Contacts of the helix formed by residues 185 - 197 (chain L) in PDB entry 3RWR
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 GLU 185 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183L PRO 3.6 5.9 + - - +
184L PHE* 1.3 85.2 - - - +
186L GLU* 1.3 70.2 + - + +
187L ASN* 2.8 15.4 + - + +
188L SER* 3.0 40.0 + - - +
189L PHE* 3.2 11.1 + - - +
191L GLU* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 186 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151L ARG* 3.6 27.8 + - - +
154L ALA* 4.0 18.5 - - + +
184L PHE* 3.7 22.9 - - + -
185L GLU* 1.3 70.4 - - - +
187L ASN* 1.3 67.7 + - + +
189L PHE* 3.9 4.9 - - - +
190L LEU* 3.4 28.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 187 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185L GLU* 2.8 17.4 + - + +
186L GLU* 1.3 79.3 - - + +
188L SER* 1.3 66.9 + - - +
189L PHE 2.9 1.7 + - - -
190L LEU* 3.1 32.0 + - - +
191L GLU* 3.1 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185L GLU* 3.0 33.5 + - - -
187L ASN* 1.3 78.7 - - - +
189L PHE* 1.3 66.6 + - - +
191L GLU* 3.1 31.8 + - - +
192L GLN* 3.5 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 189 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150L VAL* 5.1 1.1 - - + -
184L PHE* 4.0 17.9 - + + -
185L GLU 3.2 3.2 + - - -
186L GLU 3.9 10.3 - - - +
187L ASN 2.9 1.2 + - - -
188L SER* 1.3 77.0 - - - +
190L LEU* 1.3 76.6 + - + +
192L GLN* 3.1 41.5 + - + +
193L PHE* 3.3 11.1 + + - +
649M GLN* 4.0 21.5 - - + -
652M GLU* 3.4 43.5 - - + -
653M LEU* 3.3 42.4 - - + -
656M LEU* 5.8 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150L VAL* 6.1 3.6 - - + -
186L GLU* 3.4 30.5 - - + +
187L ASN* 3.1 23.1 - - - +
189L PHE* 1.3 85.0 - - + +
191L GLU* 1.3 66.6 + - + +
193L PHE* 2.8 20.1 + - - +
194L MET* 3.1 31.4 + - + +
649M GLN* 5.0 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185L GLU* 5.2 0.2 - - - +
187L ASN* 3.1 30.8 + - - +
188L SER* 3.1 30.1 + - - +
190L LEU* 1.3 79.0 - - + +
192L GLN* 1.3 56.2 + - - +
194L MET* 4.8 3.1 - - - -
195L ILE* 2.9 31.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 192 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188L SER 3.5 5.3 + - - +
189L PHE* 3.1 35.3 + - + +
191L GLU* 1.3 77.4 - - - +
193L PHE* 1.3 98.6 + - - +
195L ILE* 3.4 7.2 + - - +
196L GLU* 2.9 53.2 - - - +
197L LYS* 4.8 5.0 + - - +
652M GLU* 4.7 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 193 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189L PHE* 3.8 13.9 - + + +
190L LEU* 2.8 10.6 + - - +
192L GLN* 1.3 94.0 - - - +
194L MET* 1.3 60.4 + - - +
195L ILE 2.8 11.4 + - - -
196L GLU 3.0 0.2 + - - -
197L LYS* 2.7 76.4 + - + -
198L LEU* 3.0 12.2 + - + -
201L ALA* 4.6 5.2 - - + -
645M ALA* 4.4 3.6 - - + -
648M CYS* 3.6 35.9 - - + -
649M GLN* 3.4 34.5 - - + +
652M GLU* 4.3 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 194 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190L LEU* 3.1 30.4 + - + +
191L GLU* 4.7 3.1 - - - +
193L PHE* 1.3 83.8 - - - +
195L ILE* 1.3 70.9 + - + +
196L GLU 3.7 0.2 - - - -
198L LEU* 3.7 34.6 - - + +
199L PRO* 5.4 0.9 - - - +
649M GLN* 4.3 15.7 - - - +
717M LEU* 3.9 30.3 - - + -
720M ALA* 4.3 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 195 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191L GLU* 2.9 25.8 - - - +
192L GLN* 3.7 8.7 - - - +
193L PHE 2.8 1.2 + - - -
194L MET* 1.3 93.2 - - + +
196L GLU* 1.3 68.4 + - + +
199L PRO* 5.4 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 196 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192L GLN* 2.9 43.7 - - - +
193L PHE 3.0 0.2 + - - -
194L MET 3.7 0.2 - - - -
195L ILE* 1.3 90.1 - - + +
197L LYS* 1.3 73.6 + - - +
199L PRO* 4.4 6.0 - - - +
200L GLU* 4.9 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 197 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192L GLN* 4.8 4.8 + - - +
193L PHE* 2.7 55.3 + - + +
196L GLU* 1.3 85.2 - - + +
198L LEU* 1.3 66.7 + - - +
199L PRO* 3.0 6.6 - - - +
200L GLU* 3.1 28.7 + - + +
201L ALA* 3.4 9.7 + - - +
648M CYS* 5.8 2.2 - - + +
652M GLU* 3.1 37.8 + - - -
----------------------------------------------------------
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