Contacts of the helix formed by residues 203 - 215 (chain A) in PDB entry 1YV5
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 THR 203 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A VAL 3.7 14.8 - - - +
201A ARG* 3.0 13.2 + - - +
202A PHE* 1.3 77.7 - - - +
204A GLU* 1.3 58.4 + - - +
205A LYS* 3.8 8.6 + - - +
206A ARG* 3.2 23.0 + - - +
207A TYR* 3.0 28.1 + - - +
281A CYS* 4.5 0.2 - - - -
286A VAL* 4.0 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A THR* 1.3 69.0 - - - +
205A LYS* 1.3 56.4 - - - +
207A TYR* 3.0 12.0 + - - +
208A LYS* 2.8 70.8 + - - +
251A GLU* 5.5 0.2 - - - +
255A ILE* 6.0 0.5 - - - +
283A TRP* 3.8 12.9 + - - -
286A VAL* 3.5 20.8 - - + +
287A GLN* 2.9 25.1 + - - +
290A GLN* 4.1 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A THR* 4.0 7.4 - - - +
204A GLU* 1.3 77.2 - - - +
206A ARG* 1.3 63.0 + - - +
208A LYS* 3.3 10.4 + - - +
209A SER* 3.2 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU* 4.0 26.3 + - - +
190A LEU* 4.6 12.9 + - - +
191A THR* 3.0 39.6 + - + +
201A ARG* 3.8 19.7 - - - +
203A THR* 3.2 20.7 + - - +
205A LYS* 1.3 80.1 - - - +
207A TYR* 1.3 63.5 + - - +
209A SER* 3.4 7.9 + - - -
210A ILE* 3.0 39.3 + - + +
281A CYS* 4.7 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A THR 3.0 18.9 + - - +
204A GLU* 3.0 18.1 + - - +
206A ARG* 1.3 75.9 - - - +
208A LYS* 1.3 62.5 + - + +
210A ILE* 3.0 9.0 + - + +
211A VAL* 3.0 55.3 + - + +
214A LYS* 6.2 0.2 - - - -
251A GLU* 5.5 1.1 - - + -
254A GLN 3.6 2.3 + - - -
255A ILE* 3.3 47.4 + - + +
258A ASP* 2.5 30.9 + - - -
281A CYS* 3.2 28.9 - - - -
282A SER 4.1 1.1 - - - -
283A TRP* 3.4 24.1 - + + +
286A VAL* 4.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLU* 2.8 45.1 + - - +
205A LYS* 3.6 8.0 - - - +
207A TYR* 1.3 79.8 - - + +
209A SER* 1.3 56.2 + - - +
211A VAL* 3.7 8.2 - - - +
212A LYS* 3.0 30.6 + - - +
251A GLU* 4.1 30.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU* 4.2 14.3 - - - +
205A LYS* 3.2 14.3 + - - +
206A ARG* 3.6 13.1 - - - -
207A TYR 3.3 0.2 - - - -
208A LYS* 1.3 72.3 - - - +
210A ILE* 1.3 71.4 + - - +
212A LYS* 4.4 5.6 - - - -
213A TYR* 3.3 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A GLY* 4.1 2.4 - - - +
187A LEU* 4.0 24.5 - - + -
188A ASP* 4.1 23.6 - - + +
191A THR* 4.0 18.6 - - - +
206A ARG* 3.0 26.7 + - + +
207A TYR* 3.0 8.5 + - + +
209A SER* 1.3 79.2 - - - +
211A VAL* 1.3 61.1 + - + +
213A TYR* 3.2 1.4 + - - +
214A LYS* 2.9 53.7 + - + +
281A CYS* 4.0 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A TYR* 3.0 49.4 + - + +
208A LYS* 3.7 11.4 - - - +
210A ILE* 1.3 75.6 - - + +
212A LYS* 1.3 69.7 + - - +
214A LYS* 4.0 12.6 - - - -
215A THR* 3.0 19.6 + - - -
216A ALA* 3.1 9.7 + - - +
250A GLY 5.2 0.3 - - - +
251A GLU* 4.2 26.2 - - + +
254A GLN* 3.2 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LYS 3.0 21.5 + - - +
209A SER* 3.7 7.9 - - - +
210A ILE 3.4 0.2 - - - -
211A VAL* 1.3 80.0 - - - +
213A TYR* 1.3 90.2 + - + +
216A ALA* 3.2 25.4 + - + +
217A PHE* 3.3 27.5 - - + -
247A LEU* 4.4 25.1 - - + -
251A GLU* 6.1 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A GLN* 3.1 38.1 - - + +
181A THR* 3.4 8.8 + - - -
183A ILE* 4.3 16.6 - - + -
184A GLY* 3.6 21.1 - - - +
187A LEU* 4.9 7.6 - - + -
209A SER* 3.3 28.2 + - - +
210A ILE 3.2 1.6 + - - -
211A VAL 3.2 0.2 - - - -
212A LYS* 1.3 110.8 + - + +
214A LYS* 1.3 64.7 + - - +
215A THR 3.5 0.5 + - - -
217A PHE* 4.0 27.5 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A THR* 3.5 10.3 - - - +
184A GLY* 3.6 20.5 - - - -
185A GLN* 3.9 15.0 - - - +
188A ASP* 3.1 24.3 + - + +
207A TYR* 6.2 0.4 - - - -
210A ILE* 2.9 37.1 + - + +
211A VAL* 4.0 6.1 - - - -
213A TYR* 1.3 78.0 - - - +
215A THR* 1.3 64.1 + - - +
218A TYR* 3.4 7.7 - - - -
254A GLN* 3.6 30.3 - - - +
258A ASP* 5.0 2.0 + - - -
901A RIS 2.4 61.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ARG* 5.4 1.8 - - - +
211A VAL 3.0 8.8 + - - -
213A TYR 3.4 0.4 - - - -
214A LYS* 1.3 84.1 - - - +
216A ALA* 1.3 61.7 + - - +
217A PHE 3.4 2.1 + - - -
218A TYR* 3.6 9.7 + - + -
219A SER* 2.4 46.1 + - - +
250A GLY 4.2 9.9 - - - +
253A PHE* 4.1 21.8 - - + -
254A GLN* 2.6 34.4 + - + +
901A RIS 3.0 18.7 + - + +
----------------------------------------------------------
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