Contacts of the strand formed by residues 273 - 279 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222H TYR* 3.2 6.1 - - - -
223H VAL* 2.9 37.2 + - + +
272H ALA* 1.3 75.0 - - - +
274H LEU* 1.3 73.7 + - - +
275H ILE 3.4 0.7 + - - -
294H PHE* 3.7 13.5 - - - -
295H CYS 3.4 35.4 - - - +
296H LEU* 3.8 10.1 - - + -
297M GLN* 4.5 0.9 - - - +
353M GLU* 3.1 36.6 - - - +
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Residues in contact with LEU 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220H ALA* 4.0 9.6 - - + -
221H LEU 3.7 7.9 - - - +
222H TYR* 3.7 33.6 - - + +
273H CYS* 1.3 82.8 - - - +
275H ILE* 1.3 62.1 + - - +
276H LYS 3.5 28.7 - - - +
277H GLU* 3.8 30.3 - - + +
292H SER* 4.8 0.2 + - - -
293H ALA 4.5 3.6 - - - +
297M GLN* 5.3 0.8 + - - -
350M ARG 5.7 0.7 - - - +
351M GLY* 3.9 32.0 + - - +
352M GLU* 5.0 4.3 - - + +
353M GLU* 4.5 5.8 + - - +
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Residues in contact with ILE 275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221H LEU* 2.9 48.1 + - + +
222H TYR* 4.3 4.3 - - - +
223H VAL* 3.5 36.8 - - + -
273H CYS 3.8 0.2 - - - +
274H LEU* 1.3 77.6 - - - +
276H LYS* 1.3 66.6 + - - +
290H PHE* 3.8 7.5 - - + -
292H SER* 2.7 34.0 + - - +
293H ALA 4.1 4.5 - - - +
294H PHE* 3.9 17.7 - - + -
309H THR* 4.7 2.0 - - + -
358H ILE* 3.9 35.2 - - + -
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Residues in contact with LYS 276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191H LEU* 5.8 0.2 - - + -
192H PHE* 4.0 20.6 - - + -
220H ALA* 3.3 4.5 - - - -
221H LEU* 2.9 43.0 + - + +
274H LEU* 3.5 7.2 - - - +
275H ILE* 1.3 85.1 - - - +
277H GLU* 1.3 74.1 + - - +
278H VAL* 4.1 8.9 - - + +
283H VAL* 5.7 3.6 - - - -
287H GLU* 2.8 39.6 + - - +
288H LEU* 4.9 6.5 - - - -
290H PHE* 3.9 34.7 - - + +
292H SER* 6.1 0.2 - - - -
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Residues in contact with GLU 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218H ARG* 3.1 37.1 + - - +
219H ALA 3.7 2.7 - - - -
220H ALA* 4.5 1.8 - - + +
274H LEU* 3.8 25.8 - - + +
276H LYS* 1.3 87.6 - - - +
278H VAL* 1.3 70.9 + - - +
279H ASP 4.2 0.4 + - - -
283H VAL* 4.9 2.9 - - - +
349M ARG* 3.4 38.2 + - - -
350M ARG 5.8 0.5 - - - +
352M GLU* 5.4 1.4 - - - +
381M GLN* 4.5 5.6 - - - +
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Residues in contact with VAL 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186H TRP* 5.2 0.9 - - + -
191H LEU* 4.8 1.6 - - + -
192H PHE* 3.9 30.1 - - + -
197H LEU* 4.2 12.8 - - + -
218H ARG* 3.4 10.9 + - - +
219H ALA* 2.8 48.0 + - + +
276H LYS* 4.1 11.2 - - + -
277H GLU* 1.3 85.9 - - - +
279H ASP* 1.3 59.8 + - - +
280H ILE* 3.5 18.3 + - + -
283H VAL* 3.9 28.0 - - + -
288H LEU* 5.0 1.3 - - + -
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Residues in contact with ASP 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217H ASP 3.9 5.4 - - - +
218H ARG* 5.0 6.3 - - + +
277H GLU* 4.2 1.2 - - - +
278H VAL* 1.3 73.1 - - - +
280H ILE* 1.3 64.4 + - - +
281H TYR* 3.4 26.2 - - - +
282H THR* 3.0 40.9 + - - +
283H VAL* 3.0 19.5 + - + +
381M GLN* 6.0 1.8 - - - +
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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