Contacts of the strand formed by residues 273 - 279 (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 CYS 273 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222L TYR* 3.3 5.4 - - - -
223L VAL* 3.0 34.9 + - + +
272L ALA* 1.3 74.7 - - - +
274L LEU* 1.3 75.1 + - - +
275L ILE 3.5 0.2 + - - -
293L ALA 4.4 1.1 - - - -
294L PHE* 3.6 28.7 - - - -
295L CYS 3.4 28.9 - - - +
296L LEU* 3.8 10.1 - - + -
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Residues in contact with LEU 274 (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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220L ALA* 3.9 11.2 - - + -
221L LEU 3.6 14.6 - - - +
222L TYR* 3.6 33.6 - - + +
273L CYS* 1.3 84.4 - - - +
275L ILE* 1.3 59.7 + - - +
276L LYS 3.8 20.9 - - - +
277L GLU* 3.7 29.2 - - + +
292L SER* 5.0 0.2 + - - -
293L ALA 4.5 3.5 - - - +
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Residues in contact with ILE 275 (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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221L LEU* 2.9 48.4 + - + +
222L TYR 4.2 4.3 - - - +
223L VAL* 3.4 36.3 - - + -
273L CYS 3.5 0.6 + - - +
274L LEU* 1.3 78.6 - - - +
276L LYS* 1.3 64.7 + - - +
290L PHE* 3.8 6.9 - - + -
292L SER* 2.5 34.9 + - - +
293L ALA 4.3 4.0 - - - +
294L PHE* 3.9 16.8 - - + -
309L THR* 4.6 2.0 - - + -
358L ILE* 3.9 36.6 - - + -
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Residues in contact with LYS 276 (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* 5.3 0.5 - - - +
192L PHE* 3.9 22.7 - - + -
219L ALA 4.1 0.2 - - - +
220L ALA* 3.3 3.1 - - - -
221L LEU* 2.8 44.9 + - + +
274L LEU* 3.8 5.4 - - - +
275L ILE* 1.3 82.1 - - - +
277L GLU* 1.3 76.0 + - - +
278L VAL* 4.2 7.8 - - + +
283L VAL* 5.7 3.6 - - - -
287L GLU* 2.8 39.3 + - - +
288L LEU* 4.8 7.4 - - - -
290L PHE* 4.0 34.4 - - + +
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Residues in contact with GLU 277 (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* 3.2 36.4 + - - +
219L ALA 3.7 2.9 - - - +
220L ALA* 4.5 2.2 - - + +
274L LEU* 3.7 27.4 - - + +
276L LYS* 1.3 87.1 - - - +
278L VAL* 1.3 73.9 + - - +
279L ASP 4.3 0.9 - - - +
283L VAL* 4.8 2.9 - - - +
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Residues in contact with VAL 278 (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* 5.2 1.3 - - + -
191L LEU* 4.9 0.9 - - + -
192L PHE* 4.0 29.8 - - + -
197L LEU* 4.2 11.9 - - + -
218L ARG* 3.6 8.6 - - - +
219L ALA* 2.9 44.9 + - + +
276L LYS* 4.2 10.1 - - + +
277L GLU* 1.3 85.6 - - - +
279L ASP* 1.3 59.0 + - - +
280L ILE* 3.4 20.1 + - + -
283L VAL* 3.8 29.8 - - + -
288L LEU* 4.9 2.5 - - + -
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Residues in contact with ASP 279 (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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217L ASP 3.9 4.9 - - - +
218L ARG* 5.2 6.3 - - + +
277L GLU* 4.3 1.2 - - - +
278L VAL* 1.3 73.1 - - - +
280L ILE* 1.3 58.3 + - - +
281L TYR* 3.0 25.1 - - - +
282L THR* 2.8 54.3 + - - +
283L VAL* 3.0 17.2 + - + +
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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