Contacts of the strand formed by residues 370 - 379 (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 LEU 370 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189C TYR 4.8 2.0 - - - +
190C CYS* 5.0 1.8 - - + -
192C PHE* 3.9 16.8 - - + +
193C TYR* 3.7 36.6 - - + +
195C SER* 4.6 8.7 - - - +
360C MET* 3.8 25.8 - - + -
361C LYS 3.6 13.7 - - - +
362C PRO* 4.6 2.5 - - + -
368C ARG 4.9 0.2 - - - +
369C ASP* 1.3 81.0 - - - +
371C ASP* 1.3 64.5 + - - +
372C PHE* 3.8 34.5 + - + -
392C LYS* 3.3 5.0 - - - +
393C MET* 2.9 39.4 + - + +
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Residues in contact with ASP 371 (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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360C MET* 3.1 26.9 - - - +
361C LYS* 3.1 34.8 + - + +
363C ASN* 3.3 32.2 + - - +
364C ALA 4.8 0.5 + - - -
369C ASP* 4.3 0.7 + - - +
370C LEU* 1.3 75.9 - - - +
372C PHE* 1.3 62.4 + - - +
391C TYR 3.6 4.3 - - - +
392C LYS* 3.2 33.2 + - - +
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Residues in contact with PHE 372 (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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190C CYS* 3.6 29.6 - - + -
221C LEU* 6.1 0.2 - - + -
258C PRO* 4.8 0.2 - - + -
340C PHE* 3.9 24.0 - + + -
358C ILE* 4.3 17.0 - - + -
359C SER 3.3 8.1 - - - -
360C MET* 3.6 29.2 - - + -
370C LEU* 3.8 36.3 - - + -
371C ASP* 1.3 78.9 - - - +
373C THR* 1.3 71.2 + - - +
374C VAL* 4.2 2.5 - - + -
390C ASP* 3.5 5.2 - - - +
391C TYR* 2.9 49.0 + - + +
393C MET* 3.9 19.5 - - + -
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Residues in contact with THR 373 (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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357C THR* 3.7 2.3 + - - +
358C ILE* 3.5 2.6 - - - -
359C SER* 3.1 43.3 + - - +
372C PHE* 1.3 76.7 + - - +
374C VAL* 1.3 62.0 + - - +
375C ASP* 3.6 22.4 - - - +
388C SER* 3.8 10.1 - - - +
389C ASN 3.3 5.8 - - - +
390C ASP* 2.9 23.9 + - - +
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Residues in contact with VAL 374 (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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294C PHE* 4.5 7.4 - - + -
307C LEU* 3.8 29.4 - - + -
340C PHE* 4.8 10.8 - - + -
342C LEU* 5.8 3.4 - - + -
357C THR 3.4 6.7 - - - +
358C ILE* 4.2 22.4 - - + -
372C PHE* 5.0 2.2 - - + -
373C THR* 1.3 76.3 - - - +
375C ASP* 1.3 71.6 + - - +
376C LEU* 4.2 7.4 + - + +
387C VAL 4.0 0.9 - - - +
388C SER* 3.5 0.7 - - - -
389C ASN* 2.8 36.7 + - + +
391C TYR* 4.0 27.8 - - + +
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Residues in contact with ASP 375 (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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294C PHE* 3.8 4.0 - - - -
356C GLY* 3.0 22.7 - - - -
357C THR* 2.9 32.1 + - + +
373C THR* 3.6 11.2 + - - +
374C VAL* 1.3 72.8 - - - +
376C LEU* 1.3 60.7 + - - +
377C ASP* 5.1 3.8 - - - +
387C VAL 3.2 6.7 - - - +
388C SER* 2.5 34.9 + - - -
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Residues in contact with LEU 376 (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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294C PHE* 4.7 2.5 - - + -
307C LEU* 4.3 24.0 - - + -
342C LEU* 4.3 28.7 - - + -
346C LEU* 4.0 24.0 - - + -
354C ILE* 3.6 27.1 - - + -
355C TYR 3.5 3.1 - - - +
374C VAL* 4.6 7.4 - - + +
375C ASP* 1.3 75.4 - - - +
377C ASP* 1.3 74.2 + - - +
378C PHE* 4.4 2.0 - - + +
385C THR* 4.5 11.7 - - - +
386C SER* 3.2 2.4 - - - -
387C VAL* 2.9 42.9 + - + +
389C ASN* 6.1 1.1 - - - +
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Residues in contact with ASP 377 (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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353C GLU 4.3 0.7 - - - +
354C ILE* 3.9 0.9 - - - -
355C TYR* 2.7 50.8 + - + +
356C GLY* 4.6 1.2 - - - -
375C ASP* 5.1 3.5 - - - +
376C LEU* 1.3 81.5 + - - +
378C PHE* 1.3 62.3 + - - +
385C THR 3.5 2.2 - - - -
386C SER* 3.3 25.9 + - - -
387C VAL 4.3 1.6 + - - +
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Residues in contact with PHE 378 (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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298C ILE* 4.2 3.4 - - + -
346C LEU* 4.4 21.8 - - + -
347C THR 4.0 6.1 - - - -
348C VAL* 3.6 21.3 - - + -
352C GLU* 3.5 37.5 - - + -
353C GLU 3.2 32.5 - - - -
354C ILE* 3.9 8.5 - - + -
376C LEU* 4.5 4.0 - - + -
377C ASP* 1.3 76.2 - - - +
379C LYS* 1.3 60.9 + - - +
380C GLY* 3.5 18.4 - - - -
383C CYS* 3.5 34.5 - - - -
384C GLU* 3.1 7.0 - - - +
385C THR* 2.8 39.2 + - - +
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Residues in contact with LYS 379 (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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352C GLU* 5.5 1.7 - - - +
353C GLU 4.7 2.9 + - - +
378C PHE* 1.3 77.3 - - - +
380C GLY* 1.3 63.8 + - - +
383C CYS 4.1 2.2 - - - -
384C GLU* 3.5 37.2 - - + +
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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