Contacts of the strand formed by residues 218 - 226 (chain N) in PDB entry 5DST
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 ARG 218 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216N PRO* 3.9 2.0 - - - +
217N ASP* 1.3 81.6 - - - +
219N ALA* 1.3 66.4 + - - +
220N ALA* 3.8 25.3 - - - +
222N TYR* 5.2 3.0 + - - -
274N LEU* 5.9 0.2 - - - +
277N GLU* 3.2 32.5 + - - +
278N VAL 3.4 9.8 + - - +
279N ASP* 5.1 5.6 - - + +
280N ILE* 4.1 3.8 - - - +
312N ASN* 5.7 4.0 + - - +
313N ILE* 3.6 6.3 - - - +
314N GLU* 2.8 70.2 + - + +
316N THR* 4.1 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186N TRP* 4.3 15.7 - - + -
191N LEU* 4.2 15.3 - - + -
218N ARG* 1.3 81.3 + - - +
220N ALA* 1.3 62.5 - - - +
276N LYS 4.7 0.2 - - - -
277N GLU* 3.8 0.3 - - - -
278N VAL* 2.9 44.6 + - + +
280N ILE* 5.0 0.2 - - + -
312N ASN 3.4 7.2 - - - -
313N ILE* 3.7 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191N LEU* 4.5 3.0 - - - +
218N ARG* 3.8 20.6 - - - +
219N ALA* 1.3 77.2 - - - +
221N LEU* 1.3 61.5 + - - +
222N TYR* 3.7 23.7 - - + +
274N LEU* 3.9 12.1 - - + -
276N LYS 3.3 6.1 - - - +
277N GLU* 4.8 1.8 - - - -
311N PHE* 3.0 8.2 - - - +
312N ASN* 2.9 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190N CYS* 4.0 30.7 - - - +
191N LEU* 4.1 11.2 - - + +
192N PHE* 4.2 19.5 - - + -
220N ALA* 1.3 73.6 - - - +
222N TYR* 1.3 56.9 + - - +
274N LEU* 3.6 4.3 - - - +
275N ILE* 2.8 56.6 + - + -
276N LYS* 2.8 23.5 + - + +
290N PHE* 4.8 6.1 - - + -
309N THR* 4.2 15.0 - - + -
310N TYR 3.5 17.9 - - - +
311N PHE* 4.0 11.2 - - + -
358N ILE* 5.9 1.1 - - + -
360N MET* 5.0 3.8 - - - -
372N PHE* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 222 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218N ARG* 5.2 3.1 + - - -
220N ALA* 3.7 30.4 - - + +
221N LEU* 1.3 75.7 - - - +
223N VAL* 1.3 61.4 + - - +
272N ALA* 4.3 4.9 - - + -
273N CYS 3.2 22.9 - - - +
274N LEU* 3.6 31.0 - - + +
275N ILE* 4.2 3.8 - - - -
309N THR* 3.1 30.8 - - - +
310N TYR* 2.8 54.4 + + + +
312N ASN* 3.3 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222N TYR* 1.3 72.5 - - - +
224N VAL* 1.3 69.6 + - - +
272N ALA* 3.4 1.7 - - - +
273N CYS* 3.0 33.6 + - + +
275N ILE* 3.5 31.2 - - + -
294N PHE* 4.0 23.8 - - + -
296N LEU* 3.5 9.4 - - + +
307N LEU* 4.6 21.5 - - + -
308N VAL 3.3 7.0 - - - +
309N THR* 3.7 23.6 - - + -
310N TYR* 5.3 0.4 - - - -
340N PHE* 6.1 0.2 - - + -
358N ILE* 4.9 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223N VAL* 1.3 79.6 - - - +
225N ALA* 1.3 65.7 + - - +
226N ILE* 4.1 5.6 - - + -
268N VAL* 3.4 40.8 - - + -
270N THR* 3.7 5.2 - - - -
271N ASN 3.4 18.2 - - - +
272N ALA* 3.8 15.9 - - + -
296N LEU* 3.9 7.9 - - - -
307N LEU* 3.4 4.7 - - - +
308N VAL* 2.8 39.6 + - + +
310N TYR* 4.2 14.8 - - + -
328N PRO* 5.6 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224N VAL* 1.3 75.6 - - - +
226N ILE* 1.3 68.0 + - - +
269N VAL* 3.0 24.9 + - - +
270N THR* 3.1 27.7 + - + -
296N LEU* 3.8 5.5 - - + +
304N VAL* 3.9 21.8 - - + -
306N ALA 3.4 9.6 - - - +
307N LEU* 3.9 11.7 - - + -
354N ILE* 4.1 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 226 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224N VAL* 4.1 3.4 - - + -
225N ALA* 1.3 80.9 - - - +
227N GLU* 1.3 61.4 + - - +
228N ASP* 3.9 28.0 - - + +
263N VAL* 4.0 22.4 - - + -
267N GLN* 3.3 20.2 - - + +
268N VAL* 4.0 19.3 - - + -
269N VAL* 4.2 4.5 - - - -
303N TYR 4.1 2.5 - - - -
304N VAL* 3.2 4.6 - - - -
305N HIS 2.9 23.7 + - - -
306N ALA* 2.9 25.7 + - + +
308N VAL* 3.5 34.3 - - + -
339N VAL* 4.6 3.1 - - + -
----------------------------------------------------------
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