Contacts of the strand formed by residues 384 - 393 (chain C) 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 GLU 384 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378C PHE 3.1 11.4 - - - +
379C LYS* 3.5 37.5 - - + +
380C GLY 5.0 2.0 - - - +
383C CYS* 1.3 79.8 - - - +
385C THR* 1.3 73.3 + - - +
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Residues in contact with THR 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344C ASP* 5.8 6.5 - - + +
346C LEU* 4.0 22.9 - - + +
376C LEU* 3.8 6.4 - - - +
377C ASP* 3.5 1.6 - - - -
378C PHE* 2.8 36.7 + - - +
383C CYS* 5.6 3.7 - - + -
384C GLU* 1.3 84.6 - - - +
386C SER* 1.3 59.3 - - - +
387C VAL* 3.8 20.1 - - + +
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Residues in contact with SER 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C LEU 3.2 6.1 - - - -
377C ASP* 3.3 28.5 + - - -
385C THR* 1.3 75.1 - - - +
387C VAL* 1.3 61.8 + - - +
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Residues in contact with VAL 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343C GLU* 4.1 12.6 - - + +
374C VAL 4.5 0.4 - - - -
375C ASP* 3.2 5.5 - - - +
376C LEU* 2.9 40.9 + - + +
377C ASP* 4.3 1.1 + - - +
385C THR* 3.8 25.8 - - + +
386C SER* 1.3 80.9 + - - +
388C SER* 1.3 63.5 + - - +
389C ASN* 3.1 35.2 - - - +
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Residues in contact with SER 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C THR* 3.8 10.6 - - - +
374C VAL 3.5 0.7 - - - -
375C ASP* 2.5 27.7 + - - -
387C VAL* 1.3 76.3 - - - +
389C ASN* 1.3 65.6 + - - +
390C ASP* 4.4 2.8 + - - -
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Residues in contact with ASN 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C LYS* 5.4 9.3 - - - +
342C LEU* 4.1 24.4 - - - +
343C GLU* 3.6 19.6 + - - +
373C THR* 3.3 3.6 - - - +
374C VAL* 2.8 41.1 + - + +
376C LEU* 6.1 1.6 - - - +
387C VAL* 3.1 31.1 - - - +
388C SER* 1.3 75.8 + - - +
390C ASP* 1.3 63.4 + - - +
391C TYR* 3.3 35.3 + - + +
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Residues in contact with ASP 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C LYS* 2.9 38.7 - - + +
372C PHE 3.5 5.4 - - - +
373C THR* 2.9 26.5 + - - +
388C SER* 4.4 3.5 + - - -
389C ASN* 1.3 74.9 - - - +
391C TYR* 1.3 65.8 + - - +
392C LYS* 6.3 1.1 - - + -
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Residues in contact with TYR 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C MET 3.4 27.1 - - - -
256C LYS* 3.2 13.2 - - + +
257C GLU 4.6 0.4 - - - -
258C PRO* 4.2 16.2 - - + -
340C PHE* 3.8 28.8 - + + +
341C TYR 2.5 35.1 + - - -
342C LEU* 4.2 5.4 - - - +
371C ASP* 3.6 0.9 - - - +
372C PHE* 2.9 41.2 + - + +
374C VAL* 4.0 22.2 - - + +
389C ASN* 3.3 45.2 + - + -
390C ASP* 1.3 79.0 - - - +
392C LYS* 1.3 69.5 + - - +
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Residues in contact with LYS 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C LYS* 2.8 18.4 + - + +
257C GLU* 3.6 8.3 - - - +
258C PRO* 3.3 15.1 - - - +
363C ASN* 3.5 29.3 - - - +
369C ASP* 6.0 3.3 - - + +
370C LEU 3.3 4.9 - - - +
371C ASP* 3.2 20.1 + - - +
372C PHE* 5.3 0.2 - - - -
390C ASP* 6.3 1.1 - - + -
391C TYR* 1.3 78.1 - - - +
393C MET* 1.3 63.5 + - - +
394C ARG 3.5 4.8 + - - +
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Residues in contact with MET 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C TYR* 3.8 22.0 - - + +
190C CYS* 4.1 26.0 - - - -
193C TYR* 3.4 49.3 - - + -
258C PRO* 3.7 25.6 - - + +
260C VAL* 4.4 8.5 - - + -
338C THR* 4.2 11.0 - - - -
369C ASP* 3.7 13.4 - - - +
370C LEU* 2.9 22.9 + - + +
372C PHE* 3.9 11.8 - - + -
392C LYS* 1.3 69.4 - - - +
394C ARG* 1.3 88.0 - - + +
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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