Contacts of the helix formed by residues 156 - 166 (chain B) in PDB entry 1UU1
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 GLU 156 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ARG* 4.8 17.0 + - + +
154B VAL 5.1 2.7 - - - +
155B PHE* 1.3 74.6 - - - +
157B ARG* 1.3 66.0 + - - +
158B GLU* 2.8 26.6 - - - +
159B GLU* 2.8 44.7 + - + +
160B ILE* 3.2 8.3 - - - +
184B TYR* 3.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B PHE 3.9 0.4 + - - -
156B GLU* 1.3 71.9 - - - +
158B GLU* 1.3 69.3 + - - +
159B GLU 3.1 0.5 + - - -
160B ILE* 3.3 4.5 + - - +
161B GLU* 3.0 42.0 + - - +
182B GLU* 4.9 14.5 - - - +
183B SER 5.9 1.2 + - - -
184B TYR* 3.0 38.3 + - - +
187B PHE* 3.3 32.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ARG* 4.6 15.4 + - - +
156B GLU* 2.8 31.3 - - + +
157B ARG* 1.3 82.1 + - - +
159B GLU* 1.3 59.2 + - - +
161B GLU* 3.6 12.7 - - + +
162B ARG* 2.8 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU 4.9 0.7 - - - +
130B ARG* 3.3 40.3 + - - +
131B ILE* 2.8 46.0 + - + +
153B HIS* 5.8 0.3 - - - -
155B PHE* 3.5 15.2 - - + -
156B GLU* 2.8 47.0 + - + +
158B GLU* 1.3 77.3 - - - +
160B ILE* 1.3 66.7 + - + +
162B ARG* 3.3 27.8 + - - +
163B ILE* 3.5 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 5.0 0.7 - - + -
144B ILE* 4.6 11.9 - - + -
146B ASN* 4.3 5.2 - - - +
155B PHE* 3.8 22.7 - - + -
156B GLU 3.2 26.0 - - - +
157B ARG 3.3 2.0 + - - +
159B GLU* 1.3 73.7 - - + +
161B GLU* 1.3 56.1 + - - +
163B ILE* 3.1 10.7 + - - +
164B LEU* 2.7 48.6 + - + +
170B VAL* 4.1 24.9 - - + +
172B LEU* 4.2 21.8 - - + -
184B TYR* 3.3 36.8 - - + +
194B LEU* 5.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ARG* 3.0 40.1 + - - +
158B GLU* 3.6 11.1 - - + +
160B ILE* 1.3 77.4 - - - +
162B ARG* 1.3 50.5 + - - +
164B LEU* 3.1 11.6 - - - +
165B LYS* 2.8 49.5 + - + +
187B PHE* 3.4 21.1 - - + -
191B TYR* 2.8 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ARG* 3.9 23.6 - - - +
131B ILE* 4.5 19.8 + - - +
132B PRO 5.4 0.4 + - - -
133B GLU* 4.7 18.5 + - - +
158B GLU* 2.8 18.2 + - - +
159B GLU* 3.3 30.7 + - - +
160B ILE 3.2 0.2 - - - -
161B GLU* 1.3 73.7 - - - +
163B ILE* 1.3 68.5 + - - +
165B LYS* 3.1 25.1 + - - +
166B THR* 3.1 21.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PHE* 4.0 3.6 - - + -
131B ILE* 3.4 47.3 - - + -
134B VAL* 5.4 8.1 - - + -
136B VAL* 4.4 9.6 - - + -
142B VAL* 3.7 36.6 - - + -
144B ILE* 3.4 16.2 - - + -
159B GLU 3.5 9.0 - - - +
160B ILE 3.1 5.7 + - - +
162B ARG* 1.3 79.6 - - + +
164B LEU* 1.3 63.0 + - - +
166B THR* 2.6 31.6 + - - +
168B ALA* 4.1 5.8 + - + +
170B VAL* 3.7 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ILE* 2.7 22.8 + - + +
161B GLU* 3.1 11.7 - - - +
163B ILE* 1.3 78.2 - - - +
165B LYS* 1.3 62.8 + - - +
166B THR 3.2 0.9 + - - -
167B GLY* 3.3 5.9 + - - -
170B VAL* 3.4 31.2 - - + -
187B PHE* 3.7 33.2 - - + -
191B TYR* 3.5 33.1 - - + -
193B ASN* 3.1 43.2 + - - +
194B LEU* 4.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLU* 2.8 32.3 + - + +
162B ARG* 3.1 18.9 + - - +
164B LEU* 1.3 73.3 - - - +
166B THR* 1.3 57.3 + - - +
167B GLY* 3.1 6.0 + - - -
191B TYR* 4.5 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B VAL* 5.9 2.7 - - + +
136B VAL* 3.4 23.9 - - + +
137B GLY* 3.5 13.0 - - - -
138B GLU 4.1 0.9 + - - -
162B ARG* 3.1 21.8 - - + +
163B ILE* 2.6 21.9 + - - +
165B LYS* 1.3 73.9 - - + +
167B GLY* 1.3 59.0 + - - +
168B ALA* 3.0 18.4 + - - +
----------------------------------------------------------
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