Contacts of the helix formed by residues 156 - 167 (chain H) in PDB entry 3JCK
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 156 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A THR* 4.4 22.0 - - - -
421A TYR* 5.0 2.9 - - - -
422A MET* 4.6 12.1 - - - +
151H TRP* 3.0 53.9 + - - +
154H GLU* 3.6 7.1 + - - -
155H GLY* 1.3 74.9 - - - +
157H TYR* 1.3 63.3 + - - +
158H GLN* 3.6 2.5 - - - -
159H LYS* 4.3 9.5 + - - +
160H ALA* 4.1 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 157 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A TYR* 3.6 35.6 - + + +
425A ARG* 4.5 9.5 + - + -
428A ARG* 4.8 3.1 + - - -
152H LEU* 4.4 28.1 + - + -
155H GLY* 3.2 33.3 - - - -
156H SER* 1.3 71.5 - - - +
158H GLN* 1.3 58.2 + - - +
159H LYS 3.2 2.0 - - - -
160H ALA* 2.5 29.8 + - + +
161H TRP* 2.9 12.6 + - - -
185H ILE* 4.1 29.2 - - + -
188H GLU* 4.2 21.9 + - + +
189H ILE* 4.3 14.8 - - + -
192H ASN* 3.6 28.7 + - - -
210H PHE* 4.7 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 158 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A GLN* 3.5 20.9 + - + +
418A THR* 5.6 8.5 - - - +
421A TYR* 4.8 11.1 + - + -
156H SER* 3.6 1.4 - - - -
157H TYR* 1.3 77.5 - - - +
159H LYS* 1.3 64.5 + - + +
161H TRP* 3.4 13.6 + - - -
162H ASP* 2.9 57.7 + - - +
210H PHE* 3.2 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 159 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ASP* 6.4 2.4 - - - +
418A THR* 6.5 0.9 - - - -
147H LYS* 5.4 4.0 - - - +
151H TRP* 3.5 60.8 - - + +
156H SER* 4.3 8.6 + - - +
157H TYR 3.2 0.6 - - - -
158H GLN* 1.3 78.2 - - + +
160H ALA* 1.3 63.4 + - - +
162H ASP* 3.1 15.4 + - - +
163H LEU* 2.9 25.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H LEU* 4.7 14.8 - - + +
151H TRP* 4.2 17.1 - - + +
152H LEU* 4.9 8.7 - - + +
156H SER 4.1 1.4 + - - +
157H TYR* 2.5 24.3 + - + +
159H LYS* 1.3 72.2 - - - +
161H TRP* 1.3 55.9 + - - +
163H LEU* 2.7 33.7 + - - +
164H LEU* 2.9 15.3 + - + +
185H ILE* 4.5 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 161 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157H TYR 2.9 8.8 + - - +
158H GLN* 3.7 14.6 - - - +
160H ALA* 1.3 72.5 - - - +
162H ASP* 1.3 71.3 + - - +
164H LEU* 2.9 34.8 + - + +
165H GLN* 3.0 43.1 + - + +
182H LYS* 3.4 38.4 - - + -
185H ILE* 5.0 8.6 - - + +
186H ARG* 3.2 28.5 - - + -
210H PHE* 3.2 59.4 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 162 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158H GLN* 2.9 45.4 + - - +
159H LYS* 3.1 20.8 + - - +
160H ALA 3.0 0.2 - - - -
161H TRP* 1.3 81.5 - - - +
163H LEU* 1.3 61.6 + - + +
165H GLN* 2.9 19.4 + - - +
166H SER* 2.9 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144H TYR* 3.0 29.0 - - + +
147H LYS* 3.6 39.0 - - + -
148H LEU* 3.4 42.8 - - + +
151H TRP* 4.1 7.0 - - + -
159H LYS 2.9 15.2 + - - +
160H ALA* 2.7 17.1 + - - +
162H ASP* 1.3 73.2 - - + +
164H LEU* 1.3 53.6 + - - +
166H SER* 2.6 32.5 + - - +
167H GLY 2.9 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144H TYR* 3.7 16.7 + - - +
148H LEU* 4.0 17.9 - - + -
160H ALA 2.9 12.6 + - - +
161H TRP* 2.9 39.7 + - + +
163H LEU* 1.3 76.0 - - - +
165H GLN* 1.3 68.4 + - - +
166H SER 3.5 0.2 + - - -
167H GLY* 3.7 6.2 + - - -
168H SER* 4.8 1.9 + - - -
178H THR* 4.4 29.2 + - + +
181H LEU* 4.6 16.4 - - + -
182H LYS* 4.4 19.7 - - + +
185H ILE* 4.2 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 165 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161H TRP* 3.0 48.0 + - + +
162H ASP* 2.9 14.1 + - - +
164H LEU* 1.3 83.1 + - - +
166H SER* 1.3 57.3 + - - +
167H GLY 3.4 0.4 - - - -
168H SER* 3.1 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 166 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144H TYR* 4.1 5.2 - - - -
162H ASP* 2.9 14.0 + - - +
163H LEU* 2.6 29.4 + - - +
165H GLN* 1.3 71.7 - - - +
167H GLY* 1.3 56.2 + - - -
168H SER* 3.2 2.7 - - - -
169H GLN* 3.0 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 167 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144H TYR* 3.6 26.2 - - - -
163H LEU 2.9 7.7 + - - -
164H LEU 3.7 3.4 + - - -
165H GLN 3.4 1.0 - - - -
166H SER* 1.3 76.8 - - - +
168H SER* 1.3 62.9 + - - +
169H GLN* 3.2 2.7 + - - -
170H ASN* 3.4 5.3 + - - +
171H ILE 3.1 15.1 + - - -
174H PHE* 3.2 24.5 - - - -
175H ASP* 5.6 0.2 - - - -
----------------------------------------------------------
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