Contacts of the helix formed by residues 151 - 156 (chain A) in PDB entry 4UC5
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 151 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 4.8 9.0 - - + -
125A LEU* 4.4 12.6 - - + -
146A PHE* 4.4 4.3 - - - -
147A LEU 4.9 3.3 + - - -
148A ASP* 2.9 28.0 + - - +
150A ILE* 1.3 71.8 - - - +
152A PRO* 1.3 74.9 - - - +
154A TYR* 2.9 27.6 + - - +
155A TYR* 3.4 32.1 + - - +
212B LEU* 3.5 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PHE* 3.6 37.9 - - + -
148A ASP 3.5 18.4 - - - +
149A MET 3.7 2.5 - - - +
150A ILE 3.1 9.9 - - - +
151A THR* 1.3 97.2 - - - +
153A GLN* 1.3 61.1 + - + +
156A ALA* 2.9 39.0 + - + +
177A LEU* 4.1 17.9 - - + -
181A LEU* 4.3 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PRO* 3.5 30.0 - - + +
25A LEU* 4.9 4.2 - - - +
149A MET 5.1 1.3 - - - +
150A ILE 3.0 14.0 + - - +
151A THR 3.0 0.4 + - - -
152A PRO* 1.3 77.3 - - + +
154A TYR* 1.3 61.0 + - - +
157A ASP* 5.4 1.5 - - - +
213A SER* 4.3 11.8 + - - +
214A VAL* 2.9 32.8 + - + +
215A THR* 4.0 6.7 - - - +
216A LYS* 2.8 51.2 + - + +
223A VAL* 5.9 1.6 - - - +
8B ASP* 4.7 0.3 - - - +
9B ASP* 3.9 9.9 + - - +
15B VAL* 5.1 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.1 11.3 - - + +
19A LEU 2.7 29.9 + - - -
20A PRO* 3.8 0.5 - - - +
21A PRO* 3.5 32.6 - - + +
24A HIS* 3.4 37.5 - + + +
25A LEU* 5.3 2.6 - - - +
125A LEU* 3.8 33.7 - - + +
129A ARG* 2.9 28.7 + - + +
150A ILE* 3.7 32.3 - - + -
151A THR* 2.9 16.9 + - + +
153A GLN* 1.3 81.4 - - - +
155A TYR* 1.3 66.1 + - + +
157A ASP* 4.4 0.9 - - - -
214A VAL* 5.4 0.4 - - + -
212B LEU* 5.6 1.3 - - + -
220B SER* 3.9 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A PHE* 4.4 8.2 - + - -
110A ILE* 3.3 34.6 - - + +
125A LEU* 4.4 9.2 - - + -
128A ALA* 4.6 11.9 - - + -
129A ARG* 3.7 17.3 - - + +
132A LEU* 3.7 24.0 - - + -
144A THR* 4.2 11.6 - - + +
145A GLU 5.0 4.9 + - - -
146A PHE* 3.6 27.1 - + - -
151A THR* 3.4 34.9 + - - +
152A PRO 3.4 1.0 + - - -
154A TYR* 1.3 84.8 - - + +
156A ALA* 1.3 68.2 + - - +
157A ASP* 3.2 10.5 - - - -
158A LEU* 3.0 18.1 + - + +
159A ILE* 3.6 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 3.1 12.1 + - - -
146A PHE* 4.1 13.0 - - + -
152A PRO* 2.9 35.9 + - + +
153A GLN 5.0 0.2 - - - -
155A TYR* 1.3 73.5 - - - +
157A ASP* 1.3 58.8 + - - +
158A LEU 2.9 12.3 + - - -
159A ILE* 2.9 22.5 + - - +
181A LEU* 4.7 7.9 - - + -
182A SER* 5.5 4.7 - - - +
183A CYS* 5.8 1.1 - - - -
7B THR 5.1 0.2 - - - -
8B ASP* 6.1 0.4 - - - +
----------------------------------------------------------
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