Contacts of the helix formed by residues 163 - 173 (chain C) in PDB entry 5LSW
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 ILE 163 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C TYR* 3.7 25.3 - - + +
123C LEU* 4.5 15.7 - - + -
143C ILE* 4.2 17.9 - - + -
158C LEU* 3.4 33.9 - - + +
159C LEU* 5.3 1.1 - - + -
161C THR* 3.2 11.8 + - - +
162C GLU* 1.3 76.9 - - - +
164C ILE* 1.3 65.7 + - + +
166C LEU* 3.3 6.2 + - + +
167C CYS* 2.9 46.8 + - - -
185C ILE* 4.3 11.4 - - + -
189C ILE* 3.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C LEU* 4.1 13.7 - - + -
161C THR 4.9 0.8 + - - +
163C ILE* 1.3 79.7 - - + +
165C PRO* 1.3 72.7 - - + +
167C CYS* 3.2 7.2 + - - +
168C LEU* 3.0 40.2 + - + +
186C LEU* 4.3 16.4 - - + -
189C ILE* 4.0 22.2 - - + -
198C TYR* 3.8 25.6 - - + -
199C ILE* 3.6 33.4 - - + -
205C ARG* 5.8 5.6 - - + -
209C VAL* 4.9 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C THR 5.4 0.7 - - - +
162C GLU* 3.3 30.7 - - + +
164C ILE* 1.3 98.0 - - + +
166C LEU* 1.3 59.4 + - - +
168C LEU* 3.8 10.2 - - + +
169C ARG* 3.1 23.2 + - - +
208C HIS* 5.3 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C TYR* 3.5 44.2 - - + -
123C LEU* 4.3 33.4 - - + +
124C HIS* 3.3 39.9 - - + +
162C GLU* 3.2 22.6 + - + +
163C ILE* 3.5 11.7 - - + +
164C ILE 3.2 1.0 - - - -
165C PRO* 1.3 77.9 - - + +
167C CYS* 1.3 63.0 + - - +
169C ARG* 3.4 11.0 + - - +
170C ILE* 3.3 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C LEU* 6.3 0.4 - - - -
140C LEU* 5.4 3.4 - - - -
163C ILE* 2.9 31.9 + - - +
164C ILE* 3.7 5.8 - - - +
166C LEU* 1.3 75.8 - - - +
168C LEU* 1.3 58.9 + - + +
170C ILE* 3.2 3.9 + - - -
171C MET* 2.8 39.5 + - - +
182C ALA* 3.7 31.2 - - - +
185C ILE* 3.7 35.2 - - - -
186C LEU* 4.5 8.3 - - + -
189C ILE* 5.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C ILE* 3.0 36.2 + - + +
165C PRO* 3.8 6.1 - - + +
167C CYS* 1.3 76.4 - - - +
169C ARG* 1.3 62.0 + - - +
171C MET* 3.3 24.5 + - + +
172C GLU* 3.0 24.4 + - - +
186C LEU* 4.3 13.9 - - + -
208C HIS* 3.6 37.2 - - + +
209C VAL* 4.2 21.8 - - + +
212C ILE* 3.5 32.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C LEU 3.3 20.8 + - - -
124C HIS* 4.1 11.9 + - - +
125C THR 2.9 25.6 + - - -
126C VAL* 3.5 29.5 - - - +
136C ARG* 4.6 4.0 - - - +
165C PRO 3.1 16.9 + - - +
166C LEU* 3.7 9.1 + - - +
167C CYS 3.3 0.2 - - - -
168C LEU* 1.3 76.4 - - - +
170C ILE* 1.3 72.9 + - - +
172C GLU* 3.4 8.5 + - - +
173C SER* 3.1 49.3 + - - +
212C ILE* 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C LEU* 4.1 27.8 - - + +
136C ARG* 4.8 7.6 - - + -
140C LEU* 4.1 26.5 - - + -
166C LEU 3.3 15.4 + - - +
167C CYS* 3.2 8.3 + - - +
169C ARG* 1.3 94.0 - - - +
171C MET* 1.3 63.5 + - - +
173C SER 4.9 0.2 - - - -
174C GLY* 2.9 31.4 + - - +
178C SER* 3.5 42.0 - - - +
179C LYS* 3.3 5.9 - - - +
182C ALA* 3.7 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C CYS 2.8 31.0 + - - +
168C LEU* 3.6 20.2 - - + +
170C ILE* 1.3 71.2 - - - +
172C GLU* 1.3 61.5 + - - +
179C LYS* 3.2 27.9 - - - +
182C ALA* 3.8 7.0 - - + +
183C THR* 3.3 47.1 - - + +
186C LEU* 3.7 27.6 - - + -
212C ILE* 4.2 2.2 - - + -
213C LEU* 3.8 10.5 - - + -
216C MET* 3.4 49.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C LEU 3.0 15.1 + - - +
169C ARG* 3.8 7.7 - - - +
170C ILE 3.1 0.4 - - - -
171C MET* 1.3 79.7 - - - +
173C SER* 1.3 63.4 + - - +
174C GLY 3.8 0.4 - - - -
179C LYS* 3.7 12.6 + - - -
212C ILE* 4.3 28.0 - - + +
215C LYS* 4.1 32.4 + - + +
216C MET* 5.3 2.0 - - - -
219C GLN* 4.2 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C VAL* 5.5 5.8 - - - +
128C LYS* 5.4 7.6 - - - -
169C ARG* 3.1 33.2 + - - +
170C ILE* 3.9 0.7 - - - -
172C GLU* 1.3 83.8 + - - +
174C GLY* 1.3 61.3 + - - +
179C LYS* 4.5 1.1 - - - +
----------------------------------------------------------
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