Contacts of the helix formed by residues 163 - 174 (chain D) in PDB entry 5JKL
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 163 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D MET 4.5 2.7 + - - -
159D GLY* 3.1 21.1 + - - -
160D ALA* 4.2 1.0 - - - -
161D PRO 3.8 6.2 - - - +
162D ARG* 1.3 76.0 - - - +
164D GLY* 1.3 62.7 + - - +
165D LEU* 3.5 12.1 - - - +
166D ALA* 2.8 39.1 + - - +
167D GLU* 3.5 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 5.7 0.5 - - - +
161D PRO 4.8 3.6 - - - -
162D ARG 3.4 7.3 + - - -
163D SER* 1.3 73.4 - - - +
165D LEU* 1.4 53.4 + - - +
167D GLU* 3.4 7.9 + - - +
168D TYR* 2.9 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D SER* 3.5 8.5 - - - +
164D GLY* 1.4 73.6 - - - +
166D ALA* 1.4 59.0 + - - +
168D TYR* 3.3 13.5 + - + +
169D LEU* 2.9 61.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D LEU* 4.6 1.8 - - + +
158D MET* 3.4 48.9 - - + +
160D ALA* 3.8 17.3 - - + +
163D SER* 2.8 24.4 + - - +
165D LEU* 1.4 72.3 - - - +
167D GLU* 1.3 63.3 + - - +
169D LEU* 4.8 1.3 - - - -
170D PHE* 3.0 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 4.2 19.8 - - + +
51D PHE* 3.8 7.2 - - + -
95D SER* 3.5 14.0 - - - -
96D GLY* 2.8 29.0 + - - -
97D LEU* 2.9 30.9 + - - +
155D LEU* 4.1 12.3 - - + -
160D ALA* 3.7 19.5 - - + +
161D PRO* 3.9 7.2 - - - +
163D SER 3.5 7.1 + - - +
164D GLY* 3.4 10.3 + - - +
165D LEU 3.3 0.4 - - - -
166D ALA* 1.3 76.8 - - - +
168D TYR* 1.3 62.0 + - - +
170D PHE* 3.4 0.3 + - - +
171D ASP* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ALA 6.1 0.4 - - - -
48D LEU* 4.0 15.3 - - + +
164D GLY 2.9 18.0 + - - +
165D LEU* 3.6 14.6 - - + +
167D GLU* 1.3 77.2 - - - +
169D LEU* 1.3 82.7 + - + +
171D ASP 3.3 0.9 + - - -
172D LYS* 3.1 75.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D MET* 4.0 16.8 - - + -
165D LEU* 2.9 45.9 + - + +
166D ALA* 5.1 0.7 - - - +
168D TYR* 1.3 98.0 - - + +
170D PHE* 1.3 58.1 + - - +
172D LYS* 3.3 1.2 + - + -
173D HIS* 2.9 59.7 + - + +
205D CL 4.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D PHE* 3.7 23.6 - + - -
100D MET* 4.5 2.0 - - + -
151D HIS* 3.6 34.5 - + + -
154D ASN* 3.8 23.3 - - + -
155D LEU* 3.6 22.4 - - + -
158D MET* 3.9 23.2 - - - +
166D ALA 3.0 17.9 + - - +
167D GLU 3.8 1.8 - - - +
169D LEU* 1.3 72.7 - - - +
171D ASP* 1.3 64.3 + - - +
173D HIS* 4.5 0.9 - - - +
174D THR* 2.9 55.9 + - + +
175D LEU* 3.2 31.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 3.3 18.8 - - + -
49D LYS* 4.2 2.9 + - - +
50D ASN* 3.0 56.8 + - - +
51D PHE* 3.0 28.5 + - + -
167D GLU 2.9 18.6 + - - +
168D TYR 3.4 5.2 - - - +
170D PHE* 1.3 77.4 - - - +
172D LYS* 1.3 85.9 + - - +
175D LEU* 3.6 5.0 + - - -
176D GLY 3.2 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 172 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ALA 5.7 1.0 + - - -
48D LEU* 4.6 4.0 - - - +
50D ASN* 4.3 7.4 - - - +
168D TYR* 3.1 69.4 + - + +
169D LEU* 3.7 5.4 - - - +
170D PHE 3.2 0.2 - - - -
171D ASP* 1.3 108.1 + - - +
173D HIS* 1.3 76.2 + - + +
176D GLY 3.5 21.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D LEU* 2.9 47.8 + - + +
170D PHE* 5.2 0.7 - - - -
172D LYS* 1.3 84.8 - - + +
174D THR* 1.3 65.7 + - - +
176D GLY 4.7 1.8 - - - -
202D FE 2.3 30.6 - - - -
205D CL 3.2 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D HIS* 3.8 20.4 - - + +
154D ASN* 5.8 1.6 - - - +
170D PHE* 2.9 52.3 + - + -
173D HIS* 1.3 83.1 + - - +
175D LEU* 1.3 65.1 + - + +
176D GLY 3.3 2.4 + - - -
----------------------------------------------------------
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