Contacts of the strand formed by residues 160 - 166 (chain D) in PDB entry 3LUE
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 160 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D PRO* 3.2 7.2 - - - +
110D LEU* 3.4 0.3 - - - +
153D MET* 3.5 19.7 - - - -
154D ASP 3.1 12.1 - - - +
155D SER* 2.9 20.1 + - - +
159D VAL* 1.3 74.0 - - - +
161D HIS* 1.3 63.2 + - - +
162D THR* 5.3 1.1 - - + -
177D ARG* 3.3 4.0 - - - -
178D LEU* 2.7 44.0 + - + -
180D LEU 2.8 22.5 + - - -
181D ALA* 4.1 0.2 - - - +
261D LEU* 5.0 0.5 - - - +
274D ILE* 3.4 27.5 - - + +
277D THR* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D PRO* 1.6 40.1 - - + +
110D LEU* 2.1 38.8 + - - -
136D ILE* 4.2 21.2 - - + +
138D ALA* 4.7 0.7 - - - +
152D VAL 3.7 1.0 - - - +
153D MET* 3.5 2.8 - - - -
154D ASP* 2.9 33.9 + - + +
160D THR* 1.3 74.5 - - - +
162D THR* 1.3 65.5 + - - +
163D VAL* 3.9 14.6 - - + -
175D ILE* 3.3 23.8 - - + +
176D LEU 3.0 17.5 - - - +
177D ARG* 3.3 14.6 - - + +
277D THR* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 162 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D ILE* 4.3 4.9 - - + -
152D VAL 3.4 5.2 - - - +
153D MET* 3.6 19.1 - - + -
160D THR* 5.3 1.6 - - + -
161D HIS* 1.3 77.8 - - - +
163D VAL* 1.3 60.2 + - - +
175D ILE* 3.3 5.9 - - - -
176D LEU* 3.0 29.3 + - - +
274D ILE* 4.9 1.3 - - + +
277D THR* 3.4 25.3 + - + +
278D THR* 3.4 38.6 - - - +
281D SER* 3.0 25.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 163 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ILE* 5.4 2.0 - - + -
138D ALA* 5.0 6.5 - - + -
139D VAL* 3.6 33.7 - - + -
151D ILE* 3.2 23.2 - - - +
152D VAL* 3.2 16.6 + - + +
161D HIS* 3.9 21.1 - - + +
162D THR* 1.3 78.2 - - - +
164D PRO* 1.3 60.2 - - - +
165D ILE* 3.8 15.8 + - + +
170D ALA* 3.8 23.6 - - + -
175D ILE* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D GLY 3.8 5.2 - - - +
151D ILE* 4.0 7.2 - - + -
162D THR 4.1 0.2 - - - +
163D VAL* 1.3 84.1 - - - +
165D ILE* 1.3 55.0 + - - +
170D ALA* 3.5 2.4 - - - -
171D LEU* 2.7 43.1 + - + +
174D ALA* 3.5 31.0 - - + +
175D ILE* 4.1 2.2 - - + +
281D SER* 3.8 14.6 - - - -
285D CYS* 3.2 37.2 - - - -
293D LEU* 3.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 2.1 20.6 - - - +
44B MET* 1.3 112.8 - - + +
61B LYS* 3.1 5.0 - - - -
139D VAL* 5.3 3.6 - - + -
142D LEU* 1.5 58.3 - - + -
148D THR 3.4 1.3 - - - +
149D THR* 3.2 0.5 - - - +
150D GLY 2.9 17.9 + - - +
152D VAL* 4.1 5.4 - - + -
163D VAL* 3.9 21.1 - - + +
164D PRO* 1.3 74.5 - - - +
166D TYR* 1.3 57.6 + - - +
169D TYR 3.2 6.1 - - - +
170D ALA* 3.8 13.5 - - + -
171D LEU* 4.7 0.7 - - - -
293D LEU* 4.1 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 3.0 2.6 - - - -
57B GLU 2.1 28.0 - - - -
58B ALA* 1.5 49.7 - - - +
61B LYS* 0.8 350.1 - - + +
64B ILE* 3.0 20.2 - - + +
65B LEU* 2.3 42.1 - - + +
165D ILE* 1.3 61.9 - - - +
167D GLU* 1.3 70.9 + - + +
168D GLY 3.4 0.2 - - - -
169D TYR* 2.9 27.8 + - - +
289D ILE* 3.8 2.2 - - + -
----------------------------------------------------------
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