Contacts of the strand formed by residues 273 - 279 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B TYR* 3.3 7.2 - - - -
223B VAL* 3.0 36.7 + - + +
272B ALA* 1.3 74.1 - - - +
274B LEU* 1.3 70.8 + - - +
275B ILE* 3.6 0.6 + - - -
293B ALA 4.3 0.2 - - - -
294B PHE* 3.5 15.7 - - - -
295B CYS 3.5 35.4 - - - +
296B LEU* 3.9 10.3 - - + +
297G GLN* 4.3 0.9 - - - +
353G GLU* 3.1 36.6 - - - +
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B ALA* 3.9 10.5 - - + -
221B LEU 3.7 6.1 - - - +
222B TYR* 3.6 35.6 - - + +
272B ALA 4.3 0.2 + - - -
273B CYS* 1.3 79.3 - - - +
275B ILE* 1.3 63.3 + - - +
276B LYS 3.7 27.6 - - - +
277B GLU* 3.7 29.6 - - + +
292B SER* 4.8 0.3 + - - -
293B ALA 4.4 2.9 - - - +
297G GLN* 5.1 0.8 + - - -
350G ARG 5.3 2.0 - - - +
351G GLY* 3.9 34.4 + - - +
352G GLU* 4.9 4.3 - - + +
353G GLU* 4.4 7.4 + - - +
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Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B LEU* 2.9 49.9 + - + +
222B TYR 4.3 4.3 - - - +
223B VAL* 3.6 34.3 - - + -
273B CYS* 4.0 0.9 - - - +
274B LEU* 1.3 78.3 - - - +
276B LYS* 1.3 64.7 + - - +
290B PHE* 3.7 6.5 - - + -
292B SER* 2.5 35.2 + - - +
293B ALA 4.1 4.7 - - - +
294B PHE* 3.9 17.7 - - + -
309B THR* 4.7 2.0 - - + -
358B ILE* 3.9 35.2 - - + -
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Residues in contact with LYS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B LEU* 5.4 0.3 - - - +
192B PHE* 3.9 23.6 - - + -
220B ALA* 3.3 4.3 - - - -
221B LEU* 2.9 44.4 + - + +
274B LEU* 3.7 7.4 - - - +
275B ILE* 1.3 83.6 - - - +
277B GLU* 1.3 74.2 + - - +
278B VAL* 4.2 8.9 - - + +
283B VAL* 5.8 2.5 - - - -
287B GLU* 2.7 40.9 + - - +
288B LEU* 4.8 6.5 - - - -
290B PHE* 3.9 34.4 - - + +
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Residues in contact with GLU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ARG* 3.2 34.8 + - - +
219B ALA 3.8 2.9 - - - +
220B ALA* 4.5 2.2 - - + +
274B LEU* 3.7 27.0 - - + +
276B LYS* 1.3 88.1 - - - +
278B VAL* 1.3 70.2 + - - +
279B ASP 4.2 0.6 + - - -
283B VAL* 4.9 2.9 - - - +
349G ARG* 3.4 38.3 + - - -
350G ARG 5.5 2.5 - - - +
352G GLU* 5.5 1.7 - - - +
381G GLN* 4.8 4.7 - - - +
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Residues in contact with VAL 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B TRP* 5.3 1.1 - - + -
191B LEU* 4.9 0.9 - - + -
192B PHE* 4.0 30.5 - - + -
197B LEU* 4.2 12.6 - - + -
218B ARG* 3.5 12.4 + - - +
219B ALA* 2.9 44.1 + - + +
276B LYS* 4.2 10.8 - - + +
277B GLU* 1.3 83.7 - - - +
279B ASP* 1.3 59.2 + - - +
280B ILE* 3.6 19.0 + - + -
283B VAL* 3.9 30.7 - - + -
288B LEU* 4.9 1.3 - - + -
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Residues in contact with ASP 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ASP 4.0 5.0 - - - +
218B ARG* 5.1 6.9 - - + +
277B GLU* 4.2 1.2 + - - +
278B VAL* 1.3 70.1 - - - +
280B ILE* 1.3 61.2 + - - +
281B TYR* 3.1 28.5 - - - +
282B THR* 2.9 51.8 + - - +
283B VAL* 2.9 17.9 + - + +
381G GLN* 5.8 4.0 - - - +
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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