Contacts of the strand formed by residues 273 - 279 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222E TYR* 3.3 6.5 - - - -
223E VAL* 3.0 36.2 + - + +
272E ALA* 1.3 74.4 - - - +
274E LEU* 1.3 78.8 + - - +
293E ALA 4.4 1.1 - - - -
294E PHE* 3.5 16.6 - - - -
295E CYS* 3.3 42.8 - - - +
296E LEU* 3.8 9.6 - - + -
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Residues in contact with LEU 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E ALA* 3.9 10.1 - - + -
221E LEU 3.6 14.8 - - - +
222E TYR* 3.7 35.1 - - + +
273E CYS* 1.3 82.7 - - - +
275E ILE* 1.3 63.4 + - - +
276E LYS 3.8 22.0 - - - +
277E GLU* 3.8 28.5 - - + +
293E ALA 4.3 4.5 - - - +
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Residues in contact with ILE 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E LEU* 2.9 46.6 + - + +
222E TYR 4.3 4.5 - - - +
223E VAL* 3.6 35.7 - - + -
273E CYS 3.5 0.2 + - - -
274E LEU* 1.3 80.6 - - - +
276E LYS* 1.3 67.8 + - - +
290E PHE* 3.8 7.4 - - + -
292E SER* 2.6 34.3 + - - +
293E ALA 4.2 3.8 - - - +
294E PHE* 3.8 17.3 - - + -
309E THR* 4.7 1.8 - - + -
358E ILE* 3.8 35.2 - - + -
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Residues in contact with LYS 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E LEU* 5.3 0.2 - - - +
192E PHE* 3.9 22.4 - - + -
219E ALA 4.1 0.3 - - - +
220E ALA* 3.2 4.2 - - - -
221E LEU* 2.8 45.1 + - + +
274E LEU* 3.8 6.5 - - - +
275E ILE* 1.3 83.2 - - - +
277E GLU* 1.3 75.6 + - - +
278E VAL* 4.2 8.8 - - + +
283E VAL* 5.8 3.1 - - - -
287E GLU* 2.8 38.9 + - - +
288E LEU* 4.8 6.5 - - - -
290E PHE* 3.8 37.3 - - + +
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Residues in contact with GLU 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E ARG* 3.2 38.0 + - - +
219E ALA 3.7 3.4 - - - +
220E ALA* 4.4 1.3 - - + +
274E LEU* 3.8 26.8 - - + +
276E LYS* 1.3 85.1 - - - +
278E VAL* 1.3 72.6 + - - +
279E ASP 4.2 1.1 + - - +
283E VAL* 4.9 2.9 - - - +
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Residues in contact with VAL 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E TRP* 5.2 0.7 - - + -
191E LEU* 4.9 1.1 - - + -
192E PHE* 4.0 28.5 - - + -
197E LEU* 4.2 11.7 - - + -
218E ARG* 3.4 11.8 - - - +
219E ALA* 2.8 44.7 + - + +
276E LYS* 4.2 12.6 - - + +
277E GLU* 1.3 84.9 - - - +
279E ASP* 1.3 59.9 + - - +
280E ILE* 3.4 18.8 + - + -
283E VAL* 3.9 28.9 - - + -
288E LEU* 4.9 2.9 - - + -
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Residues in contact with ASP 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E ASP 4.0 5.6 - - - +
218E ARG* 5.0 6.7 - - + +
277E GLU* 4.2 1.0 - - - +
278E VAL* 1.3 70.2 - - - +
280E ILE* 1.3 58.7 + - - +
281E TYR* 3.0 27.5 + - - +
282E THR* 2.9 48.3 + - - +
283E VAL* 3.0 17.5 + - + +
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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