Contacts of the helix formed by residues 146 - 150 (chain F) in PDB entry 3STJ
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 ASN 146 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F SER* 3.2 23.6 - - - -
64F LEU* 3.8 14.0 - - + +
65F GLY 3.7 12.8 - - - +
66F SER* 2.7 16.5 + - - +
93F GLN* 5.6 1.2 + - - -
145F GLY* 1.3 72.5 - - - -
147F PRO* 1.4 62.6 - - - +
148F PHE 3.5 0.9 + - - -
149F GLY* 3.4 21.5 + - - -
151F GLY* 3.0 44.3 - - - +
152F GLN* 3.9 2.3 + - - -
185F GLY* 3.3 19.4 + - - -
186F ASN* 4.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 147 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D ILE* 3.8 21.3 - - + -
145F GLY 3.3 14.1 - - - +
146F ASN* 1.4 82.3 - - - +
148F PHE* 1.4 62.4 + - + +
149F GLY 3.0 6.2 + - - -
150F LEU* 3.1 25.2 + - + +
151F GLY 4.3 0.7 - - - +
153F THR* 3.6 26.2 - - + +
155F THR* 6.3 0.2 - - + -
183F ASN* 3.9 13.2 - - + -
184F ARG 3.2 11.2 - - - +
185F GLY* 4.1 2.7 - - - -
186F ASN* 3.4 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 148 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D LEU* 4.0 34.9 - - + +
208D PRO* 4.3 25.6 - - + -
213D VAL* 4.2 5.4 - - + -
215D ILE* 3.9 18.6 - - + -
146F ASN 3.5 0.6 + - - -
147F PRO* 1.4 75.1 - - + +
149F GLY* 1.3 60.4 + - - +
150F LEU* 3.2 6.8 + - + +
183F ASN* 3.7 35.4 - - + -
184F ARG* 2.8 47.8 + - + -
185F GLY* 4.4 0.8 - - - -
210F GLY 5.1 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F LEU* 4.2 23.9 - - - +
146F ASN* 3.4 17.9 + - - -
147F PRO 3.0 2.6 + - - -
148F PHE* 1.3 77.0 - - - +
150F LEU* 1.3 61.1 + - - +
151F GLY 3.4 2.5 - - - -
185F GLY* 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D ARG* 3.4 32.2 + - - +
167D LEU* 3.7 29.1 - - + +
177D GLN* 3.9 14.4 - - - +
206D LEU* 3.7 25.6 - - + -
215D ILE* 3.6 34.5 - - + -
217D PHE* 4.4 3.8 - - + -
146F ASN* 3.4 0.4 - - - +
147F PRO* 3.1 20.7 + - + +
148F PHE* 4.2 7.0 - - + +
149F GLY* 1.3 77.7 - - - +
151F GLY* 1.3 58.2 + - - +
153F THR* 4.6 1.6 - - - +
----------------------------------------------------------
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