Contacts of the helix formed by residues 168 - 179 (chain L) in PDB entry 1IJ4
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 LYS 168 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L PHE* 4.1 21.8 - - - -
133L ILE* 5.7 0.4 - - - -
161L LYS* 4.7 11.7 - - + -
162L ILE 2.8 28.7 + - - +
163L LEU* 2.8 20.0 + - - +
165L THR* 2.8 35.8 + - + +
166L PHE* 3.5 8.2 + - - +
167L GLU* 1.4 87.7 + - + +
169L LEU* 1.3 62.7 + - - +
170L LYS 3.3 1.8 - - - +
171L ASP* 3.6 27.1 - - + +
172L LEU* 3.2 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L PHE* 3.7 24.7 - - + +
30L ASP* 4.3 19.5 - - + +
31L VAL* 3.5 44.0 - - + +
34L LYS* 4.1 17.9 - - + +
166L PHE 4.4 13.5 - - - +
167L GLU 2.9 7.2 + - - +
168L LYS* 1.3 75.2 - - - +
170L LYS* 1.4 58.5 + - - +
171L ASP 3.8 0.2 + - - -
173L PHE* 3.8 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 170 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L LYS* 5.7 3.6 - - - +
167L GLU* 2.7 51.1 + - + +
169L LEU* 1.4 76.6 - - - +
171L ASP* 1.3 70.5 + - - +
174L THR* 2.6 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 171 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161L LYS* 2.9 41.8 + - - +
167L GLU* 4.9 0.2 - - - +
168L LYS* 3.3 27.9 + - + +
170L LYS* 1.3 91.2 - - - +
172L LEU* 1.3 59.9 + - - +
173L PHE 3.1 1.2 + - - -
174L THR* 3.2 3.5 + - - -
175L GLU* 2.9 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L PHE* 4.1 9.2 - - + -
131L TYR* 3.7 33.2 - - + -
133L ILE* 3.5 29.4 - - + -
161L LYS* 3.7 24.0 - - + -
168L LYS* 3.2 33.2 + - + +
171L ASP* 1.3 85.1 + - - +
173L PHE* 1.3 82.9 + - + +
174L THR 3.7 0.2 - - - -
175L GLU* 3.4 10.4 - - - +
176L LEU* 3.3 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 173 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L LEU* 4.0 14.1 - - + -
27L PHE* 4.4 3.1 - + - -
31L VAL* 3.4 47.6 - - + -
34L LYS* 2.8 49.4 + - + -
35L LEU* 3.8 28.8 - - + +
109L ILE* 3.7 19.7 - - + -
133L ILE* 5.2 0.2 - - + -
169L LEU* 3.8 17.8 + - + +
171L ASP 3.3 0.8 - - - -
172L LEU* 1.3 109.2 - - + +
174L THR* 1.3 56.9 + - - +
176L LEU* 3.9 28.3 - - + +
177L GLN* 3.4 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 174 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L LYS* 4.8 7.1 + - - +
170L LYS* 2.6 29.8 + - - +
171L ASP 3.2 3.0 + - - -
173L PHE* 1.3 77.1 - - - +
175L GLU* 1.4 59.5 + - - +
176L LEU 3.5 0.2 - - - -
177L GLN* 3.2 13.8 + - + +
178L LYS* 3.0 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 175 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131L TYR* 2.5 36.9 + - - -
158L GLU* 4.6 4.7 - - - +
161L LYS* 2.8 27.6 + - - +
171L ASP* 2.9 23.6 + - - +
172L LEU* 3.4 17.2 - - - +
174L THR* 1.4 71.4 - - - +
176L LEU* 1.3 55.8 + - - +
178L LYS* 3.2 22.0 + - - +
179L LYS* 2.8 63.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4L VAL* 4.6 6.6 - - + +
6L LEU* 4.3 4.7 - - + -
40L TYR* 3.2 23.7 + - + +
105L THR* 5.9 3.4 - - + -
107L VAL* 4.1 30.1 - - + -
109L ILE* 6.1 0.2 - - + -
129L ILE* 4.9 7.0 - - + -
131L TYR* 3.4 42.2 - - + +
172L LEU* 3.3 19.6 + - + +
173L PHE* 3.9 24.9 - - + +
174L THR 3.5 0.4 - - - -
175L GLU* 1.3 72.5 - - - +
177L GLN* 1.3 58.1 + - - +
179L LYS* 4.6 11.6 + - + +
180L ILE* 3.5 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 177 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L LYS* 2.9 30.5 + - - -
35L LEU* 3.5 20.0 - - + +
38L THR* 5.5 7.9 - - - +
40L TYR* 3.6 10.5 + - + +
173L PHE 3.4 5.9 + - - +
174L THR* 3.2 15.0 + - + +
176L LEU* 1.3 75.6 - - - +
178L LYS* 1.4 62.3 + - - +
180L ILE* 3.4 18.8 + - - +
181L TYR* 4.1 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 178 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174L THR* 3.0 19.4 + - + +
175L GLU* 3.2 27.3 + - + +
177L GLN* 1.4 73.6 - - - +
179L LYS* 1.3 64.6 + - + +
180L ILE 3.3 1.1 - - - -
181L TYR* 2.9 50.0 + - + +
182L VAL* 2.7 51.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 179 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131L TYR* 3.3 12.1 + - - +
158L GLU* 2.8 43.8 + - - +
159L PHE* 4.2 7.9 - - + -
175L GLU* 2.8 61.8 + - - +
176L LEU* 4.6 10.9 - - + +
177L GLN 3.6 1.0 - - - -
178L LYS* 1.3 75.9 - - + +
180L ILE* 1.3 59.6 + - - +
181L TYR* 3.4 2.5 - - - -
182L VAL* 4.2 14.6 - - - +
----------------------------------------------------------
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