Contacts of the strand formed by residues 384 - 393 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378K PHE 3.1 13.2 - - - +
379K LYS* 3.4 37.5 - - + +
380K GLY 5.0 1.3 - - - +
383K CYS* 1.3 79.8 - - - +
385K THR* 1.3 74.8 + - - +
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Residues in contact with THR 385 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344K ASP* 6.0 5.6 - - + +
346K LEU* 4.1 22.3 - - + +
376K LEU* 4.3 7.1 - - - +
377K ASP* 3.5 0.3 - - - -
378K PHE* 2.9 34.6 + - - +
383K CYS* 5.3 5.0 - - + -
384K GLU* 1.3 87.6 - - - +
386K SER* 1.3 63.9 + - - +
387K VAL* 3.8 19.8 - - + +
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Residues in contact with SER 386 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376K LEU 3.3 6.1 - - - -
377K ASP* 3.3 26.7 + - - -
385K THR* 1.3 75.9 - - - +
387K VAL* 1.3 63.0 + - - +
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Residues in contact with VAL 387 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343K GLU* 4.3 11.4 - - + +
374K VAL 3.8 0.8 - - - +
375K ASP* 3.2 5.4 - - - +
376K LEU* 2.8 43.3 + - + +
377K ASP* 4.3 1.5 + - - +
385K THR* 3.8 26.0 - - + +
386K SER* 1.3 81.0 + - - +
388K SER* 1.3 62.4 + - - +
389K ASN* 3.1 32.5 - - - +
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Residues in contact with SER 388 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373K THR* 3.8 11.4 - - - +
374K VAL 3.6 4.0 - - - -
375K ASP* 2.8 23.1 + - - -
387K VAL* 1.3 76.5 - - - +
389K ASN* 1.3 66.2 + - - +
390K ASP* 4.4 3.4 + - - -
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Residues in contact with ASN 389 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256K LYS* 5.5 7.9 - - - +
341K TYR 4.4 0.4 + - - -
342K LEU* 3.9 25.9 - - - +
343K GLU* 3.6 18.7 - - - +
373K THR* 3.3 4.3 - - - +
374K VAL* 2.9 40.6 + - + +
376K LEU* 6.1 2.4 - - - +
387K VAL* 3.1 29.3 - - - +
388K SER* 1.3 75.5 - - - +
390K ASP* 1.3 63.6 + - - +
391K TYR* 3.4 35.6 + - + +
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Residues in contact with ASP 390 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256K LYS* 2.9 36.5 - - + +
372K PHE 3.6 4.0 - - - +
373K THR* 2.8 31.5 + - - +
388K SER* 4.4 2.9 + - - -
389K ASN* 1.3 73.7 - - - +
391K TYR* 1.3 68.1 + - - +
392K LYS* 6.3 1.6 - - + -
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Residues in contact with TYR 391 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255K MET 3.4 26.5 - - - -
256K LYS* 3.0 15.0 - - + +
257K GLU 4.6 0.2 - - - -
258K PRO* 4.2 16.4 - - + -
340K PHE* 3.8 28.2 + + + +
341K TYR 2.4 37.6 + - - -
342K LEU* 4.2 4.7 - - - +
370K LEU 4.5 0.2 - - - -
371K ASP* 3.5 0.7 - - - +
372K PHE* 2.8 45.0 + - + +
374K VAL* 3.9 22.6 - - + +
389K ASN* 3.4 43.0 + - + -
390K ASP* 1.3 77.2 - - - +
392K LYS* 1.3 68.7 + - - +
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Residues in contact with LYS 392 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256K LYS* 2.8 13.5 + - + +
257K GLU* 3.6 10.6 - - - +
258K PRO* 3.4 15.1 - - - +
363K ASN* 3.4 19.6 - - - +
369K ASP* 6.0 3.6 - - + +
370K LEU 3.3 4.3 - - - +
371K ASP* 3.4 27.9 + - - +
390K ASP* 6.3 1.6 - - + -
391K TYR* 1.3 78.1 - - - +
393K MET* 1.3 63.6 + - - +
394K ARG 3.5 4.6 + - - +
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Residues in contact with MET 393 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189K TYR* 3.7 22.4 - - + +
190K CYS* 4.0 26.7 - - - -
193K TYR* 3.5 46.4 - - + -
258K PRO* 3.8 25.1 - - + +
260K VAL* 4.4 8.3 - - + -
338K THR* 4.2 11.9 - - - -
369K ASP* 3.7 13.7 - - - +
370K LEU* 2.9 21.6 + - + +
372K PHE* 3.9 13.2 - - + -
392K LYS* 1.3 69.7 - - - +
394K ARG* 1.3 88.2 + - + +
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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