Contacts of the helix formed by residues 207 - 214 (chain A) in PDB entry 2DW1
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 207 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A VAL 4.1 0.8 + - - -
206A VAL* 1.3 77.9 - - - +
208A LYS* 1.3 61.1 + - - +
209A ALA* 3.2 18.0 + - - +
210A MET* 2.9 28.1 + - - +
211A VAL* 3.4 8.0 + - - +
251A TRP* 4.2 5.6 - - + -
255A ASP* 3.3 14.2 - - - +
259A VAL* 4.0 20.2 - - + +
289A LEU* 4.2 7.4 - - + +
290A LEU 3.0 11.5 + - - +
291A THR* 2.5 38.6 + - - -
293A ILE* 4.2 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASP* 1.3 67.5 - - - +
209A ALA* 1.3 65.7 + - - +
210A MET 3.1 0.2 - - - -
211A VAL* 3.2 8.9 + - + -
212A THR* 3.0 32.2 + - - +
251A TRP 3.3 18.3 + - - +
252A SER 3.3 16.7 + - - +
253A ASN* 2.6 30.6 + - - +
254A GLU* 4.2 7.5 - - + +
255A ASP* 2.7 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASP* 3.1 20.2 - - - +
208A LYS* 1.3 79.1 - - - +
210A MET* 1.3 57.7 + - - +
212A THR* 3.5 5.5 + - - -
213A LYS* 3.0 27.5 + - - +
255A ASP* 4.7 2.8 + - - +
292A ALA* 3.5 18.3 - - + +
293A ILE* 3.9 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A VAL* 3.4 29.8 - - + -
207A ASP* 2.9 13.2 + - - +
209A ALA* 1.3 75.2 - - - +
211A VAL* 1.3 66.2 + - - +
213A LYS* 3.3 2.1 + - + +
214A ASN* 3.0 43.3 + - - +
221A ILE* 4.5 7.2 - - + -
224A ARG* 5.0 6.5 - - - +
225A MET* 4.8 3.6 - - - -
290A LEU* 3.3 46.0 - - + -
291A THR* 4.1 1.1 - - - -
292A ALA* 3.6 27.6 - - + +
319A ASP* 3.5 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A VAL* 4.5 3.6 - - + -
207A ASP 3.9 10.8 - - - +
208A LYS* 3.2 11.8 + - + +
210A MET* 1.3 76.7 - - - +
212A THR* 1.3 63.9 + - - +
214A ASN* 3.1 7.3 + - - +
216A GLY* 2.8 43.8 + - - -
218A LEU* 4.2 7.4 - - + -
221A ILE* 4.7 7.9 - - + -
250A ILE* 3.4 32.5 - - + -
251A TRP 4.4 0.4 - - - -
252A SER* 3.8 33.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LYS* 3.0 30.0 + - - +
209A ALA* 3.8 5.7 - - - -
211A VAL* 1.3 77.0 - - - +
213A LYS* 1.3 66.0 + - - +
215A ASN* 2.8 17.0 + - - +
216A GLY 4.7 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ALA 3.0 18.6 + - - +
210A MET* 3.3 6.5 + - - +
212A THR* 1.3 76.3 - - - +
214A ASN* 1.3 63.3 + - - +
215A ASN* 3.5 2.8 + - - +
292A ALA* 3.8 19.8 + - + +
319A ASP* 3.1 47.0 + - - +
320A TYR 5.6 0.4 + - - -
321A SER* 6.2 1.2 - - - +
322A GLU* 4.2 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A MET* 3.0 32.3 + - - +
211A VAL 3.8 2.2 - - - +
212A THR 3.0 0.4 - - - -
213A LYS* 1.3 84.8 - - - +
215A ASN* 1.3 69.6 + - - +
216A GLY 3.1 1.6 - - - +
217A ASP* 3.0 20.2 + - - +
220A LYS* 3.6 30.2 + - + +
221A ILE* 3.0 38.6 - - + +
224A ARG* 5.4 7.1 + - - +
319A ASP* 4.8 2.4 + - - -
322A GLU* 4.6 12.6 + - - +
----------------------------------------------------------
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