Contacts of the helix formed by residues 146 - 150 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G VAL 5.7 0.2 - - - +
28G SER* 3.2 25.8 + - - -
64G LEU* 3.8 9.5 - - + +
65G GLY 3.8 11.9 - - - +
66G SER* 2.9 16.2 + - - +
93G GLN* 5.7 1.6 + - - -
145G GLY* 1.3 71.5 - - - -
147G PRO* 1.4 65.4 - - - +
148G PHE 3.4 1.0 + - - -
149G GLY* 3.2 29.2 + - - -
150G LEU 3.3 0.2 - - - +
151G GLY* 3.0 45.9 - - - +
152G GLN* 3.5 4.0 + - - +
185G GLY* 3.3 18.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 147 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G GLY 3.5 8.5 - - - +
146G ASN* 1.4 85.6 - - - +
148G PHE* 1.4 67.1 + - + +
149G GLY 3.1 2.0 + - - -
150G LEU* 3.1 24.5 + - + +
151G GLY 4.5 0.2 - - - +
153G THR* 3.6 23.8 - - + +
155G THR* 6.2 0.2 - - + -
183G ASN* 3.9 16.8 - - + -
184G ARG 3.3 7.6 - - - +
185G GLY* 4.1 0.7 - - - -
186G ASN* 3.3 29.1 - - - +
215H ILE* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 148 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G ASN 3.4 0.6 + - - -
147G PRO* 1.4 76.4 - - + +
149G GLY* 1.3 60.7 + - - +
150G LEU* 3.2 5.9 + - + +
183G ASN* 3.7 35.7 - - + -
184G ARG* 2.8 44.8 + - + -
185G GLY* 4.4 0.2 - - - -
210G GLY 5.6 1.1 - - - -
211G GLY* 5.4 0.4 - - - -
206H LEU* 3.9 35.1 - - + +
208H PRO* 4.1 28.5 - - + -
213H VAL* 4.1 5.4 - - + -
215H ILE* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G LEU* 4.2 22.6 - - - +
146G ASN* 3.2 21.5 + - - -
147G PRO 3.1 2.2 + - - -
148G PHE* 1.3 76.7 - - - +
150G LEU* 1.3 59.5 + - - +
185G GLY* 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G ASN* 3.3 0.6 - - - +
147G PRO 3.1 20.7 + - - +
148G PHE* 4.3 6.1 - - + +
149G GLY* 1.3 78.4 - - - +
151G GLY* 1.3 58.9 + - - +
153G THR* 4.6 1.3 - - - +
164H ARG* 3.4 32.8 + - - +
167H LEU* 3.5 32.2 - - + +
177H GLN* 3.9 14.1 - - - +
206H LEU* 3.8 23.3 - - + -
215H ILE* 3.6 34.8 - - + -
217H PHE* 4.3 3.8 - - + -
----------------------------------------------------------
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