Contacts of the strand formed by residues 218 - 226 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PRO* 3.9 1.9 - - - +
217A ASP* 1.3 82.9 + - - +
219A ALA* 1.3 62.6 + - - +
220A ALA* 3.8 24.4 - - - +
222A TYR* 5.2 3.0 + - - -
274A LEU* 5.9 0.2 - - - +
277A GLU* 3.1 34.1 + - - +
278A VAL 3.4 8.5 - - - +
279A ASP* 5.1 6.7 - - + +
280A ILE* 4.7 2.8 - - - +
312A ASN* 5.9 4.2 + - - +
313A ILE* 3.7 5.4 - - - +
314A GLU* 2.8 68.4 + - + +
316A THR* 4.0 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TRP* 4.4 14.8 - - + -
191A LEU* 4.2 16.8 - - + -
218A ARG* 1.3 78.5 + - - +
220A ALA* 1.3 62.3 + - - +
276A LYS 4.0 0.2 - - - +
277A GLU* 3.6 2.4 - - - +
278A VAL* 2.7 49.5 + - + +
280A ILE* 5.0 0.7 - - + -
312A ASN 3.4 7.0 - - - -
313A ILE* 3.7 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LEU* 4.5 2.4 - - - +
218A ARG* 3.8 20.4 - - - +
219A ALA* 1.3 77.2 - - - +
221A LEU* 1.3 60.3 + - - +
222A TYR* 3.8 22.9 - - + +
274A LEU* 3.8 14.4 - - + -
276A LYS 3.3 6.1 - - - +
277A GLU* 4.7 1.3 - - - -
311A PHE* 3.0 7.9 - - - +
312A ASN* 2.8 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A CYS* 4.1 30.5 - - - +
191A LEU* 4.2 10.1 - - + -
192A PHE* 4.3 19.1 - - + -
220A ALA* 1.3 74.6 - - - +
222A TYR* 1.3 62.6 + - - +
274A LEU* 3.7 4.0 - - - +
275A ILE* 2.9 52.0 + - + +
276A LYS* 2.9 22.9 + - + +
290A PHE* 4.8 2.0 - - + -
309A THR* 4.2 14.1 - - + +
310A TYR 3.6 17.0 - - - +
311A PHE* 4.1 10.5 - - + -
358A ILE* 5.8 1.1 - - + -
360A MET* 4.8 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ARG* 5.2 2.6 + - - -
220A ALA* 3.8 30.0 - - + +
221A LEU* 1.3 76.7 - - - +
223A VAL* 1.3 62.6 + - - +
272A ALA* 4.3 4.5 - - + -
273A CYS* 3.1 28.7 - - - +
274A LEU* 3.6 25.7 - - + +
275A ILE* 4.3 4.5 - - - -
308A VAL 4.4 0.2 - - - -
309A THR* 3.0 30.0 - - - +
310A TYR* 2.8 55.4 + + + +
312A ASN* 3.1 25.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A TYR* 1.3 72.6 - - - +
224A VAL* 1.3 68.8 + - - +
272A ALA* 3.4 1.9 - - - +
273A CYS* 2.9 39.0 + - + +
275A ILE* 3.6 31.9 - - + -
294A PHE* 4.1 15.9 - - + -
296A LEU* 3.5 11.5 - - + +
307A LEU* 4.6 21.5 - - + -
308A VAL 3.3 6.1 - - - +
309A THR* 3.5 24.9 - - + -
310A TYR* 5.2 0.2 - - - -
358A ILE* 4.9 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A VAL* 1.3 81.8 - - - +
225A ALA* 1.3 64.2 + - - +
226A ILE* 4.0 7.6 - - + -
268A VAL* 3.5 38.4 - - + -
270A THR* 3.7 5.8 - - - +
271A ASN 3.4 18.4 - - - +
272A ALA* 3.8 14.6 - - + -
296A LEU* 3.9 7.4 - - - +
307A LEU* 3.4 3.8 - - - +
308A VAL* 2.8 40.5 + - + +
310A TYR* 4.2 14.4 - - + -
328A PRO* 5.5 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A VAL* 1.3 76.1 - - - +
226A ILE* 1.3 64.3 + - - +
268A VAL* 3.6 1.4 - - - -
269A VAL* 2.8 25.7 + - - -
270A THR* 3.1 27.7 + - + -
296A LEU* 3.8 3.0 - - + +
304A VAL* 3.8 26.0 - - + -
306A ALA 3.5 6.1 - - - +
307A LEU* 4.0 11.9 - - + -
354A ILE* 4.1 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A VAL* 4.0 2.9 - - + -
225A ALA* 1.3 79.9 - - - +
227A GLU* 1.3 59.9 + - - +
228A ASP* 3.9 27.4 - - + +
263A VAL* 4.0 22.7 - - + -
267A GLN* 3.4 13.2 - - + +
268A VAL* 3.8 26.2 - - + -
269A VAL* 4.2 4.3 - - - -
303A TYR 4.1 3.1 - - - -
304A VAL* 3.4 3.6 - - - -
305A HIS 3.0 23.2 + - - -
306A ALA* 2.9 29.1 + - + +
308A VAL* 3.6 31.2 - - + -
339A VAL* 4.6 4.7 - - + -
----------------------------------------------------------
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