Contacts of the helix formed by residues 205 - 216 (chain A) in PDB entry 3SJN
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 THR 205 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TRP 2.6 12.4 + - - +
204A HIS* 1.3 79.0 - - + +
206A CYS* 1.3 73.0 + - - +
207A GLY* 3.6 5.8 + - - -
208A HIS* 3.8 25.6 - - + +
209A SER* 3.1 28.1 + - - -
228A VAL* 3.7 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A THR* 1.3 78.3 + - - +
207A GLY* 1.3 55.7 + - - +
209A SER* 3.6 4.2 + - - -
210A ALA* 3.2 23.4 + - - +
228A VAL* 4.2 5.1 - - - +
235A SER* 3.8 40.3 + - - +
238A LYS* 4.0 24.5 - - + -
239A LEU* 3.4 19.2 - - - +
242A GLN* 4.9 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A THR* 3.3 7.5 + - - -
206A CYS* 1.3 76.9 - - - +
208A HIS* 1.3 64.7 + - - +
210A ALA* 3.4 5.2 + - - +
211A MET* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLY 4.0 12.1 - - - -
173A ASP 5.7 0.4 - - - -
175A PRO* 3.7 29.5 - - + +
178A ASP* 5.1 0.9 - - - -
202A LYS 5.2 0.4 - - - -
203A TRP* 3.4 55.2 + + - +
204A HIS* 5.3 3.6 - + - -
205A THR* 3.6 15.3 + - + +
206A CYS 3.5 0.4 - - - -
207A GLY* 1.3 75.3 - - - +
209A SER* 1.3 61.4 + - - +
211A MET* 4.0 5.7 - - + +
212A MET* 3.2 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TRP* 3.3 39.6 - - - +
205A THR 3.1 17.2 + - - -
206A CYS 3.8 0.7 - - - -
207A GLY 3.3 0.2 - - - -
208A HIS* 1.3 79.4 - - - +
210A ALA* 1.3 60.4 + - - +
212A MET 3.6 0.2 + - - -
213A ALA* 3.2 24.6 + - - +
227A PRO* 3.4 14.0 - - - +
228A VAL* 3.7 4.0 - - - +
239A LEU* 3.8 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A CYS 3.2 17.2 + - - +
207A GLY* 3.4 6.0 + - - +
208A HIS 3.4 0.4 - - - -
209A SER* 1.3 73.9 - - - +
211A MET* 1.3 64.2 + - - +
213A ALA* 3.4 10.4 + - - +
214A LYS* 3.4 14.9 + - - +
239A LEU* 3.7 14.1 - - + +
242A GLN* 4.6 21.2 - - + +
243A VAL* 4.3 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLY 3.2 17.1 + - - +
208A HIS* 4.0 8.1 - - + +
209A SER 3.4 0.2 - - - -
210A ALA* 1.3 79.0 - - - +
212A MET* 1.3 62.9 + - + +
213A ALA 3.5 0.2 + - - -
214A LYS* 3.7 13.8 + - + +
215A ARG* 3.4 57.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PRO* 3.7 35.9 - - - +
178A ASP* 3.6 28.7 - - + +
179A TYR* 4.5 1.3 - - + +
203A TRP* 3.6 30.3 - - + +
208A HIS* 3.2 37.1 + - + +
211A MET* 1.3 81.7 - - + +
213A ALA* 1.3 59.0 + - - +
215A ARG* 3.6 14.3 + - + +
216A LEU* 3.2 50.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TRP* 4.6 2.4 - - + -
209A SER 3.2 18.3 + - - +
210A ALA 3.7 1.6 - - - +
211A MET 3.3 0.6 - - - -
212A MET* 1.3 76.6 - - - +
214A LYS* 1.3 60.3 + - - +
216A LEU* 3.4 2.0 + - - -
217A GLU* 3.1 15.8 + - - +
224A ILE* 4.0 13.7 - - + -
243A VAL* 3.5 28.0 - - + -
245A GLN* 2.8 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ALA 3.4 12.6 + - - +
211A MET* 3.7 13.9 + - + +
212A MET 3.5 0.2 - - - -
213A ALA* 1.3 78.1 - - - +
215A ARG* 1.3 63.0 + - + +
217A GLU* 3.3 38.6 + - - +
218A GLU* 4.8 0.9 + - - +
242A GLN 5.0 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PRO* 6.3 1.3 - - - -
179A TYR* 3.3 30.2 - - + -
211A MET* 3.4 48.9 + - + +
212A MET* 3.9 17.5 - - + +
213A ALA 3.3 0.4 - - - -
214A LYS* 1.3 81.8 - - + +
216A LEU* 1.3 58.8 + - + +
217A GLU 3.3 1.4 + - - -
218A GLU* 3.7 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A MET* 6.0 0.4 - - + -
178A ASP* 5.2 0.9 - - + +
179A TYR* 3.8 34.1 - - + -
182A VAL* 3.8 32.8 - - + -
197A ILE* 4.2 6.1 - - + -
203A TRP* 4.1 18.8 - - + -
212A MET* 3.2 36.5 + - + +
213A ALA* 3.4 6.3 + - - +
214A LYS 3.3 0.2 - - - -
215A ARG* 1.3 74.5 - - - +
217A GLU* 1.3 63.2 + - - +
218A GLU 3.2 2.9 - - - -
219A PHE* 3.3 24.9 + - + +
220A ASN 4.1 2.1 + - - -
221A LEU* 4.1 31.4 + - + +
224A ILE* 6.1 0.4 - - + -
245A GLN* 4.3 2.9 + - - +
----------------------------------------------------------
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