Contacts of the helix formed by residues 159 - 170 (chain O) in PDB entry 3A68
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 159 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40O LYS 3.3 11.7 - - - +
41O TYR* 3.4 14.2 - - - -
42O VAL 5.0 0.3 + - - -
45O SER* 4.3 10.7 + - - +
105O ARG* 3.0 44.5 + - - -
154O ALA* 2.8 21.1 + - - +
155O THR* 4.8 0.6 - - - +
157O ASN* 3.2 6.0 - - + +
158O GLY* 1.3 74.6 - - - +
160O VAL* 1.3 61.6 + - - +
161O GLN* 3.5 2.9 + - - +
162O LEU* 3.0 19.8 + - + +
163O ALA* 3.2 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148F LEU* 4.1 19.7 - - + +
151F HIS* 3.5 44.6 - - + +
152F SER* 6.1 1.3 - - - +
167F GLU* 3.7 9.9 - - + +
171F LEU* 3.5 19.5 - - + -
158O GLY* 3.2 12.6 + - - +
159O ASP* 1.3 72.2 + - - +
161O GLN* 1.3 57.7 + - - +
163O ALA* 3.3 7.1 + - - +
164O ASP* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 161 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148F LEU* 5.1 4.8 - - + +
171F LEU* 3.6 38.3 - - + +
172F GLY* 3.7 17.5 - - - +
175F VAL* 3.6 23.9 - - + +
101O TYR* 2.5 39.6 + - - -
105O ARG* 3.7 9.7 + - - +
159O ASP* 3.4 1.6 + - - +
160O VAL* 1.3 79.1 - - - +
162O LEU* 1.3 60.1 + - - +
164O ASP* 3.6 10.3 + - + +
165O PHE* 2.9 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41O TYR* 4.4 5.4 - - + -
45O SER* 3.8 31.4 - - - +
49O VAL* 4.0 14.8 - - + -
101O TYR* 3.2 36.4 + - + +
105O ARG* 4.0 1.1 - - - +
150O LEU* 4.4 15.3 - - + -
153O VAL* 5.6 0.2 - - + -
154O ALA* 3.6 22.0 - - + +
159O ASP* 3.0 25.2 + - - +
161O GLN* 1.3 74.2 - - - +
163O ALA* 1.3 64.0 + - - +
165O PHE* 3.3 3.2 + - + +
166O VAL* 3.0 45.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151O HIS* 3.5 27.5 - - + +
154O ALA* 3.7 15.8 - - + +
155O THR* 4.1 13.7 - - + -
159O ASP 3.2 11.9 + - - +
160O VAL* 3.6 10.3 - - - +
161O GLN 3.3 0.2 - - - -
162O LEU* 1.3 78.6 - - - +
164O ASP* 1.3 63.0 + - - +
166O VAL* 3.4 1.3 + - - -
167O GLU* 3.0 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 164 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F GLU* 3.6 37.2 - - + +
168F THR* 4.5 5.2 + - - -
171F LEU* 5.5 0.8 - - + +
172F GLY* 5.2 2.8 + - - -
160O VAL 2.9 16.2 + - - +
161O GLN* 3.6 15.5 + - + +
162O LEU 3.2 0.2 - - - -
163O ALA* 1.3 75.9 - - - +
165O PHE* 1.3 58.3 + - - +
167O GLU* 3.3 8.2 + - - +
168O THR* 2.8 51.1 + - - -
341O CA 2.5 27.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 165 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97O LYS* 3.9 18.8 - - + -
98O LEU* 3.8 15.3 - - + -
101O TYR* 3.6 60.8 - + + -
104O LYS* 6.1 2.7 - - - -
161O GLN* 2.9 24.1 + - - +
162O LEU* 3.6 4.0 - - + +
164O ASP* 1.3 78.0 + - - +
166O VAL* 1.3 69.1 + - + +
168O THR* 4.8 2.9 - - - -
169O GLU* 2.8 53.0 + - + +
170O TYR* 3.6 27.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147O LEU* 3.8 31.9 - - + +
150O LEU* 3.5 32.5 - - + -
151O HIS* 4.3 13.5 - - + +
162O LEU* 3.0 31.5 + - + +
163O ALA* 3.8 4.0 - - - +
165O PHE* 1.3 84.7 - - + +
167O GLU* 1.3 62.4 + - - +
170O TYR* 3.0 25.1 + - + +
171O LEU* 3.1 22.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F GLU* 4.1 0.7 - - - +
160G VAL* 4.2 4.4 - - + +
164G ASP* 3.3 37.9 - - + +
151O HIS* 3.0 18.3 + - - +
163O ALA 3.0 19.1 + - - +
164O ASP* 3.3 11.1 - - - +
166O VAL* 1.3 78.2 - - - +
168O THR* 1.3 66.8 + - - +
171O LEU* 3.5 37.6 + - + +
172O GLY 3.8 5.4 + - - -
341O CA 2.3 29.8 - - - -
342O CA 2.6 28.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 168 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F THR* 5.7 0.3 + - - -
164G ASP* 4.7 6.5 + - - -
164O ASP* 2.8 42.7 + - - +
165O PHE* 4.1 2.2 - - - -
167O GLU* 1.3 79.7 - - - +
169O GLU* 1.3 75.8 + - - +
173O GLU* 3.6 1.0 - - - +
215O CA 2.4 29.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 169 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97O LYS* 3.2 35.3 + - + +
165O PHE* 2.8 44.5 + - + +
168O THR* 1.3 90.2 - - - +
170O TYR* 1.3 79.3 - - + +
173O GLU* 3.3 24.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 170 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56O GLU* 4.3 5.8 - - - -
94O HIS* 2.7 50.2 + + + -
97O LYS* 3.4 24.3 - - - +
98O LEU* 3.2 24.3 + - + +
147O LEU* 3.9 34.2 - - + +
165O PHE* 3.6 32.1 - + - -
166O VAL* 3.0 18.9 + - + +
168O THR 3.5 0.6 - - - -
169O GLU* 1.3 93.4 - - + +
171O LEU* 1.3 62.3 + - - +
172O GLY 3.5 1.6 - - - -
173O GLU* 3.4 5.6 + - + +
174O GLN* 2.8 33.3 + - - +
----------------------------------------------------------
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