Contacts of the helix formed by residues 174 - 188 (chain B) in PDB entry 5I94
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 LEU 174 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU* 3.9 28.3 - - + -
167B LEU* 4.0 20.0 - - + -
168B ARG 4.3 8.1 - - - +
169B THR* 5.5 0.2 - - - -
171B ASP* 2.8 27.3 + - + +
173B ARG* 1.3 85.3 - - - +
175B LYS* 1.3 61.7 + - - +
177B CYS* 3.5 4.0 + - + +
178B MET* 3.0 34.6 + - + +
206B ASN* 3.3 18.1 - - + +
209B LEU* 4.2 17.9 - - + -
210B LEU* 3.9 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ASP 3.5 4.1 + - - +
172B PRO* 3.4 19.7 + - + +
173B ARG 3.5 1.2 - - - -
174B LEU* 1.3 74.2 - - - +
176B GLU* 1.3 76.7 + - - +
177B CYS 3.3 0.2 + - - -
178B MET* 3.3 4.4 + - - -
179B ASP* 2.9 56.0 + - - +
182B ARG* 5.9 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B PRO 4.6 2.6 - - - +
173B ARG* 3.7 9.0 - - - +
175B LYS* 1.3 87.9 + - - +
177B CYS* 1.3 57.7 + - - +
179B ASP* 3.7 6.0 - - - +
180B MET* 3.1 33.7 + - + +
205B SER* 3.4 26.2 - - - +
206B ASN* 2.7 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PHE* 4.7 2.9 - - - -
174B LEU* 3.9 4.3 - - + +
175B LYS 3.2 0.4 - - - -
176B GLU* 1.3 77.7 - - - +
178B MET* 1.3 85.6 + - - +
180B MET* 3.5 3.0 + - - +
181B LEU* 3.1 28.7 + - - +
202B CYS 3.3 27.6 - - - +
203B VAL* 4.4 7.0 - - - -
205B SER* 4.3 0.4 - - - -
206B ASN* 3.2 21.3 + - - +
210B LEU* 4.1 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PHE* 4.3 0.9 - - + -
159B ILE* 4.3 6.5 - - + -
162B LEU* 3.6 28.9 - - + -
169B THR* 3.3 41.7 - - - +
174B LEU* 3.0 25.9 + - + +
175B LYS* 3.9 4.0 - - - +
177B CYS* 1.3 102.9 - - - +
179B ASP* 1.3 61.1 + - - +
181B LEU* 3.4 21.7 + - + +
182B ARG* 3.0 54.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LYS* 2.9 54.5 + - - +
176B GLU* 3.7 5.9 - - - +
178B MET* 1.3 74.3 - - - +
180B MET* 1.3 60.9 + - + +
182B ARG* 3.4 27.2 + - - +
183B LEU* 2.9 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLU* 3.1 20.5 + - + +
177B CYS 3.7 5.4 - - - +
179B ASP* 1.3 76.3 - - + +
181B LEU* 1.3 51.6 + - - +
183B LEU* 3.1 18.4 + - + +
184B THR* 2.7 38.8 + - - -
201B LYS* 3.3 47.1 - - - +
202B CYS* 3.9 19.1 - - - +
204B GLN* 5.8 1.3 - - - +
205B SER* 4.7 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL* 4.6 11.9 - - + -
158B PHE* 3.8 28.9 - - + -
159B ILE* 3.9 14.8 - - + -
177B CYS* 3.1 13.0 + - - +
178B MET* 3.6 28.9 - - + +
180B MET* 1.3 77.9 - - - +
182B ARG* 1.3 57.8 + - + +
184B THR* 3.1 6.2 + - - +
185B LEU* 2.8 37.6 + - + +
194B LEU* 4.1 28.0 - - + -
202B CYS* 3.7 26.0 - - + -
203B VAL* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B THR* 5.2 9.5 + - - +
175B LYS* 5.9 1.6 - - - +
178B MET* 3.0 38.4 + - - +
179B ASP* 3.4 27.6 + - - +
181B LEU* 1.3 74.2 - - - +
183B LEU* 1.3 64.3 + - - +
185B LEU* 3.5 15.0 + - + +
186B GLN* 3.3 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ASP* 2.9 20.5 + - + +
180B MET* 3.3 20.0 - - - +
182B ARG* 1.3 76.2 - - - +
184B THR* 1.3 58.3 + - - +
186B GLN* 3.3 22.8 + - + +
187B THR* 3.2 45.2 + - + +
201B LYS* 6.2 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B MET 2.7 18.1 + - - -
181B LEU* 3.4 9.2 - - - +
182B ARG 3.1 0.2 - - - -
183B LEU* 1.3 74.4 - - - +
185B LEU* 1.3 66.2 + - + +
186B GLN 3.0 5.2 + - - -
187B THR* 3.3 9.1 + - - +
188B THR* 3.1 36.2 + - + +
194B LEU* 4.3 16.8 - - + -
198B LEU* 3.8 30.0 - - + +
201B LYS* 3.6 22.6 + - - +
202B CYS* 4.1 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL* 3.9 39.9 - - + -
181B LEU* 2.8 20.9 + - + +
182B ARG* 3.5 16.1 + - + +
184B THR* 1.3 78.8 - - + +
186B GLN* 1.3 60.7 + - + +
188B THR* 3.6 15.4 - - - +
189B SER* 4.2 4.7 + - - -
192B VAL* 4.1 28.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ARG 3.3 13.2 + - - +
183B LEU* 3.4 32.1 - - - +
184B THR 3.0 0.8 - - - -
185B LEU* 1.3 79.7 - - + +
187B THR* 1.3 61.2 + - + +
188B THR 3.2 8.3 + - - -
189B SER* 4.1 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 3.2 30.8 + - + +
184B THR* 3.3 12.0 + - - +
186B GLN* 1.3 78.3 - - + +
188B THR* 1.3 68.8 + - - +
189B SER 4.2 0.2 - - - -
201B LYS* 5.7 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B THR* 3.1 20.5 + - + +
185B LEU* 3.6 12.6 - - - +
186B GLN 3.2 0.4 - - - -
187B THR* 1.3 95.0 - - - +
189B SER* 1.3 67.3 + - - +
190B ASP* 3.2 37.7 + - - +
191B GLY* 4.1 2.4 + - - -
192B VAL* 5.2 3.8 - - - +
198B LEU* 5.6 7.6 - - + +
----------------------------------------------------------
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