Contacts of the helix formed by residues 186 - 201 (chain A) in PDB entry 4NAK
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 186 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LEU 3.7 9.4 - - - +
185A VAL* 1.3 71.9 - - - +
187A THR* 1.3 65.5 + - - +
188A GLU* 3.8 16.6 - - + +
189A ASP* 3.0 26.9 + - - +
190A VAL* 3.0 24.6 + - - +
279A SER* 3.6 10.7 + - - -
281A THR* 3.9 12.8 + - - -
413A K 3.2 11.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A THR* 3.7 22.3 + - - +
118A ARG* 4.2 12.3 + - - -
119A MET* 4.2 24.0 - - + -
185A VAL 3.9 1.6 + - - -
186A ASN* 1.3 71.8 - - - +
188A GLU* 1.3 67.1 + - + +
190A VAL* 3.2 4.9 + - - +
191A GLU* 2.8 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ASN* 3.2 11.4 - - + +
187A THR* 1.3 87.3 + - + +
189A ASP* 1.3 61.9 + - - +
191A GLU* 3.5 9.9 - - - +
192A LYS* 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A VAL* 4.9 0.2 - - + -
186A ASN* 3.0 14.1 + - - +
188A GLU* 1.3 80.6 - - - +
190A VAL* 1.3 63.8 - - - +
192A LYS* 3.3 14.2 + - - +
193A VAL* 3.1 23.6 + - - +
205A LEU* 3.5 21.1 - - + +
277A GLN 4.1 11.3 - - - +
278A GLY* 4.2 9.3 - - - -
279A SER* 2.7 24.3 + - - -
413A K 2.6 29.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A THR* 4.6 5.8 - - + -
116A PHE* 3.7 29.6 - - + -
119A MET* 3.5 26.7 - - + -
176A CYS* 4.8 1.6 - - - -
185A VAL* 3.7 24.5 - - + -
186A ASN 3.0 17.2 + - - +
187A THR* 3.6 7.6 - - - +
189A ASP* 1.3 72.7 - - - +
191A GLU* 1.3 66.9 + - - +
193A VAL* 3.3 8.4 + - + +
194A LEU* 2.9 35.5 + - + +
205A LEU* 5.2 0.2 - - - -
237A PRO* 4.4 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A MET* 3.7 19.2 - - + +
120A PRO* 5.2 3.8 - - - +
121A GLU* 3.3 30.5 - - - +
187A THR* 2.8 29.3 + - + +
188A GLU* 3.5 11.9 - - - +
190A VAL* 1.3 77.4 - - - +
192A LYS* 1.3 61.7 + - - +
194A LEU* 3.8 4.6 - - - +
195A LYS* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLU 3.1 14.5 + - - +
189A ASP* 3.5 19.2 + - - +
190A VAL 3.2 0.4 - - - -
191A GLU* 1.3 75.7 - - - +
193A VAL* 1.3 58.7 + - - +
195A LYS* 3.3 21.1 + - - +
196A ASP* 3.0 43.9 + - - +
205A LEU* 5.0 1.1 - - + -
276A SER* 4.1 5.6 - - - -
277A GLN* 2.7 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ASP 3.1 16.5 + - - +
190A VAL* 3.4 20.4 - - + +
192A LYS* 1.3 73.8 - - - +
194A LEU* 1.3 58.7 + - - +
197A GLY* 2.8 26.5 + - - -
203A ALA* 3.6 32.6 - - - +
204A VAL* 3.8 3.1 - - - +
205A LEU* 3.8 26.5 - - + +
237A PRO* 4.0 13.5 - - + +
239A VAL* 3.9 18.3 - - + +
276A SER* 3.5 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 3.8 42.8 - - + -
119A MET* 3.8 29.4 - - + -
121A GLU* 4.5 14.4 - - + -
122A VAL* 5.0 4.0 - - + -
174A LEU* 3.5 13.0 - - + +
176A CYS* 4.1 9.0 - - + -
190A VAL* 2.9 25.2 + - + +
191A GLU* 3.8 5.6 - - - +
193A VAL* 1.3 77.4 - - - +
195A LYS* 1.3 56.0 + - - +
197A GLY 3.3 0.3 + - - -
198A SER* 2.9 28.2 + - - -
239A VAL* 3.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLU 3.1 17.9 + - - +
192A LYS* 3.5 18.6 - - - +
194A LEU* 1.3 75.6 - - - +
196A ASP* 1.3 86.8 + - - +
198A SER* 3.3 7.7 + - - -
199A ALA* 3.1 26.7 + - - +
402A DTT 3.2 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LYS* 3.0 24.7 + - - +
193A VAL 4.0 0.2 - - - +
195A LYS* 1.3 98.8 + - - +
197A GLY* 1.3 60.0 + - - +
199A ALA* 3.7 4.0 - - - +
200A VAL* 2.9 35.9 + - + +
203A ALA* 3.7 5.8 - - + +
274A TYR* 3.4 32.7 - - + -
276A SER* 2.6 35.3 + - - +
402A DTT 4.5 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 3.9 10.2 - - - +
193A VAL 2.8 18.7 + - - -
194A LEU 3.3 1.5 + - - -
196A ASP* 1.3 74.7 - - - +
198A SER* 1.3 58.5 + - - +
201A GLY* 2.8 33.4 + - - -
202A ALA 4.3 1.8 - - - -
203A ALA* 3.5 17.2 - - - +
239A VAL* 3.9 13.7 - - - -
241A LYS* 4.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 3.9 19.1 - - - +
194A LEU 2.9 16.9 + - - -
195A LYS* 3.3 8.0 + - - -
197A GLY* 1.3 75.3 - - - +
199A ALA* 1.3 61.6 + - - +
241A LYS* 3.3 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LYS 3.1 17.8 + - - +
196A ASP* 3.7 5.4 - - - +
198A SER* 1.3 81.2 - - - +
200A VAL* 1.3 65.2 + - + +
241A LYS* 4.9 2.4 + - - -
402A DTT 4.3 8.7 - - - -
409A K 3.8 21.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ASP* 2.9 18.6 + - - +
199A ALA* 1.3 84.5 - - + +
201A GLY* 1.3 51.8 + - - +
202A ALA 3.6 19.3 - - - +
241A LYS* 5.1 1.1 - - - -
271A HIS* 2.6 30.1 + - - -
272A PRO* 3.6 32.0 - - + +
274A TYR* 3.8 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLY 2.8 18.0 + - - -
199A ALA 3.6 1.0 - - - -
200A VAL* 1.3 78.0 - - - +
202A ALA* 1.3 60.0 + - - +
240A ILE* 3.4 0.7 - - - -
241A LYS* 3.0 49.6 + - - +
244A LEU* 3.7 11.7 - - - +
271A HIS* 3.7 8.1 - - - -
----------------------------------------------------------
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