Contacts of the strand formed by residues 264 - 268 (chain D) in PDB entry 3TKY
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 264 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D LEU* 3.7 21.8 - - + -
206D THR 3.6 2.7 + - - +
207D ILE* 3.3 21.8 - - + +
208D VAL* 3.1 24.5 + - - +
262D GLY 3.4 0.4 - - - -
263D ASP* 1.3 79.7 + - - +
265D ILE* 1.3 65.6 + - - +
290D LEU* 3.6 2.2 - - - -
295D LYS* 3.3 22.4 - - + +
297D ILE* 4.0 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D ILE* 4.4 2.0 - - - -
208D VAL* 3.2 27.4 - - + +
210D VAL* 3.4 30.7 - - + -
259D VAL* 3.6 24.5 - - + -
260D PRO 4.3 0.2 - - - +
262D GLY 5.5 0.7 - - - +
264D ALA* 1.3 75.7 - - - +
266D PHE* 1.3 58.9 + - - +
267D ILE* 4.0 5.6 - - + -
286D CYS* 3.7 33.2 - - + +
289D ALA* 4.1 6.7 - - + +
290D LEU* 3.5 22.6 - - + +
295D LYS 3.2 4.9 + - - -
296D VAL* 3.0 15.1 - - + +
297D ILE* 2.8 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D MET* 3.7 27.8 - - + -
194D ILE* 5.5 2.0 - - + -
201D PHE* 4.1 10.1 - + + -
207D ILE* 4.2 18.0 - - + +
208D VAL 2.8 9.6 + - - +
209D ASP* 3.1 30.0 - - + +
210D VAL 2.8 28.9 + - - -
217D VAL* 3.3 26.0 - - + -
221D ILE* 4.9 3.6 - - + -
265D ILE* 1.3 71.7 - - - +
267D ILE* 1.3 60.5 + - - +
268D LYS* 3.5 32.1 - - + -
297D ILE* 3.5 35.4 - - + -
299D ALA* 4.0 16.6 - - + -
361D VAL* 5.4 2.2 - - + -
370D SAH 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D VAL* 3.5 32.3 - - + +
265D ILE* 4.0 8.3 - - + -
266D PHE* 1.3 79.4 - - - +
268D LYS* 1.3 60.8 + - - +
269D TRP 4.2 0.7 + - - -
270D ILE* 3.6 22.0 - - + -
271D CYS* 3.9 27.6 - - - +
282D LEU* 5.0 8.5 - - + -
283D LEU* 4.0 17.3 - - + -
286D CYS* 4.8 5.6 - - - -
296D VAL* 3.7 18.8 - - + -
297D ILE 3.0 11.8 + - - +
298D VAL* 3.6 10.5 - - + +
299D ALA* 3.2 21.0 + - - +
300D GLU* 5.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D ASN* 4.6 6.3 - - - +
187D SER* 3.0 47.3 + - - +
190D THR* 4.9 11.8 - - - +
191D MET* 4.8 6.7 - - - -
194D ILE* 5.3 3.8 - - + -
209D ASP* 4.7 0.2 + - - -
210D VAL 4.6 0.4 + - - -
217D VAL* 4.5 5.8 - - + -
266D PHE* 3.5 37.6 + - + -
267D ILE* 1.3 72.5 - - - +
269D TRP* 1.3 87.5 + - + +
270D ILE* 2.9 9.6 + - - +
299D ALA* 3.5 19.3 - - + +
359D THR* 5.2 6.6 + - + +
370D SAH 2.6 36.7 + - - +
----------------------------------------------------------
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