Contacts of the helix formed by residues 187 - 201 (chain L) in PDB entry 6QX2
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 ASN 187 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100L ARG* 3.4 5.7 - - - +
101L TYR* 3.7 1.8 - - - -
186L HIS* 1.3 73.0 - - - +
188L LEU* 1.3 60.6 + - - +
189L THR* 3.2 35.2 + - - -
190L GLU* 3.3 30.6 + - + +
191L LEU* 3.0 29.6 + - - +
215L GLY 5.0 2.0 + - - -
217L ASP* 3.0 33.7 + - + +
482L ASP* 2.9 23.3 + - - +
483L ASP 3.3 14.1 + - - -
484L ARG* 3.4 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101L TYR* 2.9 31.8 + - + +
131L ILE* 4.1 16.2 - - + -
164L PHE* 3.9 22.2 - - + -
165L PRO* 4.0 15.5 - - + -
169L ALA* 4.5 7.0 - - + -
186L HIS 3.7 0.6 + - - -
187L ASN* 1.3 68.7 - - - +
189L THR* 1.3 61.3 + - - +
191L LEU* 3.2 6.8 + - + +
192L ILE* 2.9 52.8 + - + +
476L ILE* 4.5 6.3 - - + -
480L PHE* 3.8 36.8 - - + +
481L GLY* 4.1 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 189 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187L ASN* 3.2 10.3 + - - -
188L LEU* 1.3 78.4 - - - +
190L GLU* 1.3 64.1 + - + +
192L ILE* 3.3 1.7 + - - +
193L ASN* 3.0 42.4 + - - +
477L ARG* 3.9 21.8 - - + -
481L GLY* 3.1 24.3 - - - -
482L ASP 3.2 11.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187L ASN* 3.3 24.9 + - + +
189L THR* 1.3 76.6 - - + +
191L LEU* 1.3 58.1 + - - +
193L ASN* 3.4 8.8 + - - +
194L GLY 2.9 23.9 + - - -
212L ASP* 3.2 24.7 - - - +
213L ILE* 3.6 15.3 - - + +
214L GLU* 3.1 29.5 + - - +
215L GLY 4.0 1.9 - - - +
484L ARG* 2.8 51.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 191 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165L PRO* 3.7 24.0 - - + +
168L LEU* 3.8 26.2 - - + -
169L ALA* 3.4 42.6 - - + +
186L HIS* 3.8 19.5 - - + -
187L ASN 3.0 16.7 + - - +
188L LEU* 3.2 11.0 + - - +
190L GLU* 1.3 74.4 - - - +
192L ILE* 1.3 58.0 + - - +
194L GLY* 3.0 4.9 + - - -
195L VAL* 2.9 31.2 + - - +
213L ILE* 3.9 25.1 - - + +
352L LEU* 4.6 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 192 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165L PRO* 4.2 7.4 - - + -
188L LEU* 2.9 37.0 + - + +
189L THR 4.0 2.5 - - - +
191L LEU* 1.3 72.0 - - - +
193L ASN* 1.3 61.0 + - - +
195L VAL* 3.1 8.8 + - - +
196L LEU* 2.9 42.3 + - + +
473L LEU* 3.6 51.8 - - + +
474L THR 4.6 0.2 - - - +
476L ILE* 3.9 15.0 - - + -
477L ARG* 3.7 39.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 193 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189L THR* 3.0 31.9 + - - +
190L GLU* 3.6 9.4 - - - +
192L ILE* 1.3 75.7 - - - +
194L GLY* 1.3 56.3 + - - +
196L LEU* 3.4 7.7 + - - +
197L SER* 3.0 32.9 + - - -
212L ASP* 3.6 20.7 + - + +
477L ARG* 2.7 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 194 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190L GLU 2.9 14.4 + - - -
191L LEU 3.0 5.6 + - - -
193L ASN* 1.3 74.9 - - - +
195L VAL* 1.3 54.7 - - - +
197L SER* 3.3 4.2 + - - -
198L LEU* 3.0 24.9 + - - +
209L LEU* 3.5 19.7 - - - +
212L ASP* 3.6 16.7 - - - +
213L ILE* 4.3 8.5 - - - -
352L LEU* 4.5 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165L PRO* 4.7 5.6 - - + -
191L LEU 2.9 23.3 + - - +
192L ILE* 3.1 9.8 + - - +
194L GLY* 1.3 68.1 - - - +
196L LEU* 1.3 55.8 + - - +
198L LEU* 3.3 8.0 + - - +
199L SER* 2.8 33.4 + - - -
352L LEU* 3.7 26.2 - - + +
355L TYR* 4.2 20.9 - - + -
356L LEU* 3.9 27.5 - - + +
473L LEU* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192L ILE* 2.9 29.5 + - + +
193L ASN* 3.6 7.0 - - - +
195L VAL* 1.3 72.5 - - - +
197L SER* 1.3 63.6 + - - +
199L SER* 2.8 21.8 + - - -
200L LYS* 3.2 20.2 + - + +
470L ARG* 3.7 47.3 - - + +
473L LEU* 4.6 11.4 - - + -
474L THR* 3.6 16.6 - - - +
477L ARG* 3.7 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 197 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193L ASN 3.0 9.2 + - - -
194L GLY 3.4 6.3 - - - -
196L LEU* 1.3 74.2 - - - +
198L LEU* 1.3 62.7 + - - +
200L LYS* 3.2 12.8 + - - +
201L ASN* 3.1 22.3 + - - +
204L ILE* 3.8 20.5 - - - +
209L LEU* 4.8 0.2 - - - -
212L ASP* 2.7 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194L GLY 3.0 13.6 + - - +
195L VAL* 3.5 9.9 - - - +
197L SER* 1.3 74.8 - - - +
199L SER* 1.3 57.3 + - - +
201L ASN 3.1 30.8 + - - +
202L PRO* 3.4 11.1 - - + +
204L ILE* 3.6 26.3 - - + +
209L LEU* 4.6 5.8 - - + -
349L LYS* 4.0 13.0 - - + -
352L LEU* 3.7 17.5 - - + +
353L VAL* 3.7 49.8 - - + +
356L LEU* 4.1 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 199 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195L VAL* 2.8 19.0 + - - -
196L LEU* 2.8 16.7 + - - -
198L LEU* 1.3 72.0 - - - +
200L LYS* 1.3 53.0 + - - +
202L PRO* 5.3 2.4 - - - +
356L LEU* 3.6 30.3 - - - -
466L LEU* 3.5 15.7 - - - +
470L ARG* 2.9 52.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196L LEU* 3.2 20.7 + - + +
197L SER* 3.6 9.0 - - - +
198L LEU 3.1 0.4 - - - -
199L SER* 1.3 78.7 - - - +
201L ASN* 1.3 58.2 + - + +
202L PRO* 4.0 6.7 - - - +
470L ARG* 3.7 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 201 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197L SER 3.1 9.6 + - - +
198L LEU* 3.1 10.5 + - - +
200L LYS* 1.3 81.0 - - + +
202L PRO* 1.3 66.2 - - - +
203L ASP* 3.0 21.6 + - - +
204L ILE* 3.1 45.3 + - + +
208L GLU* 4.5 11.9 + - - -
----------------------------------------------------------
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