Contacts of the strand formed by residues 252 - 258 (chain D) in PDB entry 1YFL
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 252 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D VAL* 4.6 12.3 - - + -
214D GLU 2.9 9.4 - - - +
215D HIS* 3.1 36.5 + - + +
216D HIS* 4.1 2.8 + - - -
236D ASN* 2.9 46.5 + - - +
251D GLY* 1.3 75.6 + - - -
253D ASP* 1.3 61.3 + - - +
254D GLU* 3.5 10.9 + - + +
119E ASP* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D VAL* 3.4 4.7 - - - -
213D LEU* 3.1 32.3 + - + +
214D GLU* 2.8 35.1 + - + +
234D HIS* 2.9 44.4 + - - +
235D LEU 4.7 1.0 + - - -
236D ASN* 4.5 4.9 + - - +
237D LYS 5.1 4.0 - - - +
251D GLY 4.3 0.4 - - - -
252D THR* 1.3 69.6 - - - +
254D GLU* 1.3 64.6 + - - +
255D VAL* 3.4 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LYS* 4.6 1.9 - - - -
14D LEU* 2.9 29.2 - - - +
174D TYR* 4.2 15.1 + - + +
210D SER* 5.6 1.6 - - - -
211D ASN 3.7 4.7 - - - +
212D VAL* 3.8 22.2 - - + -
235D LEU* 3.0 33.2 + - + +
236D ASN* 4.2 10.0 - - - +
252D THR* 3.5 11.3 + - + +
253D ASP* 1.3 73.2 + - - +
255D VAL* 1.3 63.2 + - - +
120E LYS* 2.4 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D SER* 3.5 5.9 + - - -
211D ASN 3.0 35.7 + - - +
213D LEU* 3.4 33.9 - - + -
232D VAL* 4.1 5.6 - - + -
233D LYS 3.1 10.5 - - - +
234D HIS* 3.3 29.6 - - + +
235D LEU* 3.8 7.4 - - - +
253D ASP* 3.4 9.6 - - - +
254D GLU* 1.3 80.7 - - - +
256D TYR* 1.3 61.2 + - - +
257D ILE* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D LEU* 3.7 29.8 - - + -
21D HIS* 3.5 37.3 + + + -
22D PHE* 3.5 25.8 - + - -
167D PHE* 3.5 6.8 - - - -
169D TYR* 4.1 13.7 - + - -
207D PHE 4.8 0.2 + - - -
208D GLY* 3.3 20.4 - - - -
209D LEU 3.4 33.4 - - - -
210D SER* 4.0 5.6 - - - +
233D LYS* 2.7 42.3 + - + +
235D LEU* 4.7 4.7 - - + -
255D VAL* 1.3 73.2 - - - +
257D ILE* 1.3 59.7 + - - +
258D PHE* 3.3 36.4 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D PHE* 3.9 3.0 - - + -
208D GLY* 3.7 0.5 - - - -
209D LEU* 2.7 53.1 + - + +
213D LEU* 4.3 2.0 - - + -
223D LEU* 3.6 33.2 - - + -
226D TRP* 3.6 25.1 - - + -
227D SER* 3.5 22.0 - - - -
230D TYR* 4.0 10.5 - - + -
231D ASN 3.2 10.8 - - - +
232D VAL* 3.8 17.5 - - + -
255D VAL* 3.7 22.2 - - + -
256D TYR* 1.3 73.8 - - - +
258D PHE* 1.3 63.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D HIS* 4.3 31.4 - + + +
206D LYS* 5.0 4.0 - - - -
207D PHE* 3.4 20.0 - - - +
208D GLY* 4.0 6.5 - - - -
230D TYR* 3.3 6.3 - - - +
231D ASN* 2.9 69.9 + - + +
233D LYS* 4.0 13.9 - - + -
256D TYR* 3.3 43.3 - + + -
257D ILE* 1.3 75.9 - - - +
259D ASN* 1.3 77.7 + - - +
----------------------------------------------------------
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