Contacts of the helix formed by residues 250 - 258 (chain A) in PDB entry 3L2P
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 250 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A CYS* 1.3 79.0 - - - +
251A PRO* 1.4 69.4 - - - +
252A ASP* 3.0 45.3 + - - +
253A ASP* 3.2 34.8 + - - +
254A MET* 3.9 4.0 + - - +
270A PHE* 4.7 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A VAL* 4.2 12.8 - - + +
241A LYS* 5.5 3.1 - - - -
244A SER* 3.8 25.8 - - - +
249A CYS 3.6 8.2 - - - +
250A ASN* 1.4 89.2 - - - +
252A ASP* 1.3 66.0 + - - +
253A ASP 3.3 0.4 - - - -
254A MET* 3.8 9.8 + - + +
255A ALA* 3.4 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ASN* 3.0 19.9 + - - +
251A PRO* 1.3 81.0 - - - +
253A ASP* 1.3 67.9 + - - +
255A ALA* 3.2 8.5 + - - +
256A ARG* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ASN* 3.2 35.3 + - - +
252A ASP* 1.3 77.3 - - - +
254A MET* 1.3 64.5 + - - +
256A ARG* 3.2 9.8 + - - +
257A ASP* 3.0 21.0 + - - +
270A PHE* 3.7 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A VAL* 3.7 48.7 - - + +
243A PHE* 4.3 5.2 - - + -
244A SER* 4.2 10.3 - - - -
247A PHE* 5.1 1.3 - - + -
249A CYS* 4.2 21.1 - - - -
250A ASN 3.9 2.4 + - - +
251A PRO* 3.8 5.1 + - - +
252A ASP 3.4 0.2 - - - -
253A ASP* 1.3 78.5 - - - +
255A ALA* 1.3 55.7 + - - +
257A ASP* 3.1 8.0 + - - +
258A LEU* 2.8 31.8 + - - +
266A THR* 3.8 9.2 - - + +
267A ILE* 3.4 33.4 - - + -
270A PHE* 3.7 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A VAL* 4.7 4.4 - - + +
251A PRO 3.4 12.7 + - - +
252A ASP* 3.2 13.8 + - - +
253A ASP 3.2 0.8 - - - -
254A MET* 1.3 76.2 - - - +
256A ARG* 1.3 64.1 + - - +
258A LEU* 3.1 27.0 + - + +
259A GLU* 3.6 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASP 3.2 11.2 + - - +
253A ASP* 3.2 11.0 + - - +
255A ALA* 1.3 78.0 - - - +
257A ASP* 1.3 57.5 + - - +
259A GLU* 3.1 48.5 + - - +
260A GLN* 3.5 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ASP 3.0 12.6 + - - +
254A MET* 3.1 11.9 + - - +
256A ARG* 1.3 74.1 - - - +
258A LEU* 1.3 57.7 + - - +
259A GLU 2.9 5.6 - - - -
260A GLN* 3.0 33.1 + - - +
261A GLY 4.3 0.9 + - - -
262A ASP 5.2 0.2 + - - -
265A GLU* 4.8 1.6 - - - +
266A THR* 2.6 50.3 + - + +
269A VAL* 5.0 8.4 - - - +
270A PHE* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ASP* 3.8 31.3 - - + +
237A LYS* 4.7 2.5 - - - +
240A VAL* 3.8 22.9 - - + -
254A MET 2.8 14.1 + - - +
255A ALA* 3.1 19.0 + - + +
257A ASP* 1.3 76.1 - - - +
259A GLU* 1.3 57.3 + - - +
260A GLN 3.2 0.4 - - - -
261A GLY* 3.1 20.2 + - - +
262A ASP 4.6 2.0 - - - +
263A VAL* 4.0 42.0 - - + +
266A THR* 4.1 7.9 - - + +
612A TYR* 5.6 0.7 - - - +
614A GLN* 5.6 3.1 + - - +
----------------------------------------------------------
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