Contacts of the helix formed by residues 208 - 217 (chain A) in PDB entry 2PWZ
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 208 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLY* 5.6 2.4 - - - -
204A LYS* 2.9 52.3 + - - +
205A ARG* 3.6 2.9 - - - +
207A GLN* 1.3 84.6 - - - +
209A ALA* 1.3 63.6 + - - +
210A GLY 3.3 2.9 - - - -
211A THR* 3.0 32.9 + - - +
212A GLU* 3.6 4.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
153A ARG* 3.6 33.1 - - - +
157A PHE* 3.9 12.3 - - + -
205A ARG 3.0 15.7 + - - +
206A ILE 3.6 8.2 + - - +
207A GLN 3.7 0.4 - - - -
208A ASN* 1.3 77.2 - - - +
210A GLY* 1.3 62.5 + - - +
212A GLU* 3.0 25.7 - - - +
213A VAL* 3.6 2.1 + - - +
48C HIS* 3.4 18.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ARG* 3.5 24.1 - - - +
208A ASN 3.3 0.6 - - - -
209A ALA* 1.3 74.8 - - - +
211A THR* 1.3 65.4 + - - +
213A VAL* 2.9 17.0 + - - +
214A VAL* 3.1 18.4 + - - +
223A ALA* 5.4 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ASN* 3.0 26.2 + - - +
210A GLY* 1.3 73.3 - - - +
212A GLU* 1.3 53.1 + - - +
214A VAL* 3.2 10.3 + - + +
215A GLU* 2.8 54.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PHE* 4.6 0.6 - - - -
205A ARG* 3.0 44.6 + - - +
208A ASN 3.6 2.9 + - - +
209A ALA* 3.0 20.9 - - - +
211A THR* 1.3 78.9 - - - +
213A VAL* 1.3 57.7 + - - +
215A GLU* 4.0 7.2 - - - +
216A ALA* 3.3 22.2 + - - +
44C VAL* 3.9 15.9 - - + +
47C SER* 5.2 0.5 + - - -
48C HIS* 2.8 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ARG* 4.9 0.9 - - - +
209A ALA 4.0 3.1 - - - +
210A GLY 2.9 8.4 + - - +
212A GLU* 1.3 74.1 - - - +
214A VAL* 1.3 68.5 + - - +
216A ALA* 3.0 3.3 + - - +
217A LYS* 2.9 27.4 + - + +
222A SER 3.9 6.7 - - - +
223A ALA* 3.7 33.7 - - + +
41C GLY 3.7 18.6 - - - +
44C VAL* 3.9 5.8 - - + -
45C ASP* 3.8 31.0 - - + +
48C HIS* 3.8 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG* 3.7 27.4 - - - +
210A GLY 3.1 16.1 + - - +
211A THR* 3.5 11.7 - - + +
213A VAL* 1.3 77.9 - - - +
215A GLU* 1.3 62.4 + - + +
217A LYS* 3.3 5.5 + - - +
219A GLY* 2.9 34.1 + - - -
221A GLY 3.3 19.3 - - - +
222A SER* 4.3 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A THR* 2.8 39.5 + - + +
212A GLU* 4.2 6.8 + - - +
214A VAL* 1.3 76.9 - - + +
216A ALA* 1.3 61.1 + - - +
218A ALA* 3.2 13.5 + - - -
219A GLY 4.7 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLU 3.3 15.5 + - - +
213A VAL 3.0 3.1 + - - +
215A GLU* 1.3 74.9 - - - +
217A LYS* 1.3 56.5 + - - +
218A ALA* 3.1 10.0 + - - +
37C PRO 4.0 4.7 - - - +
40C PRO* 3.8 14.6 - - + +
41C GLY* 3.4 22.2 + - - +
44C VAL* 3.5 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A VAL* 2.9 20.4 + - + +
214A VAL 3.7 4.9 - - - +
215A GLU 3.2 0.4 - - - -
216A ALA* 1.3 75.6 - - - +
218A ALA* 1.3 59.5 + - - +
219A GLY 3.1 0.7 - - - -
220A GLY* 2.8 25.1 + - - -
221A GLY* 3.4 35.5 - - - +
222A SER 2.9 23.7 + - - +
224A THR* 4.1 12.9 + - - +
14C GLN* 4.9 6.9 + - - +
37C PRO* 4.1 2.9 - - - +
38C VAL* 3.7 30.2 + - + +
41C GLY* 3.4 31.2 - - - -
42C VAL* 3.9 17.3 - - - +
45C ASP* 4.2 4.3 + - - -
----------------------------------------------------------
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