Contacts of the strand formed by residues 218 - 226 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216L PRO* 3.8 1.8 - - - +
217L ASP* 1.3 82.0 - - - +
219L ALA* 1.3 63.8 + - - +
220L ALA* 3.8 27.1 - - - +
222L TYR* 5.2 2.8 + - - -
277L GLU* 3.2 32.1 + - - +
278L VAL 3.6 7.4 - - - +
279L ASP* 5.2 6.1 - - + +
280L ILE* 4.6 3.0 - - - +
312L ASN* 5.8 3.6 + - - +
313L ILE* 3.6 7.7 - - - +
314L GLU* 2.9 69.6 + - + +
316L THR* 4.0 20.9 - - + -
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Residues in contact with ALA 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186L TRP* 4.3 15.7 - - + -
191L LEU* 4.3 15.0 - - + -
218L ARG* 1.3 80.6 + - - +
220L ALA* 1.3 62.9 + - - +
276L LYS 4.1 0.4 - - - +
277L GLU* 3.7 2.3 - - - +
278L VAL* 2.9 46.6 + - + +
280L ILE* 4.9 0.4 - - + +
312L ASN 3.4 6.7 - - - -
313L ILE* 3.7 20.0 - - + -
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Residues in contact with ALA 220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191L LEU* 4.7 1.7 - - - +
218L ARG* 3.8 20.6 - - - +
219L ALA* 1.3 77.7 - - - +
221L LEU* 1.3 61.7 + - - +
222L TYR* 3.6 23.4 - - + +
274L LEU* 3.9 12.1 - - + -
276L LYS 3.3 5.2 - - - +
277L GLU* 4.8 1.6 - - - -
311L PHE* 3.1 6.4 - - - -
312L ASN* 2.9 37.1 + - + +
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Residues in contact with LEU 221 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190L CYS* 4.0 30.7 - - - +
191L LEU* 4.2 11.0 - - + +
192L PHE* 4.1 20.6 - - + -
220L ALA* 1.3 73.4 - - - +
222L TYR* 1.3 61.0 + - - +
274L LEU* 3.6 5.4 - - - +
275L ILE* 2.9 50.1 + - + -
276L LYS* 2.8 23.8 + - + +
290L PHE* 4.8 5.8 - - + -
309L THR* 4.1 15.0 - - + +
310L TYR 3.5 20.9 - - - +
311L PHE* 4.1 8.1 - - + -
358L ILE* 5.9 1.3 - - + -
360L MET* 4.9 4.3 - - - -
372L PHE* 6.1 0.4 - - + -
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Residues in contact with TYR 222 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218L ARG* 5.2 2.6 + - - -
220L ALA* 3.6 31.4 - - + +
221L LEU* 1.3 76.1 - - - +
223L VAL* 1.3 62.1 + - - +
272L ALA* 4.3 4.0 - - + -
273L CYS* 3.3 23.6 - - - +
274L LEU* 3.6 29.6 - - + +
275L ILE* 4.2 3.6 - - - -
309L THR* 3.1 30.4 - - - +
310L TYR* 2.8 54.3 + + + +
312L ASN* 3.3 22.6 + - - -
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Residues in contact with VAL 223 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222L TYR* 1.3 72.9 - - - +
224L VAL* 1.3 71.4 + - - +
272L ALA* 3.4 2.4 - - - +
273L CYS* 3.0 33.3 + - + +
275L ILE* 3.4 32.8 - - + -
294L PHE* 4.0 22.4 - - + -
296L LEU* 3.5 9.6 - - + +
307L LEU* 4.6 20.2 - - + -
308L VAL 3.3 6.3 - - - +
309L THR* 3.6 24.5 - - + -
310L TYR* 5.1 0.2 - - - -
358L ILE* 4.9 9.6 - - + -
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Residues in contact with VAL 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223L VAL* 1.3 81.9 - - - +
225L ALA* 1.3 64.3 + - - +
226L ILE* 4.0 8.3 - - + -
268L VAL* 3.5 39.3 - - + -
270L THR* 3.7 4.7 - - - +
271L ASN 3.4 17.9 - - - +
272L ALA* 3.8 14.1 - - + -
296L LEU* 3.9 7.4 - - - -
307L LEU* 3.4 5.9 - - - +
308L VAL* 2.8 38.6 + - + +
310L TYR* 4.2 15.0 - - + -
328L PRO* 5.4 2.5 - - + -
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Residues in contact with ALA 225 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224L VAL* 1.3 73.5 - - - +
226L ILE* 1.3 66.0 + - - +
268L VAL* 3.8 1.4 - - - -
269L VAL* 2.9 27.4 + - - +
270L THR* 2.9 28.8 + - + -
296L LEU* 3.8 4.9 - - + +
304L VAL* 3.9 18.4 - - + -
306L ALA 3.4 10.1 - - - +
307L LEU* 3.9 12.1 - - + -
354L ILE* 4.1 7.2 - - + -
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Residues in contact with ILE 226 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224L VAL* 4.0 3.1 - - + -
225L ALA* 1.3 79.7 - - - +
227L GLU* 1.3 59.8 + - - +
228L ASP* 3.9 27.6 - - + +
263L VAL* 4.0 20.9 - - + -
267L GLN* 3.2 21.3 - - - +
268L VAL* 3.9 20.6 - - + -
269L VAL* 4.1 6.3 - - - -
303L TYR 4.2 0.7 - - - -
304L VAL* 3.4 3.4 - - - -
305L HIS 2.9 23.7 + - - -
306L ALA* 3.0 26.1 + - + +
308L VAL* 3.6 35.0 - - + -
339L VAL* 4.6 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