Contacts of the helix formed by residues 201 - 210 (chain A) in PDB entry 1YRT
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 PHE 201 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PRO* 3.8 28.7 - - + -
197A HIS 3.7 15.3 - - - -
198A LEU* 3.0 19.5 + - + +
199A SER 3.0 1.8 + - - -
200A ASN* 1.3 82.2 - - + +
202A ARG* 1.3 66.1 + - - +
203A ASP 3.3 2.0 - - - -
204A SER* 3.8 9.9 - - - -
205A ALA* 2.8 24.9 + - - +
248A GLY 3.8 8.1 - - - +
251A SER* 3.2 39.9 - - - +
252A ALA* 3.6 31.0 - - + -
275A PHE* 3.9 31.0 - + + -
112B LEU* 3.8 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A SER 3.4 9.1 + - - +
200A ASN 3.7 0.4 - - - -
201A PHE* 1.3 77.2 - - - +
203A ASP* 1.3 85.3 + - - +
205A ALA* 3.1 4.9 + - - +
206A ARG* 2.9 61.5 + - - +
111B ASN 3.9 15.5 - - - +
112B LEU* 3.7 28.8 - - - +
113B GLY* 3.8 18.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ASN 5.1 3.5 + - - +
201A PHE* 3.3 0.4 - - - +
202A ARG* 1.3 112.3 + - - +
204A SER* 1.3 62.2 + - - +
206A ARG* 3.3 10.5 + - - +
207A SER* 2.8 33.0 + - - -
212A GLY* 5.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ASN 5.2 1.3 + - - -
201A PHE* 3.3 20.2 + - - +
203A ASP* 1.3 80.0 - - - +
205A ALA* 1.3 62.1 + - - +
207A SER* 3.5 6.3 + - - -
208A SER* 3.3 21.0 + - - -
251A SER* 3.5 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PHE 2.8 18.5 + - - +
202A ARG* 3.4 6.3 - - - +
204A SER* 1.3 76.9 - - - +
206A ARG* 1.3 57.3 + - - +
208A SER* 3.0 6.1 + - - -
209A VAL* 3.0 31.2 + - - +
244A ILE* 3.7 26.5 - - + +
247A ALA* 3.9 11.0 - - + -
248A GLY* 3.6 23.1 - - - +
112B LEU* 4.6 1.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
202A ARG* 2.9 61.1 + - + +
203A ASP* 3.9 8.6 + - - +
205A ALA* 1.3 69.0 - - + +
207A SER* 1.3 62.4 + - - +
208A SER 3.0 1.8 - - - -
209A VAL* 5.2 1.3 - - - -
210A THR* 2.7 31.6 + - - +
212A GLY* 3.0 30.0 + - - -
213A ASP 3.6 19.3 - - - +
214A SER* 3.6 33.3 - - - +
244A ILE* 5.7 8.7 - - + -
112B LEU 4.8 3.6 + - - +
113B GLY* 3.2 26.5 + - - -
114B GLU* 4.0 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ASP 2.8 21.3 + - - -
204A SER* 3.8 6.6 + - - -
206A ARG* 1.3 74.2 - - - +
208A SER* 1.3 64.2 + - - +
210A THR 3.5 8.0 - - - +
211A SER* 4.4 3.4 - - - +
212A GLY* 3.7 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A SER 3.3 9.7 + - - -
205A ALA 3.0 9.5 + - - -
206A ARG 3.0 0.6 - - - -
207A SER* 1.3 85.1 - - - +
209A VAL* 1.3 68.1 + - - +
210A THR 3.8 2.6 - - - +
246A ARG* 6.0 0.3 + - - -
247A ALA* 4.1 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ALA 3.0 7.3 + - - +
208A SER* 1.3 77.9 - - - +
210A THR* 1.3 67.9 + - - +
218A TYR* 4.4 12.0 + - - -
240A LEU* 4.0 21.0 - - + +
243A LYS* 3.3 52.5 - - + +
244A ILE* 4.2 18.2 - - + -
247A ALA* 3.6 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ARG* 2.7 20.0 + - - +
207A SER 3.5 8.8 - - - +
208A SER 3.8 2.6 - - - +
209A VAL* 1.3 83.8 - - - +
211A SER* 1.3 85.1 + - - +
213A ASP* 3.0 56.9 + - + +
214A SER 4.3 1.2 + - - -
215A VAL* 4.9 3.1 + - - +
218A TYR* 3.1 40.5 - - + +
240A LEU* 5.7 1.2 - - - +
244A ILE* 5.4 4.9 - - - +
----------------------------------------------------------
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