Contacts of the helix formed by residues 142 - 154 (chain A) in PDB entry 4OCA
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 142 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL 5.4 2.7 + - - +
117A PRO* 4.0 17.2 - - + +
141A ALA* 1.3 70.6 - - - +
143A LEU* 1.3 63.3 + - - +
144A ASP* 4.3 2.1 - - - +
145A ALA* 3.4 25.5 + - + +
146A ILE* 3.1 27.0 + - + +
169A TYR* 3.1 18.2 + - - -
170A LYS* 4.6 3.6 + - - -
290A TRP* 3.4 39.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PRO* 4.9 8.7 - - + -
135A HIS* 3.7 11.9 - - + -
141A ALA* 2.8 17.9 + - + +
142A ASP* 1.3 69.2 - - - +
144A ASP* 1.3 59.7 + - - +
146A ILE* 4.4 6.3 - - + -
147A TYR* 2.8 66.2 + - + +
157A VAL* 5.6 0.4 - - + -
159A GLU* 3.5 38.6 - - + +
169A TYR* 3.5 26.3 + - + -
172A ARG* 4.5 3.1 - - - +
174A ILE* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASP* 4.3 2.2 - - - +
143A LEU* 1.3 77.1 - - - +
145A ALA* 1.3 61.8 + - - +
147A TYR* 4.0 5.0 - - - +
148A ALA* 3.2 22.7 + - - +
169A TYR* 3.1 14.1 + - - +
170A LYS* 2.5 37.4 + - - +
172A ARG* 3.3 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PRO* 3.4 32.1 - - + -
142A ASP* 3.3 18.7 + - - +
144A ASP* 1.3 80.0 - - - +
146A ILE* 1.3 62.7 + - - +
148A ALA* 3.2 8.1 + - - +
149A LEU* 3.1 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL 4.4 9.0 - - - +
117A PRO* 4.5 11.4 - - + -
120A ILE* 4.0 20.0 - - + -
131A ILE* 4.2 21.6 - - + +
133A PRO* 3.9 27.1 - - + -
141A ALA* 4.2 12.1 - - + -
142A ASP* 3.1 25.2 + - + +
143A LEU* 4.1 6.7 - - + +
145A ALA* 1.3 74.3 - - - +
147A TYR* 1.3 67.0 + - + +
149A LEU* 3.2 11.0 + - + +
150A GLY* 3.1 17.3 + - - -
157A VAL* 4.2 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 2.8 50.2 + - + +
144A ASP* 4.0 4.9 - - - +
146A ILE* 1.3 71.8 - - + +
148A ALA* 1.3 61.2 + - - +
150A GLY* 3.0 2.5 + - - +
151A GLU* 2.9 40.2 + - + +
157A VAL* 4.4 25.1 - - + -
159A GLU* 2.3 38.0 + - - -
172A ARG* 3.8 27.4 - - - -
177A ARG* 3.4 26.7 + - + +
178A GLY* 5.2 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ASP 3.2 12.7 + - - +
145A ALA* 3.2 12.7 + - - +
147A TYR* 1.3 79.0 - - - +
149A LEU* 1.3 62.8 + - + +
151A GLU* 4.0 7.2 - - - +
152A ARG* 3.0 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PRO* 3.5 37.7 - - + +
120A ILE* 3.9 20.0 - - + -
121A GLU* 3.9 29.6 - - + +
124A ILE* 4.6 1.3 - - + +
131A ILE* 4.7 10.5 - - + -
145A ALA* 3.1 19.3 + - + +
146A ILE* 3.4 13.0 - - - +
147A TYR 3.2 0.2 - - - -
148A ALA* 1.3 80.3 - - + +
150A GLY* 1.3 60.9 + - - +
152A ARG* 4.5 6.5 - - - +
153A TYR* 3.1 42.6 + - + +
155A ILE* 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ILE* 4.8 2.4 - - - +
146A ILE 3.1 9.8 + - - -
147A TYR 3.0 7.7 + - - -
149A LEU* 1.3 77.1 - - - +
151A GLU* 1.3 52.5 + - - +
154A GLY* 2.7 29.8 + - - -
155A ILE* 2.8 34.7 + - - -
157A VAL* 4.3 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A TYR* 2.9 22.4 + - + +
148A ALA* 4.2 6.0 - - - +
150A GLY* 1.3 74.5 - - - +
152A ARG* 1.3 65.4 + - - +
154A GLY* 3.6 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLU* 3.3 19.4 + - - -
148A ALA 3.0 20.5 + - - +
149A LEU* 3.9 8.2 - - - +
151A GLU* 1.3 80.2 - - - +
153A TYR* 1.3 95.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLU* 2.8 35.9 + - + +
124A ILE* 3.3 41.5 - - + -
149A LEU* 3.1 27.2 + - + +
152A ARG* 1.3 110.9 + - + +
154A GLY* 1.3 63.5 + - - +
155A ILE* 3.8 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR 5.5 0.3 - - - +
150A GLY 2.7 13.1 + - - -
151A GLU* 3.6 6.4 + - - -
152A ARG 3.4 3.0 + - - -
153A TYR* 1.3 80.6 - - - +
155A ILE* 1.3 58.8 - - - +
156A PRO* 3.9 6.6 - - - +
----------------------------------------------------------
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