Contacts of the helix formed by residues 195 - 206 (chain D) in PDB entry 6Q2J
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 195 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D SER* 5.3 1.0 + - - -
192D ALA* 3.4 21.3 + - + +
193D GLN 3.3 1.6 - - - -
194D SER* 1.3 76.6 + - - +
196D ILE* 1.3 60.9 + - - +
197D PRO* 3.3 18.8 - - - +
198D CYS* 3.7 22.5 - - - +
199D GLN* 3.3 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 196 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B THR 5.7 5.4 - - - +
193D GLN 5.8 0.2 - - - +
194D SER 3.0 10.1 + - - +
195D ASP* 1.3 71.6 + - - +
197D PRO* 1.4 70.3 - - + +
199D GLN* 3.5 18.9 + - + +
200D GLN* 2.9 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 197 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B GLY* 5.6 3.6 - - - -
292B VAL* 3.7 35.2 - - + +
132D LEU* 4.8 17.9 - - + -
195D ASP* 3.3 16.2 - - - +
196D ILE* 1.4 96.6 - - + +
198D CYS* 1.3 58.9 + - - +
200D GLN* 3.2 7.8 + - + +
201D SER* 2.9 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 198 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D SER* 3.3 15.5 - - - +
131D CYS* 4.1 2.3 - - - +
132D LEU* 3.7 22.2 - - + +
191D CYS* 2.0 50.5 - - - -
195D ASP* 3.7 28.9 - - - +
197D PRO* 1.3 78.2 - - - +
199D GLN* 1.3 62.4 + - - +
201D SER* 3.1 9.6 + - - -
202D LYS* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 199 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D CYS* 4.3 9.6 - - + -
192D ALA 5.1 0.2 - - - -
193D GLN* 3.0 52.3 + - - +
195D ASP 3.3 15.9 + - - +
196D ILE* 3.5 19.2 + - + +
197D PRO 3.3 0.2 - - - -
198D CYS* 1.3 84.7 - - - +
200D GLN* 1.3 58.4 + - - +
202D LYS* 3.5 23.8 + - - +
203D GLU* 2.8 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B THR* 5.0 11.1 - - - +
291B GLY* 5.9 0.7 - - - -
292B VAL 3.4 26.8 - - - +
293B SER* 6.0 0.6 - - - -
196D ILE* 2.9 30.3 + - + +
197D PRO* 3.5 8.3 - - + +
199D GLN* 1.3 77.5 - - - +
201D SER* 1.3 61.1 + - - +
203D GLU* 2.9 27.5 + - - +
204D ALA* 4.0 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ILE* 6.4 0.2 - - - -
292B VAL* 4.6 11.4 + - - -
294B LEU* 4.3 17.3 - - - -
131D CYS 4.2 3.3 + - - -
132D LEU* 4.1 23.3 + - - +
135D ALA* 5.0 7.4 - - - -
197D PRO 2.9 14.7 + - - -
198D CYS* 3.1 16.3 + - - -
200D GLN* 1.3 73.7 - - - +
202D LYS* 1.3 57.4 + - - +
203D GLU 3.3 0.2 - - - -
204D ALA* 3.0 10.7 + - - +
205D LEU* 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D CYS* 3.7 30.5 - - - -
189D CYS 4.6 6.7 - - - +
190D ASP* 4.8 14.9 + - - +
191D CYS* 5.0 11.5 + - - +
198D CYS 2.9 17.5 + - - +
199D GLN* 3.5 22.9 - - - +
200D GLN 3.2 0.4 - - - -
201D SER* 1.3 77.4 + - - +
203D GLU* 1.3 61.1 + - - +
205D LEU* 4.6 1.3 - - - +
206D HIS* 3.3 39.5 + - + +
208D LYS* 3.7 24.0 - - + +
313D ARG* 5.3 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D GLN* 2.8 37.8 + - - +
200D GLN* 2.9 29.0 + - - +
201D SER 3.3 0.4 - - - -
202D LYS* 1.3 79.8 - - - +
204D ALA* 1.3 56.9 + - - +
207D SER* 3.4 5.8 - - - -
208D LYS* 3.1 51.5 + - + +
209D THR* 4.4 17.9 + - + +
213D ASN* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B SER* 6.0 0.9 - - - -
294B LEU* 3.9 35.0 - - + +
151D TYR* 4.5 0.7 - - - -
152D LEU* 3.8 23.4 - - + +
200D GLN 4.0 2.8 + - - +
201D SER* 3.0 14.7 + - - +
203D GLU* 1.3 79.6 - - - +
205D LEU* 1.3 65.8 + - - +
207D SER* 3.6 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LEU* 4.1 18.2 - - + -
131D CYS* 3.4 34.3 - - + +
134D VAL* 4.1 13.9 - - + -
135D ALA* 3.7 31.0 - - + +
138D CYS* 5.8 1.6 - - + -
148D LEU* 4.8 17.8 - - + +
151D TYR* 3.3 21.5 + - - -
174D PHE* 6.1 0.2 - - - -
175D TYR* 5.6 0.3 + - - -
186D LEU* 4.6 29.8 - - + +
189D CYS* 5.1 2.7 - - - -
201D SER* 2.9 18.7 + - - +
202D LYS* 4.6 0.4 - - - +
204D ALA* 1.3 78.3 - - - +
206D HIS* 1.3 69.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D CYS* 4.2 0.4 - - - -
151D TYR* 3.7 4.1 + - - -
175D TYR* 5.0 9.2 - - - -
186D LEU* 3.3 20.1 + - + -
187D ALA* 4.2 12.6 + - - -
189D CYS* 3.6 33.8 - - - -
202D LYS* 3.3 33.7 + - + +
205D LEU* 1.3 82.7 - - + +
207D SER* 1.3 72.7 + - - +
208D LYS* 3.6 14.8 + - + -
211D ALA* 4.4 0.2 - - - +
212D VAL* 4.1 4.6 - - + +
283D LEU* 6.2 3.4 - - + -
288D GLN* 3.7 27.1 + - - +
313D ARG* 4.2 9.3 + - - -
----------------------------------------------------------
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