Contacts of the helix formed by residues 195 - 206 (chain D) in PDB entry 3P05
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 195 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D GLN* 2.9 37.8 + - - +
156D GLY 3.2 28.5 + - - +
157D PRO* 3.3 22.1 + - + -
158D LYS* 5.2 0.2 - - - +
159D GLU 4.2 2.0 + - - -
194D ALA* 1.3 72.4 - - - +
196D PRO* 1.3 65.8 - - + +
197D ASP* 3.5 10.4 + - - +
198D CYS* 3.0 23.1 + - - +
199D LYS* 2.7 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 196 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D PRO* 5.9 1.3 - - + -
194D ALA 3.8 1.3 - - - +
195D ASN* 1.3 89.2 - - + +
197D ASP* 1.3 68.1 + - - +
199D LYS* 3.7 10.3 - - + +
200D THR* 3.0 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 197 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D PRO 5.4 3.5 - - - +
195D ASN* 3.4 10.8 + - - +
196D PRO* 1.3 81.6 - - - +
198D CYS* 1.3 63.9 + - - +
200D THR* 3.5 5.6 - - - +
201D ILE* 3.2 30.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
155D GLN* 3.5 34.8 - - - +
161D PHE* 4.3 5.4 - - + -
194D ALA* 4.3 4.7 - - + -
195D ASN* 3.0 15.9 + - - +
197D ASP* 1.3 76.6 - - - +
199D LYS* 1.3 60.1 + - - +
200D THR 3.1 0.2 + - - -
201D ILE* 3.2 8.0 + - - +
202D LEU* 2.8 35.5 + - + +
218D CYS* 3.6 40.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 199 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D VAL* 3.7 13.8 - - + +
192D GLN* 3.1 49.4 + - - +
194D ALA* 3.9 18.9 + - + +
195D ASN 2.7 21.9 + - - +
196D PRO* 3.7 10.3 - - + +
198D CYS* 1.3 71.6 - - - +
200D THR* 1.3 57.3 + - - +
202D LEU* 3.4 6.2 + - - +
203D LYS* 3.1 49.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 200 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D PRO* 3.0 20.8 + - - +
197D ASP* 3.5 6.7 - - - +
198D CYS 3.1 0.2 - - - -
199D LYS* 1.3 75.7 - - - +
201D ILE* 1.3 68.2 + - + +
202D LEU 3.3 0.5 + - - -
203D LYS* 3.3 8.3 + - - +
204D ALA* 3.3 20.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D ASP* 3.2 18.4 + - + +
198D CYS* 3.2 12.8 + - - +
200D THR* 1.3 79.5 - - + +
202D LEU* 1.3 62.0 + - - +
204D ALA* 3.4 10.1 + - - +
205D LEU* 3.4 19.0 + - + +
217D ALA* 3.8 44.0 - - + +
218D CYS* 4.5 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D PHE* 3.8 29.6 - - + -
191D VAL* 3.9 25.2 - - + +
194D ALA* 4.1 10.5 - - + -
198D CYS 2.8 30.5 + - - +
199D LYS 3.8 3.8 - - - +
201D ILE* 1.3 74.3 - - - +
203D LYS* 1.3 66.8 + - - +
205D LEU* 3.3 24.8 + - + +
206D GLY 3.9 4.7 + - - +
214D MET* 3.8 44.4 - - + +
217D ALA* 4.9 0.9 - - + -
218D CYS* 3.6 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D VAL* 4.4 18.4 - - + +
192D GLN* 5.3 6.9 + - - +
199D LYS* 3.1 33.9 + - + +
200D THR* 3.3 7.4 + - - +
202D LEU* 1.3 74.8 - - - +
204D ALA* 1.3 62.6 + - - +
206D GLY* 3.1 15.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
200D THR* 3.3 9.9 + - + +
201D ILE* 3.5 12.8 - - - +
202D LEU 3.3 0.2 - - - -
203D LYS* 1.3 79.3 - - - +
205D LEU* 1.3 60.5 + - - +
206D GLY* 3.1 1.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
201D ILE* 3.4 10.4 + - + +
202D LEU* 3.3 17.6 + - + +
203D LYS 3.2 1.0 - - - -
204D ALA* 1.3 77.8 - - - +
206D GLY* 1.3 66.7 + - - +
207D PRO 4.7 1.9 - - - +
209D ALA* 4.2 13.3 - - + +
213D GLU* 4.1 10.1 - - + +
214D MET* 4.0 31.4 - - + +
217D ALA* 3.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D LEU 3.9 3.8 + - - +
203D LYS 3.1 13.0 + - - -
204D ALA 3.1 5.9 - - - -
205D LEU* 1.3 83.2 - - - +
207D PRO* 1.3 78.9 - - - +
209D ALA* 3.8 14.2 - - - +
----------------------------------------------------------
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