Contacts of the strand formed by residues 218 - 226 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216O PRO* 3.9 1.6 - - - +
217O ASP* 1.3 81.2 + - - +
219O ALA* 1.3 63.2 + - - +
220O ALA* 3.7 26.7 - - - +
222O TYR* 5.0 3.6 + - - -
277O GLU* 3.3 32.3 + - - +
278O VAL 3.5 8.7 - - - +
279O ASP* 4.9 7.6 - - + +
280O ILE* 4.7 2.9 - - - +
312O ASN* 5.8 4.2 + - - +
313O ILE* 3.6 6.3 - - - +
314O GLU* 2.7 72.2 + - + +
316O THR* 4.0 21.5 - - + -
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Residues in contact with ALA 219 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186O TRP* 4.3 12.6 - - + -
191O LEU* 4.1 20.9 - - + -
218O ARG* 1.3 79.6 + - - +
220O ALA* 1.3 63.0 + - - +
276O LYS 4.0 0.6 - - - +
277O GLU* 3.7 2.9 - - - +
278O VAL* 2.9 42.1 + - + +
280O ILE* 5.0 0.4 - - + -
312O ASN 3.3 7.0 - - - +
313O ILE* 3.7 20.6 - - + -
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Residues in contact with ALA 220 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191O LEU* 4.7 1.7 - - - +
218O ARG* 3.7 19.5 - - - +
219O ALA* 1.3 76.0 - - - +
221O LEU* 1.3 59.3 + - - +
222O TYR* 3.5 30.8 - - + +
274O LEU* 3.8 10.5 - - + -
276O LYS 3.4 6.1 - - - +
277O GLU* 4.9 1.1 - - - -
311O PHE* 3.1 7.7 - - - -
312O ASN* 2.9 39.2 + - + +
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Residues in contact with LEU 221 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190O CYS* 4.2 22.0 - - - +
191O LEU* 4.1 19.9 - - + +
192O PHE* 4.3 19.5 - - + -
220O ALA* 1.3 73.1 - - - +
222O TYR* 1.3 60.3 + - - +
274O LEU* 3.7 2.3 - - - +
275O ILE* 2.8 58.5 + - + -
276O LYS* 2.9 22.2 + - + +
290O PHE* 4.9 5.4 - - + -
309O THR* 4.2 13.5 - - - -
310O TYR 3.5 17.5 - - - +
311O PHE* 4.1 10.8 - - + -
358O ILE* 5.9 1.1 - - + -
360O MET* 5.1 4.0 - - - -
372O PHE* 6.1 0.2 - - + -
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Residues in contact with TYR 222 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218O ARG* 5.0 3.5 + - - -
220O ALA* 3.5 32.9 - - + +
221O LEU* 1.3 76.2 - - - +
223O VAL* 1.3 62.5 + - - +
272O ALA* 4.4 7.6 - - + -
273O CYS* 3.3 6.3 - - - +
274O LEU* 3.6 41.8 - - + +
275O ILE* 4.2 3.6 - - - -
308O VAL 4.4 0.2 - - - -
309O THR* 3.0 31.0 - - - +
310O TYR* 2.8 55.5 + + + +
312O ASN* 3.4 23.4 + - - -
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Residues in contact with VAL 223 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222O TYR* 1.3 72.7 - - - +
224O VAL* 1.3 71.5 + - - +
272O ALA* 3.4 1.9 - - - +
273O CYS* 3.0 39.0 + - + +
275O ILE* 3.5 32.5 - - + -
294O PHE* 4.1 19.1 - - + -
296O LEU* 3.4 9.1 - - + +
307O LEU* 4.6 19.5 - - + -
308O VAL 3.3 6.5 - - - +
309O THR* 3.6 25.1 - - + -
310O TYR* 5.2 0.4 - - - -
358O ILE* 5.0 9.6 - - + -
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Residues in contact with VAL 224 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223O VAL* 1.3 83.3 - - - +
225O ALA* 1.3 66.2 + - - +
226O ILE* 4.0 6.3 - - + -
268O VAL* 3.4 38.8 - - + -
270O THR* 3.5 5.6 - - - +
271O ASN 3.3 18.6 - - - +
272O ALA* 3.7 14.4 - - + -
296O LEU* 3.8 8.0 - - - +
307O LEU* 3.4 6.9 - - - +
308O VAL* 2.9 37.9 + - + +
310O TYR* 4.2 14.8 - - + -
328O PRO* 5.6 1.8 - - + -
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Residues in contact with ALA 225 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224O VAL* 1.3 72.7 - - - +
226O ILE* 1.3 68.2 + - - +
268O VAL* 3.6 1.6 - - - -
269O VAL* 2.9 25.4 + - - +
270O THR* 2.8 29.1 + - + -
296O LEU* 3.8 5.3 - - + +
304O VAL* 3.8 23.8 - - + -
306O ALA 3.4 5.6 - - - +
307O LEU* 3.9 11.9 - - + -
354O ILE* 4.1 6.1 - - + -
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Residues in contact with ILE 226 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224O VAL* 4.0 3.6 - - + -
225O ALA* 1.3 81.1 - - - +
227O GLU* 1.3 56.8 - - - +
228O ASP* 3.8 27.6 - - + +
263O VAL* 4.0 21.8 - - + -
267O GLN* 3.3 18.6 - - - +
268O VAL* 3.8 20.6 - - + -
269O VAL* 4.2 6.5 - - - -
304O VAL* 3.5 3.9 - - - -
305O HIS 2.8 29.8 + - - -
306O ALA* 2.8 27.2 + - + +
308O VAL* 3.6 31.4 - - + -
339O VAL* 4.6 4.3 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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