Contacts of the helix formed by residues 153 - 158 (chain B) in PDB entry 3F2F
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 153 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 2.9 21.8 + - - -
80A GLU* 3.9 20.1 + - + +
61B THR* 3.7 12.4 + - - +
62B SER* 2.6 29.6 + - - -
152B ALA* 1.3 79.2 - - - +
154B VAL* 1.3 66.7 + - - +
155B ARG* 3.4 0.2 - - - +
156B GLN* 2.9 45.3 + - + +
157B SER* 3.0 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 5.6 4.7 - - + -
13B SER* 4.2 33.0 - - - -
62B SER* 3.8 16.3 + - - +
95B TRP* 4.6 11.0 - - + -
152B ALA 4.2 1.6 + - - -
153B ASP* 1.3 71.7 - - - +
155B ARG* 1.3 62.7 + - - +
157B SER* 3.9 5.6 - - - -
158B PHE* 2.9 44.5 + - + +
159B CYS* 3.2 10.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 4.0 23.0 - - - +
155A ARG* 5.9 2.4 - - - +
156A GLN* 4.3 13.3 - - - +
62B SER* 3.5 12.4 + - - +
64B GLU* 3.1 36.6 + - - +
81B THR* 3.8 19.2 - - - +
95B TRP* 3.3 51.1 + - + +
153B ASP* 3.1 10.2 + - - +
154B VAL* 1.3 83.3 - - - +
156B GLN* 1.3 62.1 + - - +
159B CYS* 3.3 20.1 + - + -
160B CYS* 3.0 40.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 3.1 23.5 + - - +
80A GLU* 3.6 27.2 + - + +
81A THR* 3.9 24.9 - - - +
82A SER* 4.4 11.9 + - - +
155A ARG* 5.1 4.6 - - - +
153B ASP* 2.9 41.3 + - + +
155B ARG* 1.3 80.0 - - - +
157B SER* 1.3 61.8 + - - +
160B CYS* 3.6 26.2 - - - +
161B HIS* 3.6 14.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B VAL* 3.6 3.8 - - - +
148B PRO* 3.5 34.1 - - - +
152B ALA 5.2 5.2 + - - -
153B ASP 3.0 20.6 + - - -
154B VAL* 3.8 6.8 + - - -
156B GLN* 1.3 78.2 - - - +
158B PHE* 1.3 60.7 + - - +
161B HIS* 3.3 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 5.5 4.5 - + + -
10B LEU* 3.8 36.3 - - + -
96B CYS* 4.3 11.0 - - - -
98B LEU* 3.9 22.7 - - + -
99B ASP* 5.9 0.7 - - - -
145B LEU* 4.7 6.1 - - + -
146B VAL* 3.5 34.7 - - + +
148B PRO* 3.9 14.1 - - + -
154B VAL* 2.9 23.5 + - + +
157B SER* 1.3 80.3 - - - +
159B CYS* 1.3 77.7 + - - +
160B CYS 3.2 1.8 - - - -
161B HIS* 2.9 16.9 + - - +
162B VAL* 3.4 35.5 - - + +
195B LEU* 6.2 0.2 - - + -
----------------------------------------------------------
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