Contacts of the helix formed by residues 149 - 157 (chain B) in PDB entry 2POD
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 149 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B GLY* 5.0 2.3 - - - -
124B PRO* 4.8 9.7 - - - +
147B ARG* 3.6 26.7 + - + +
148B TYR* 1.3 70.9 - - - +
150B ASP* 1.3 53.4 + - - +
151B LEU 3.5 2.0 - - - -
152B ASN* 3.4 26.9 + - - +
153B ALA* 2.8 34.0 + - - +
157B ARG* 3.4 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ASN* 3.5 11.5 + - - -
121B CYS* 3.4 24.8 - - + +
122B ALA 3.4 18.5 + - - +
123B GLY* 4.3 1.4 - - - -
148B TYR* 3.1 20.7 + - - +
149B ASP* 1.3 72.3 + - - +
151B LEU* 1.3 63.0 + - - +
153B ALA* 3.7 6.6 - - - +
154B PHE* 3.2 21.5 + - - -
161B LEU* 3.4 12.5 - - + +
347B VAL* 5.8 0.5 - - - +
348B ARG* 2.9 49.9 + - - +
349B ALA 4.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B CYS 3.3 11.3 + - - +
123B GLY* 3.6 23.4 - - - +
149B ASP 3.5 0.4 - - - -
150B ASP* 1.3 76.1 - - - +
152B ASN* 1.3 71.4 + - - +
154B PHE* 3.4 21.4 + - + -
155B LEU* 3.2 37.3 + - + +
176B TRP* 3.6 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ASP* 3.4 35.0 + - - +
151B LEU* 1.3 85.6 - - - +
153B ALA* 1.3 66.0 + - - +
155B LEU* 3.4 8.4 + - - +
156B HIS* 3.2 49.0 + - + +
157B ARG* 3.8 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ASP* 2.8 19.0 + - + +
150B ASP* 3.7 10.8 - - - +
151B LEU 3.3 0.2 - - - -
152B ASN* 1.3 76.3 - - - +
154B PHE* 1.3 56.7 + - - +
157B ARG* 2.8 58.6 + - - +
161B LEU* 3.9 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B CYS* 3.3 33.9 - - + -
150B ASP 3.2 17.2 + - - -
151B LEU* 3.4 24.4 + - + -
153B ALA* 1.3 73.9 - - - +
155B LEU* 1.3 74.5 - - + +
156B HIS 3.5 0.2 + - - -
158B ALA* 3.6 22.5 - - + +
161B LEU* 3.6 17.0 - - + +
173B MSE 4.9 0.9 - - + -
175B ILE* 3.7 26.7 - - + -
176B TRP* 3.4 50.7 - + - -
177B PRO* 3.8 23.1 - - + -
201B PRO* 3.7 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 3.2 40.1 + - + +
152B ASN* 4.3 11.4 - - - +
153B ALA 3.3 0.2 - - - -
154B PHE* 1.3 95.0 - - + +
156B HIS* 1.3 85.9 + - + +
177B PRO* 5.1 10.8 - - + +
180B PRO* 5.3 12.3 - - + -
201B PRO* 4.6 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ASN* 3.2 40.7 + - + +
154B PHE 3.3 0.6 - - - -
155B LEU* 1.3 102.1 + - + +
157B ARG* 1.4 77.3 + - + +
158B ALA 3.7 2.2 - - - -
204B LYS* 3.4 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ASP* 3.4 30.1 + - - +
152B ASN* 3.8 16.8 + - - +
153B ALA* 2.8 42.8 + - + +
156B HIS* 1.4 84.3 - - + +
158B ALA* 1.4 60.8 + - - +
159B ASP* 3.4 10.3 - - - -
160B GLU* 3.2 41.6 + - + +
161B LEU* 3.3 10.6 + - - +
204B LYS* 5.0 0.4 - - - +
----------------------------------------------------------
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