Contacts of the helix formed by residues 202 - 214 (chain A) in PDB entry 3C9G
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 SER 202 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 4.6 0.9 - - - -
200A THR 4.1 0.4 + - - -
201A GLU* 1.3 72.1 - - - +
203A GLU* 1.3 65.3 + - - +
204A ASP* 3.3 15.6 + - - +
205A LYS* 3.4 32.1 + - - +
206A VAL* 3.2 26.2 + - - +
200B THR 3.0 13.2 + - - -
202B SER* 4.4 13.8 - - - +
205B LYS* 4.6 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 4.3 18.3 - - + +
201A GLU 3.8 2.8 + - - -
202A SER* 1.3 69.8 + - - +
204A ASP* 1.3 67.7 + - - +
206A VAL 3.4 1.0 + - - -
207A LEU* 3.1 36.4 + - + +
221A ILE* 3.6 33.7 - - + +
205B LYS* 5.3 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A SER* 3.3 8.4 + - - +
203A GLU* 1.3 83.7 + - - +
205A LYS* 1.3 67.6 + - + +
207A LEU* 3.4 5.4 + - - +
208A LYS* 3.0 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A SER* 3.4 23.4 + - - +
203A GLU 3.4 0.4 - - - -
204A ASP* 1.3 85.5 - - - +
206A VAL* 1.3 62.7 + - - +
208A LYS* 3.4 6.4 + - - +
209A ALA* 3.0 24.7 + - - +
273A THR* 4.7 5.1 - - + +
199B PRO 3.2 23.6 - - - +
200B THR* 4.1 16.6 - - + +
201B GLU 3.9 19.1 + - - +
202B SER* 5.0 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A THR* 4.4 7.2 - - + -
196A LYS 4.7 0.7 - - - +
197A ILE* 3.9 29.4 - - + -
201A GLU* 4.1 24.0 - - + +
202A SER 3.2 18.1 + - - +
203A GLU 3.9 3.1 - - - +
205A LYS* 1.3 76.8 - - - +
207A LEU* 1.3 65.8 + - + +
209A ALA* 3.2 9.2 + - - +
210A ILE* 3.0 37.0 + - + +
227A VAL* 4.7 0.7 - - + -
269A LYS* 4.0 18.2 - - + -
200B THR* 4.1 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 4.0 22.4 - - + -
203A GLU* 3.1 36.4 + - + +
204A ASP* 3.9 5.4 - - - +
206A VAL* 1.3 80.6 - - + +
208A LYS* 1.3 58.9 + - + +
210A ILE* 3.2 10.9 + - + +
211A ARG* 2.9 53.1 + - - +
219A ILE* 4.4 26.5 - - + +
221A ILE* 4.1 15.3 - - + -
227A VAL* 5.1 1.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
204A ASP* 3.0 51.8 + - - +
205A LYS* 3.9 6.5 - - + +
207A LEU* 1.3 72.8 - - + +
209A ALA* 1.3 61.5 + - - +
211A ARG* 3.5 7.5 - - - +
212A ASN* 2.7 43.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
205A LYS 3.0 14.9 + - - +
206A VAL* 3.3 12.6 - - - +
208A LYS* 1.3 78.8 - - - +
210A ILE* 1.3 62.8 + - + +
212A ASN* 3.3 14.9 + - - +
213A ILE* 3.5 11.1 - - - +
269A LYS* 3.8 27.8 - - + +
272A ALA* 3.7 17.9 - - + +
273A THR* 3.8 17.7 - - + +
289A ILE* 5.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ILE* 4.0 25.6 - - + -
195A THR* 4.2 2.0 - - + -
206A VAL* 3.0 39.3 + - + +
207A LEU* 3.5 7.4 - - + +
209A ALA* 1.3 76.8 - - - +
211A ARG* 1.3 57.2 + - - +
213A ILE* 3.2 10.9 + - - +
214A PHE* 3.0 24.5 + - + +
217A ALA* 4.2 11.4 - - + -
219A ILE* 3.7 24.9 - - + -
227A VAL* 4.1 24.0 - - + -
289A ILE* 3.6 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 2.9 39.3 + - - +
208A LYS* 3.1 7.1 + - - +
210A ILE* 1.3 71.4 - - - +
212A ASN* 1.3 62.4 + - - +
213A ILE 3.1 2.2 - - - -
214A PHE 3.3 17.0 - - - +
215A PRO* 3.0 39.6 + - + +
217A ALA* 2.9 35.4 + - + +
218A GLU* 4.5 0.8 + - - +
219A ILE* 3.9 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LYS* 2.7 33.1 + - - +
209A ALA* 3.5 2.8 - - - +
210A ILE 3.2 0.6 - - - -
211A ARG* 1.3 74.2 - - - +
213A ILE* 1.3 59.4 + - + +
236A ARG* 3.1 29.7 + - - +
240A LEU* 3.8 5.9 - - - +
272A ALA 2.9 28.8 + - - +
273A THR* 3.1 23.6 + - - +
274A VAL* 4.5 0.4 - - - +
275A SER* 3.7 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ALA 3.5 15.5 - - - +
210A ILE* 3.2 6.5 + - - +
212A ASN* 1.3 82.9 - - - +
214A PHE* 1.3 92.6 - - + +
215A PRO* 3.7 1.8 - - - -
233A SER 5.3 0.2 - - - +
236A ARG* 3.3 20.8 - - - +
237A PHE* 3.7 26.2 + - + -
240A LEU* 4.5 2.9 - - + -
267A LEU* 3.9 17.3 - - + -
272A ALA* 4.0 24.7 - - + -
275A SER* 4.7 4.5 - - - -
276A ARG 5.1 1.3 - - - +
277A ILE* 3.8 28.7 - - + -
289A ILE* 6.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE* 4.1 15.9 - - + -
193A ILE* 3.9 24.9 - - + -
210A ILE* 3.0 12.2 + - + +
211A ARG* 3.3 14.3 - - - -
213A ILE* 1.3 107.5 - - + +
215A PRO* 1.3 66.6 - - - +
216A ASP* 3.1 7.4 + - - +
217A ALA* 3.1 15.7 + - + +
231A ALA* 3.7 28.0 - - + -
233A SER 3.9 16.6 - - - -
234A LEU* 5.1 1.1 - - - -
237A PHE* 4.0 22.7 - + + -
265A ILE* 6.2 0.4 - - + -
267A LEU* 4.9 2.7 - - + -
289A ILE* 5.8 2.5 - - + -
291A VAL* 4.2 26.5 - - + -
293A PHE* 4.2 10.8 - + - -
----------------------------------------------------------
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