Contacts of the helix formed by residues 161 - 172 (chain J) in PDB entry 6XAV
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 THR 161 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J GLU 5.6 1.4 + - - -
143J SER* 5.2 6.7 - - - +
144J TYR* 4.6 4.0 - - - +
160J LEU* 1.3 76.2 - - - +
162J GLU* 1.3 55.8 + - - +
163J GLU* 3.8 9.9 - - + +
164J GLN* 3.4 34.0 + - + +
165J TYR* 2.8 28.2 + - - +
96L THR* 5.7 0.2 + - - -
99L ARG* 2.3 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 162 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J GLU 5.8 0.7 - - - +
143J SER* 5.0 5.7 + - - +
144J TYR* 3.2 36.4 + - - -
161J THR* 1.3 80.2 + - - +
163J GLU* 1.3 62.2 + - - +
165J TYR* 3.2 11.7 + - - +
166J LEU* 3.0 27.9 + - - +
180J MET* 3.9 14.4 - - - +
293J ARG* 5.4 1.7 - - - -
94L GLY 5.8 0.2 - - - -
95L GLY* 4.9 11.1 + - - -
99L ARG* 3.4 27.1 - - - +
101L ALA* 4.7 15.2 - - + +
102L PRO* 6.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161J THR* 3.3 8.0 + - + +
162J GLU* 1.3 78.0 - - - +
164J GLN* 1.3 53.5 + - + +
166J LEU* 3.1 6.9 + - - +
167J ASP* 2.7 50.3 + - - +
99L ARG* 2.9 45.7 + - - -
100L PRO 5.6 0.5 - - - +
102L PRO* 5.7 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 164 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158J GLN* 5.4 4.0 + - - -
159J ILE 4.2 3.6 - - - +
160J LEU* 3.3 36.5 - - + +
161J THR* 3.4 21.7 + - + +
163J GLU* 1.3 77.5 - - + +
165J TYR* 1.3 58.0 + - - +
167J ASP* 4.3 8.5 - - - +
168J ALA* 3.0 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 165 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144J TYR* 3.8 54.3 + + + -
160J LEU* 3.6 10.5 - - + +
161J THR 2.8 15.3 + - - +
162J GLU* 3.3 15.3 - - - +
163J GLU 3.1 0.2 - - - -
164J GLN* 1.3 77.9 - - - +
166J LEU* 1.3 66.4 + - + +
168J ALA 4.1 0.3 - - - -
169J LEU* 3.2 40.1 + - + +
176J PHE* 3.5 36.8 - + - -
178J ALA* 4.1 12.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162J GLU 3.0 12.7 + - - +
163J GLU* 3.1 8.3 + - - +
165J TYR* 1.3 81.8 - - + +
167J ASP* 1.3 70.2 + - - +
169J LEU* 3.2 26.3 + - + +
170J GLU* 3.3 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 167 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163J GLU* 2.7 33.0 + - - +
164J GLN* 4.1 8.9 + - - +
166J LEU* 1.3 80.6 - - - +
168J ALA* 1.3 60.8 + - - +
170J GLU* 3.1 19.8 + - - +
171J GLU* 2.8 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 168 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154J LEU* 4.8 15.9 - - + -
160J LEU* 4.7 5.2 - - + -
164J GLN 3.0 19.7 + - - +
165J TYR 4.2 2.2 - - - +
167J ASP* 1.3 76.4 - - - +
169J LEU* 1.3 57.5 + - - +
171J GLU* 3.5 8.3 + - - +
172J PHE* 2.9 37.6 + - + +
176J PHE* 4.7 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165J TYR* 3.2 38.9 + - + +
166J LEU* 3.5 20.0 - - + +
167J ASP 3.1 0.8 - - - -
168J ALA* 1.3 76.9 - - - +
170J GLU* 1.3 64.5 + - + +
172J PHE 3.3 14.8 - - - +
173J GLY* 3.7 19.5 + - - +
176J PHE* 3.6 27.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 170 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166J LEU* 3.3 35.8 + - + +
167J ASP* 3.1 13.8 + - - +
169J LEU* 1.3 82.6 - - - +
171J GLU* 1.3 69.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 171 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167J ASP* 2.8 28.1 - - - +
168J ALA* 3.5 6.3 + - - -
170J GLU* 1.3 84.5 - - + +
172J PHE* 1.3 88.9 + - + +
173J GLY 4.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 172 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151J MET 4.3 13.5 - - - -
152J THR* 3.7 30.5 - - - +
153J ASN* 3.8 22.4 - - + -
154J LEU* 6.2 0.7 - - + -
168J ALA* 2.9 28.3 + - + +
169J LEU* 3.3 10.0 - - - -
170J GLU 3.5 0.2 - - - -
171J GLU* 1.3 100.9 - - + +
173J GLY* 1.3 58.8 + - - +
174J ASP 3.8 1.3 - - - +
175J GLU 5.9 0.7 - - - +
176J PHE* 3.2 26.0 - - + +
----------------------------------------------------------
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