Contacts of the strand formed by residues 214 - 219 (chain A) in PDB entry 1TYI
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 ALA 214 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A GLU* 4.2 18.6 - - + +
179A TYR* 4.9 6.3 - - + -
186A THR* 3.1 22.4 - - + -
204A ASP 3.5 13.1 - - - +
205A ILE* 3.2 36.1 + - - +
206A GLY* 4.6 4.7 - - - +
210A GLY 4.2 0.2 + - - -
212A TYR* 4.5 1.9 - - - -
213A TYR* 1.3 77.8 - - - +
215A VAL* 1.4 66.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A MET* 4.2 23.1 - - + -
186A THR 2.9 9.9 + - - +
187A VAL* 3.4 12.1 - - + -
188A SER 3.1 24.3 + - - +
202A LEU* 5.2 7.0 - - + -
205A ILE* 6.3 0.2 - - - -
212A TYR 4.6 2.7 - - - +
214A ALA* 1.4 80.3 - - - +
216A ASN* 1.3 68.6 + - - +
217A TYR* 2.9 43.9 - - + +
235A VAL* 5.9 0.2 - - + -
238A LYS* 4.9 12.6 - - + +
239A VAL* 6.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A HIS* 3.2 15.8 - - - -
175A GLU* 2.7 27.7 + - - +
186A THR 5.1 0.3 - - - +
188A SER 3.7 1.6 - - - -
190A HIS* 3.4 4.9 - - - +
199A THR* 2.7 22.8 + - - +
200A GLY 3.4 13.0 - - - +
201A ASP 3.0 16.6 + - - +
202A LEU* 3.4 22.1 + - - +
204A ASP* 2.9 27.1 + - - +
214A ALA* 4.7 0.5 - - - +
215A VAL* 1.3 79.9 + - - +
217A TYR* 1.3 62.7 + - - +
218A PRO* 2.9 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A VAL* 3.6 6.7 - - + -
188A SER 2.8 28.9 + - - +
189A PHE* 3.8 9.4 - + - -
190A HIS* 2.7 32.6 + - - +
202A LEU* 5.8 2.2 - - + -
215A VAL* 2.9 32.8 - - + +
216A ASN* 1.3 70.4 - - - +
218A PRO* 1.3 64.4 - - - +
219A LEU* 3.3 2.9 - - + +
231A ILE* 3.6 31.4 - - + -
235A VAL* 2.8 51.7 + - + +
238A LYS* 3.2 33.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A HIS* 3.1 17.3 - - + +
192A TYR* 3.1 38.6 - - + -
200A GLY 3.5 3.8 - - - +
201A ASP* 3.9 4.7 - - - +
202A LEU* 3.5 33.0 - - + +
216A ASN 2.9 17.9 - - - +
217A TYR* 1.3 87.0 - - - +
219A LEU* 1.3 65.0 + - - +
220A ARG* 3.9 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PHE* 3.9 14.4 - - + -
190A HIS 2.8 36.9 + - - +
192A TYR* 2.7 17.6 + - - +
195A TYR* 2.6 23.6 + - - -
217A TYR* 3.3 11.4 - - + +
218A PRO* 1.3 84.1 - - - +
220A ARG* 1.3 62.3 + - - +
223A ILE* 4.8 4.3 - - + -
228A TYR* 4.2 15.7 - - + -
231A ILE* 2.9 44.0 - - + -
265A PHE* 3.3 30.5 - - + -
----------------------------------------------------------
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