Contacts of the helix formed by residues 185 - 197 (chain B) in PDB entry 1N0N
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 185 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR 3.4 20.7 + - - +
80B ASN 2.7 20.6 + - - +
81B LEU 3.7 15.0 + - - +
82B SER* 3.9 17.0 + - - -
85B GLY* 4.8 1.6 - - - -
183B VAL 3.4 1.4 + - - -
184B ILE* 1.3 69.8 - - - +
186B TRP* 1.3 61.8 + - - +
187B GLU* 3.0 17.0 + - - +
188B ASN* 2.9 28.1 + - - +
189B VAL* 3.1 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLY* 5.6 0.2 - - - -
86B GLY 3.3 24.7 + - - -
87B GLY 3.0 18.4 + - - -
88B GLU 4.0 7.2 - - - +
89B PRO* 3.6 42.8 - - + -
93B LEU* 4.0 4.7 - - + -
97B ILE* 4.5 4.3 - - + -
104B PHE* 3.7 21.5 - + - -
107B PHE* 3.6 28.5 - + - -
126B LEU* 4.9 1.6 - - + -
156B LEU* 4.0 14.4 - - + -
181B TRP* 4.1 14.2 + + - -
184B ILE* 3.2 28.2 + - + +
185B ASN* 1.3 73.5 - - - +
187B GLU* 1.3 57.7 + - - +
189B VAL* 3.8 28.9 - - + +
190B THR* 2.8 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ASN* 3.0 12.8 + - - +
186B TRP* 1.3 77.9 - - - +
188B ASN* 1.3 64.1 - - - +
190B THR* 3.4 7.1 + - - -
191B GLU* 3.2 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR* 3.1 41.4 + - - +
80B ASN* 2.8 29.9 + - - -
185B ASN* 2.9 19.7 + - - +
187B GLU* 1.3 75.3 - - - +
189B VAL* 1.3 64.6 + - - +
191B GLU* 3.1 29.8 + - - +
192B ARG* 3.1 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASN* 4.4 5.8 - - + +
93B LEU* 3.9 16.6 - - + -
126B LEU* 4.6 5.6 - - + -
155B LEU* 3.7 41.8 - - + +
156B LEU* 4.1 18.6 - - + -
184B ILE* 4.2 9.9 - - + -
185B ASN 3.1 14.6 + - - +
186B TRP* 3.8 28.0 - - + +
188B ASN* 1.3 75.9 - - - +
190B THR* 1.3 63.5 + - - +
192B ARG* 3.3 3.3 + - - +
193B TYR* 3.0 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PRO* 4.7 4.3 - - - +
90B LYS 4.9 7.7 + - - +
93B LEU* 3.6 25.4 - - + +
186B TRP 2.8 25.1 + - - -
187B GLU* 3.5 8.1 - - - -
188B ASN 3.1 0.2 - - - -
189B VAL* 1.3 77.6 - - - +
191B GLU* 1.3 59.2 + - + +
193B TYR* 3.1 4.1 + - + +
194B MET* 2.8 52.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLU* 3.2 34.2 + - + +
188B ASN* 3.1 23.2 + - - +
190B THR* 1.3 80.9 - - + +
192B ARG* 1.3 58.6 + - + +
194B MET* 3.3 4.9 + - - +
195B ALA* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B SER 4.8 0.4 + - - -
76B ILE* 3.8 35.2 - - - +
79B THR* 2.9 28.3 + - - +
80B ASN* 3.7 4.8 - - - +
153B ILE* 5.0 2.9 - - + +
154B PRO* 3.6 16.3 + - - +
155B LEU* 3.5 34.4 - - + +
188B ASN* 3.1 29.7 + - - +
189B VAL 3.7 5.8 - - - +
190B THR 3.3 0.2 - - - -
191B GLU* 1.3 80.7 - - + +
193B TYR* 1.3 61.1 + - - +
195B ALA* 3.4 14.9 + - - +
196B CYS* 3.3 18.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLU* 3.8 10.0 + - + +
93B LEU* 3.8 35.7 - - + -
96B ALA* 3.4 24.2 - - + +
99B ARG* 5.4 2.9 + - - -
128B PHE* 4.0 20.7 - + - -
135B LEU* 4.0 24.0 - - + -
155B LEU* 3.5 17.4 - - + +
189B VAL 3.0 13.9 + - - +
190B THR* 3.1 9.4 + - - +
192B ARG* 1.3 73.3 - - - +
194B MET* 1.3 74.5 + - + +
195B ALA 3.0 5.0 + - - -
196B CYS* 3.2 6.4 + - - -
197B LYS* 2.9 66.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LYS 6.0 0.4 - - - +
91B GLY* 5.9 0.4 - - - -
92B GLU* 3.6 49.4 - - + +
93B LEU 5.0 0.9 - - - +
190B THR* 2.8 41.5 + - + +
191B GLU* 4.0 4.3 - - - +
193B TYR* 1.3 89.9 - - + +
195B ALA* 1.3 59.8 + - - +
196B CYS 3.4 0.6 + - - -
197B LYS* 3.9 6.5 - - - -
198B LYS* 3.6 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLU 2.8 19.4 + - - +
192B ARG* 3.4 11.4 - - - +
193B TYR 3.0 0.4 - - - -
194B MET* 1.3 79.5 - - - +
196B CYS* 1.3 57.7 + - + +
198B LYS* 3.6 16.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 3.8 45.6 - - + -
130B LYS* 4.6 3.8 - - + +
153B ILE* 3.8 31.9 - - + -
155B LEU* 4.2 3.8 - - - -
192B ARG 3.3 16.8 - - - +
193B TYR* 3.6 7.2 - - - -
195B ALA* 1.3 76.1 - - + +
197B LYS* 1.3 56.3 + - - +
198B LYS* 2.5 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLU* 2.7 29.9 + - - -
128B PHE* 4.1 21.3 - - + -
193B TYR* 2.9 60.4 + - + +
194B MET* 3.6 9.2 + - - +
195B ALA 3.4 0.2 - - - -
196B CYS* 1.3 79.5 - - - +
198B LYS* 1.3 71.2 + - - +
----------------------------------------------------------
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