Contacts of the helix formed by residues 192 - 205 (chain A) in PDB entry 1YVP
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 192 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASN 5.1 0.7 - - - +
159A LYS 5.1 1.9 - - - +
161A ALA* 4.6 3.7 + - - +
190A PRO 3.3 1.8 + - - -
191A ALA* 1.3 79.7 - - - +
193A GLU* 1.3 63.3 + - - +
194A GLY* 2.8 15.1 - - - +
195A LEU* 2.7 55.4 - - - +
196A THR* 3.0 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ASN* 1.3 76.0 - - - +
194A GLY* 1.3 61.6 + - - +
196A THR* 3.4 11.2 + - - +
197A MET* 3.1 21.5 + - - +
213A TYR* 2.6 38.1 + - - -
218A LEU* 4.3 9.6 - - + -
222A THR* 4.0 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ALA* 3.5 21.0 - - - +
192A ASN* 2.8 12.2 - - - +
193A GLU* 1.3 74.4 - - - +
195A LEU* 1.3 57.1 + - - +
197A MET* 3.4 7.6 + - - +
198A VAL* 3.1 32.1 + - - +
222A THR* 4.3 12.5 + - - -
225A VAL* 4.6 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TYR* 3.7 13.7 - - + +
157A ASN* 2.9 41.5 - - - +
159A LYS 3.5 22.0 - - - +
161A ALA* 4.4 8.7 - - - -
164A LEU* 4.2 16.9 - - + +
188A ILE* 6.3 0.4 - - + -
190A PRO* 3.9 11.9 - - + -
191A ALA* 3.5 13.2 - - + +
192A ASN* 2.7 39.3 - - - +
194A GLY* 1.3 70.0 - - - -
196A THR* 1.3 55.9 + - - +
198A VAL* 3.2 4.6 + - - +
199A ALA* 2.7 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PRO* 3.2 29.8 + - + +
192A ASN 3.0 17.1 + - - -
193A GLU* 3.7 16.0 + - - +
194A GLY 3.3 0.2 - - - -
195A LEU* 1.3 75.8 - - - +
197A MET* 1.3 53.3 + - - +
199A ALA* 3.2 2.3 + - - +
200A LYS* 2.8 47.6 + - - +
213A TYR* 3.7 11.7 - - - +
1D IU 4.5 7.2 - - - +
2D IU 5.4 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLU 3.1 11.2 + - - +
194A GLY* 3.4 9.4 - - - +
195A LEU 3.2 0.2 - - - -
196A THR* 1.3 76.2 - - - +
198A VAL* 1.3 56.5 + - - +
200A LYS* 3.1 4.7 + - - +
201A TYR* 2.9 27.2 + - - +
209A VAL* 4.0 16.0 - - + +
213A TYR* 3.3 43.6 + - + +
218A LEU* 4.0 2.7 - - + -
222A THR* 3.4 27.8 - - + +
225A VAL* 3.8 12.3 - - + -
226A LEU* 3.7 50.3 - - + -
229A LEU* 4.2 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ALA* 3.8 22.4 - - + +
164A LEU* 3.5 31.0 - - + -
165A ALA* 4.5 6.5 - - + +
168A VAL* 4.2 24.5 - - + -
194A GLY 3.1 16.4 + - - +
195A LEU* 3.7 6.1 - - - +
197A MET* 1.3 72.5 - - - +
199A ALA* 1.3 67.9 + - - +
201A TYR* 3.1 8.9 + - + +
202A VAL* 2.9 28.0 + - + +
225A VAL* 4.0 15.5 - - + -
229A LEU* 4.9 3.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
183A LEU* 3.8 20.2 - - + -
188A ILE* 5.5 1.6 - - + -
190A PRO* 3.9 9.2 - - + -
195A LEU 2.7 21.2 + - - +
196A THR 3.4 4.9 - - - +
198A VAL* 1.3 74.7 - - - +
200A LYS* 1.3 57.7 + - - +
202A VAL* 3.4 1.6 + - - +
203A SER* 2.9 35.9 + - - -
1D IU 3.6 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A THR* 2.8 23.6 + - - +
197A MET* 3.1 9.4 + - - +
199A ALA* 1.3 78.3 - - - +
201A TYR* 1.3 56.3 + - - +
203A SER* 4.6 0.2 - - - -
204A LYS* 2.9 27.4 + - - +
205A GLY 3.6 2.8 + - - -
208A GLU* 3.8 24.9 + - + +
209A VAL* 3.8 9.2 - - + +
212A ALA* 3.5 33.1 - - + +
213A TYR* 4.2 15.3 - - + -
1D IU 2.7 40.7 + - + +
2D IU 3.8 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A VAL* 4.4 11.7 - - + -
169A THR* 3.6 31.2 - - + +
172A LYS* 5.2 13.6 - - - +
197A MET 2.9 11.0 + - - +
198A VAL* 3.5 6.7 - - - +
200A LYS* 1.3 77.3 - - - +
202A VAL* 1.3 71.6 + - + +
205A GLY* 2.9 27.6 + - - +
206A TRP* 3.9 29.8 - + + -
209A VAL* 3.3 17.9 - - + +
229A LEU* 3.9 33.0 - - + -
232A THR* 4.1 4.0 + - - -
233A GLU* 3.3 28.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TYR* 6.2 0.7 - - + -
168A VAL* 4.1 38.1 - - + -
179A HIS* 3.5 15.0 - - + +
180A LYS* 3.3 49.4 - - + +
183A LEU* 4.1 12.6 - - + -
198A VAL* 2.9 22.4 + - + +
199A ALA 3.8 3.6 - - - +
201A TYR* 1.3 84.2 - - + +
203A SER* 1.3 59.3 + - - +
205A GLY 4.9 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LYS* 4.0 26.1 + - - +
183A LEU* 3.8 10.2 - - - +
184A ARG* 5.0 3.9 + - - +
199A ALA 2.9 18.6 + - - -
202A VAL* 1.3 79.3 - - - +
204A LYS* 1.3 68.3 + - - +
1D IU 3.4 50.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LYS 2.9 9.8 + - - +
203A SER* 1.3 83.3 + - - +
205A GLY* 1.3 62.5 + - - +
207A LYS* 5.8 0.9 - - - +
208A GLU* 3.2 47.4 + - + +
1D IU 3.6 32.3 + - + -
2D IU 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LYS 3.6 0.4 + - - -
201A TYR* 2.9 22.8 + - - -
202A VAL 4.8 0.4 + - - -
204A LYS* 1.3 79.2 - - - +
206A TRP* 1.3 65.8 + - - -
207A LYS* 3.4 2.5 - - - -
208A GLU* 3.2 13.2 + - - +
209A VAL* 3.2 15.4 + - - +
----------------------------------------------------------
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