Contacts of the helix formed by residues 176 - 180 (chain A) in PDB entry 1DXO
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 LEU 176 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PHE* 3.8 26.7 - - + -
116A PHE* 4.6 11.9 - - + -
120A PHE* 4.7 2.0 - - + -
142A ALA* 3.7 20.2 - - + -
144A LEU* 4.4 24.7 - - + -
171A ILE* 3.1 12.3 + - + +
172A GLN* 3.3 15.5 - - - +
175A ILE* 1.3 77.4 - - + +
177A HIS* 1.3 66.5 + - - +
179A CYS* 3.1 15.1 + - - +
181A PHE* 3.3 37.4 + - + +
183A VAL* 3.6 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A TYR* 3.0 37.7 - + + +
133A ASP* 3.8 34.7 + - + +
172A GLN 3.0 17.1 + - - +
173A SER* 3.8 8.9 + - - +
176A LEU* 1.3 76.2 - - - +
178A PHE* 1.3 62.2 + - - +
180A GLY* 2.7 18.8 + - - -
181A PHE 3.0 29.0 + - - +
182A GLN* 5.1 2.0 - - + -
183A VAL* 4.0 4.7 - - + +
222A PHE* 3.4 48.2 + + + +
223A ALA 4.9 4.1 + - - -
224A PRO* 6.1 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A TYR* 3.3 46.9 - + + +
128A TYR* 4.9 5.6 - + - -
130A ALA 4.6 1.6 - - - +
131A MET* 4.0 28.1 - - + -
132A TYR* 3.0 49.7 + + + -
173A SER 3.1 12.3 + - - +
174A GLY 3.3 22.0 - - - +
175A ILE 3.9 2.2 - - - +
176A LEU 3.2 0.4 - - - -
177A HIS* 1.3 76.4 - - - +
179A CYS* 1.3 57.1 + - - +
180A GLY 3.3 0.2 - - - -
105C TRP* 3.5 20.0 - + - -
106C PHE* 4.8 0.9 - + - -
161C HIS* 3.4 24.2 - + - -
302C DQN 3.4 24.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PHE* 3.8 15.7 - - - -
125A ALA* 3.1 27.4 - - - +
126A TYR* 4.3 2.2 - - - -
135A GLY* 3.7 6.5 - - - -
136A PRO* 3.2 7.3 - - - +
137A PHE* 2.9 40.9 + - + +
175A ILE 3.2 17.5 - - - -
176A LEU 3.1 8.0 + - - +
177A HIS 3.0 0.8 - - - -
178A PHE* 1.3 78.0 - - - +
180A GLY* 1.3 58.5 + - - +
181A PHE* 3.4 2.0 - - + -
105C TRP* 3.7 25.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A TYR 3.0 23.1 + - - -
133A ASP* 5.0 2.6 - - - -
135A GLY* 3.8 7.0 - - - -
138A ARG* 2.9 32.3 - - - +
177A HIS* 2.7 12.5 + - - -
179A CYS* 1.3 78.9 - - - +
181A PHE* 1.3 66.3 + - - +
182A GLN* 3.5 2.6 + - - +
----------------------------------------------------------
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