Contacts of the strand formed by residues 218 - 226 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216F PRO* 3.9 1.4 - - - +
217F ASP* 1.3 83.2 + - - +
219F ALA* 1.3 63.8 + - - +
220F ALA* 3.8 24.8 - - - +
222F TYR* 5.2 2.8 + - - -
277F GLU* 3.1 34.1 + - - +
278F VAL 3.5 7.8 + - - +
279F ASP* 5.1 7.6 - - + +
280F ILE* 4.8 2.4 - - - +
312F ASN* 5.8 3.6 + - - +
313F ILE* 3.5 6.6 - - - +
314F GLU* 2.9 70.9 + - + +
316F THR* 4.0 21.3 - - + -
349K ARG* 5.4 2.8 - - - +
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Residues in contact with ALA 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F TRP* 4.3 14.1 - - + -
191F LEU* 4.1 17.0 - - + -
218F ARG* 1.3 78.9 + - - +
220F ALA* 1.3 63.6 + - - +
277F GLU* 3.7 2.6 - - - +
278F VAL* 2.9 45.8 + - + +
280F ILE* 5.1 0.2 - - + -
312F ASN 3.4 7.2 - - - -
313F ILE* 3.6 21.5 - - + -
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Residues in contact with ALA 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191F LEU* 4.6 2.6 - - - +
218F ARG* 3.8 19.7 - - - +
219F ALA* 1.3 77.8 - - - +
221F LEU* 1.3 59.7 - - - +
222F TYR* 3.8 24.4 - - + +
274F LEU* 3.8 13.2 - - + -
276F LYS 3.2 6.7 - - - +
277F GLU* 4.8 1.3 - - - -
311F PHE* 3.1 8.4 - - - +
312F ASN* 3.0 35.5 + - + +
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Residues in contact with LEU 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F CYS* 4.1 31.9 - - - +
191F LEU* 4.2 10.5 - - + -
192F PHE* 4.3 19.7 - - + -
220F ALA* 1.3 75.1 - - - +
222F TYR* 1.3 57.5 + - - +
274F LEU* 3.7 3.3 - - - +
275F ILE* 2.8 57.5 + - + +
276F LYS* 2.7 26.3 + - + +
290F PHE* 4.9 1.8 - - + -
309F THR* 4.2 14.1 - - + -
310F TYR 3.6 17.3 - - - +
311F PHE* 4.1 11.0 - - + -
358F ILE* 5.8 0.9 - - + -
360F MET* 4.7 8.7 - - - -
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Residues in contact with TYR 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F ARG* 5.2 2.6 + - - -
220F ALA* 3.8 28.2 - - + +
221F LEU* 1.3 74.8 - - - +
223F VAL* 1.3 62.8 + - - +
272F ALA* 4.3 7.4 - - + -
273F CYS 3.2 17.3 - - - +
274F LEU* 3.6 32.5 - - + +
275F ILE* 4.4 3.6 - - - -
309F THR* 3.0 29.3 - - - -
310F TYR* 2.8 59.0 + + + +
312F ASN* 3.3 23.4 + - - -
351K GLY* 6.3 1.3 - - - -
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Residues in contact with VAL 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F TYR* 1.3 72.7 - - - +
224F VAL* 1.3 71.4 + - - +
272F ALA* 3.4 1.6 - - - +
273F CYS* 3.0 39.7 + - + +
275F ILE* 3.5 32.1 - - + -
294F PHE* 4.1 15.9 - - + -
296F LEU* 3.5 10.4 - - + +
307F LEU* 4.6 20.6 - - + -
308F VAL 3.3 7.6 - - - +
309F THR* 3.6 24.5 - - + -
310F TYR* 5.1 0.4 - - - -
358F ILE* 4.9 9.0 - - + -
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Residues in contact with VAL 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F VAL* 1.3 79.9 - - - +
225F ALA* 1.3 65.1 + - - +
226F ILE* 4.0 8.3 - - + -
268F VAL* 3.5 40.2 - - + -
270F THR* 3.7 4.3 - - - +
271F ASN 3.4 18.4 - - - +
272F ALA* 3.7 14.4 - - + -
296F LEU* 3.8 7.8 - - - +
307F LEU* 3.3 7.3 - - - +
308F VAL* 2.9 37.9 + - + +
310F TYR* 4.2 15.0 - - + -
328F PRO* 5.5 3.1 - - + -
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Residues in contact with ALA 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224F VAL* 1.3 74.4 - - - +
226F ILE* 1.3 67.6 + - - +
269F VAL* 3.0 24.4 + - - +
270F THR* 3.1 26.9 + - + -
296F LEU* 3.7 6.0 - - + +
304F VAL* 3.8 24.7 - - + -
306F ALA 3.4 5.8 - - - +
307F LEU* 3.9 12.3 - - + -
354F ILE* 4.1 5.4 - - + -
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Residues in contact with ILE 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224F VAL* 4.0 3.8 - - + -
225F ALA* 1.3 79.5 - - - +
227F GLU* 1.3 61.4 + - - +
228F ASP* 3.9 26.5 - - + +
263F VAL* 4.0 16.2 - - + -
267F GLN* 3.3 27.6 - - - +
268F VAL* 3.9 19.7 - - + -
269F VAL* 4.1 7.0 - - - -
303F TYR 4.2 0.2 - - - -
304F VAL* 3.3 4.0 - - - -
305F HIS 2.8 24.3 + - - -
306F ALA* 3.0 24.7 + - + +
308F VAL* 3.6 34.5 - - + -
339F VAL* 4.7 4.9 - - + -
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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