Contacts of the strand formed by residues 273 - 279 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D GLN* 4.6 0.4 - - - -
353D GLU* 3.3 33.4 - - - +
222I TYR* 3.3 5.9 - - - -
223I VAL* 3.0 32.4 + - + +
272I ALA* 1.3 75.2 - - - +
274I LEU* 1.3 75.9 + - - +
275I ILE 3.4 0.5 + - - -
293I ALA 4.4 0.2 - - - -
294I PHE* 3.6 30.3 - - - -
295I CYS 3.3 21.1 - - - +
296I LEU* 3.8 9.6 - - + -
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Residues in contact with LEU 274 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D GLN* 5.5 0.4 + - - -
350D ARG 5.7 1.3 - - - +
351D GLY* 4.1 29.9 + - - +
352D GLU* 5.1 5.6 - - + +
353D GLU* 4.5 5.7 + - - +
220I ALA* 4.0 9.6 - - + -
221I LEU 3.7 12.6 - - - +
222I TYR* 3.5 34.3 - - + +
273I CYS* 1.3 85.8 - - - +
275I ILE* 1.3 60.1 + - - +
276I LYS 3.9 21.1 - - - +
277I GLU* 3.6 31.2 - - + +
293I ALA 4.5 3.6 - - - +
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Residues in contact with ILE 275 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221I LEU* 2.8 49.5 + - + +
222I TYR* 4.2 4.3 - - - +
223I VAL* 3.5 36.6 - - + -
273I CYS 3.4 0.6 + - - +
274I LEU* 1.3 79.1 - - - +
276I LYS* 1.3 67.7 + - - +
290I PHE* 3.9 6.2 - - + -
292I SER* 2.5 34.7 + - - +
293I ALA 4.4 3.4 - - - +
294I PHE* 4.0 16.2 - - + -
309I THR* 4.6 2.9 - - + -
358I ILE* 3.9 35.2 - - + -
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Residues in contact with LYS 276 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191I LEU* 5.3 0.5 - - - +
192I PHE* 3.8 22.0 - - + -
219I ALA 4.1 0.3 - - - +
220I ALA* 3.3 4.2 - - - -
221I LEU* 2.9 44.5 + - + +
274I LEU* 3.8 5.8 - - - +
275I ILE* 1.3 82.4 - - - +
277I GLU* 1.3 75.7 + - - +
278I VAL* 4.1 8.2 - - + +
283I VAL* 5.6 3.8 - - - -
287I GLU* 2.7 39.4 + - - +
288I LEU* 4.7 7.2 - - - -
290I PHE* 3.8 37.3 - - + +
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Residues in contact with GLU 277 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D ARG* 3.1 40.6 + - - -
352D GLU* 5.0 0.9 - - - +
381D GLN* 4.3 11.4 - - - +
218I ARG* 3.4 34.5 + - - +
219I ALA 3.7 2.9 - - - +
220I ALA* 4.6 1.8 - - + +
274I LEU* 3.6 27.8 - - + +
276I LYS* 1.3 85.0 - - - +
278I VAL* 1.3 71.8 + - - +
279I ASP 4.2 0.8 + - - -
283I VAL* 4.9 3.1 - - - +
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Residues in contact with VAL 278 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186I TRP* 5.2 1.1 - - + -
191I LEU* 4.8 1.1 - - + -
192I PHE* 4.0 30.1 - - + -
197I LEU* 4.2 11.9 - - + -
218I ARG* 3.4 11.7 + - - +
219I ALA* 2.9 45.6 + - + +
276I LYS* 4.1 12.8 - - + +
277I GLU* 1.3 85.6 - - - +
279I ASP* 1.3 61.2 + - - +
280I ILE* 3.6 17.6 + - + -
283I VAL* 3.8 29.4 - - + -
288I LEU* 5.0 1.8 - - + -
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Residues in contact with ASP 279 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D GLN* 5.8 4.5 - - - +
217I ASP 3.8 5.6 - - - +
218I ARG* 5.2 5.6 - - + +
277I GLU* 4.2 1.0 + - - +
278I VAL* 1.3 71.4 - - - +
280I ILE* 1.3 61.5 + - - +
281I TYR* 3.3 25.9 + - - +
282I THR* 2.8 50.6 + - - +
283I VAL* 2.9 18.3 + - + +
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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