - - - +
168A GLU* 1.3 77.4 - - - +
170A TYR* 1.3 58.1 + + - +
172A LYS* 3.2 2.6 + - - +
173A ALA* 2.7 55.4 + - + +
262A MET* 3.8 37.9 - - + -
263A TRP* 4.1 2.5 - + - -
494A ALA* 3.3 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A TRP* 3.0 72.5 + + + +
167A ARG 4.3 0.4 - - - +
169A PHE* 1.3 79.0 - + - +
171A ASP* 1.3 58.8 + - - +
174A GLY* 2.8 28.8 + - - -
175A THR* 3.3 4.7 + - - -
256A MET* 3.5 12.6 - - - +
262A MET* 2.7 39.5 + - + -
263A TRP* 3.5 18.5 - + - -
469A PHE* 5.4 2.2 - + - -
470A TRP* 3.9 12.3 - + - -
485A ARG* 3.8 7.2 - - - +
491A ASP* 3.5 35.3 - - + +
494A ALA* 3.6 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ARG* 3.0 40.0 + - - +
168A GLU* 3.9 9.9 - - - +
170A TYR* 1.3 77.3 - - - +
172A LYS* 1.3 63.6 + - + +
175A THR* 3.5 12.2 + - - -
176A ALA* 3.4 20.4 + - - +
485A ARG* 2.9 32.3 + - - -
489A ASP* 4.3 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASN* 3.1 19.6 + - - +
130A VAL* 3.9 19.3 - - + +
131A LYS 3.3 28.8 + - - +
132A VAL* 3.8 18.4 - - + +
133A CYS* 5.4 1.9 - - - +
168A GLU* 3.3 35.6 + - - +
169A PHE 3.2 3.4 + - - +
171A ASP* 1.3 80.7 - - + +
173A ALA* 1.3 59.8 + - - +
176A ALA* 3.4 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASN* 3.9 7.9 + - - +
127A PHE* 4.2 9.2 - - + -
130A VAL* 3.9 14.6 - - + -
169A PHE* 2.7 50.2 + - + +
172A LYS* 1.3 73.9 - - - +
174A GLY* 1.3 60.8 + - - +
177A VAL* 3.9 7.6 - - - +
493A PRO* 3.3 18.0 - - - +
494A ALA* 3.9 9.6 - - - -
499A SER* 4.0 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A TYR 2.8 13.0 + - - -
173A ALA* 1.3 78.3 - - - +
175A THR* 1.3 64.4 + - - +
176A ALA 3.1 3.6 + - - -
177A VAL* 3.2 20.4 + - - +
178A ARG 4.1 2.6 + - - -
490A PHE* 2.8 19.6 - - - +
491A ASP 4.5 0.4 - - - -
493A PRO* 4.1 5.0 - - - +
494A ALA* 3.7 18.3 - - - +
----------------------------------------------------------
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