Contacts of the strand formed by residues 384 - 393 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378F PHE 3.3 11.0 - - - +
379F LYS* 3.4 36.5 - - + +
380F GLY 4.9 2.2 - - - +
383F CYS* 1.3 80.4 - - - +
385F THR* 1.3 74.0 + - - +
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Residues in contact with THR 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344F ASP* 5.8 8.1 - - + +
346F LEU* 4.0 22.9 - - + +
376F LEU* 4.0 6.9 - - - +
377F ASP* 3.6 0.7 - - - +
378F PHE* 2.9 35.0 + - - +
383F CYS* 5.1 6.4 - - + -
384F GLU* 1.3 83.8 - - - +
386F SER* 1.3 63.1 + - - +
387F VAL* 3.7 19.8 - - + +
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Residues in contact with SER 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376F LEU 3.3 6.1 - - - -
377F ASP* 3.5 26.8 + - - -
385F THR* 1.3 75.1 - - - +
387F VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343F GLU* 4.0 12.1 - - + +
374F VAL 3.8 0.4 - - - +
375F ASP* 3.2 4.6 - - - +
376F LEU* 2.7 47.6 + - + +
377F ASP* 4.4 0.9 + - - +
385F THR* 3.7 27.4 - - + +
386F SER* 1.3 79.9 - - - +
388F SER* 1.3 64.6 + - - +
389F ASN* 3.2 29.4 - - - +
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Residues in contact with SER 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373F THR* 3.8 10.7 - - - +
374F VAL 3.6 0.7 - - - -
375F ASP* 2.5 28.0 + - - -
387F VAL* 1.3 75.3 - - - +
389F ASN* 1.3 66.1 + - - +
390F ASP* 4.4 3.7 + - - +
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Residues in contact with ASN 389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256F LYS* 5.3 10.0 + - - +
341F TYR 4.7 0.2 + - - -
342F LEU* 4.2 23.4 - - - +
343F GLU* 3.4 22.1 + - - +
373F THR* 3.4 3.0 - - - +
374F VAL* 2.8 40.9 + - + +
376F LEU* 6.2 1.4 - - - +
387F VAL* 3.2 24.8 - - - +
388F SER* 1.3 79.3 + - - +
390F ASP* 1.3 66.1 + - - +
391F TYR* 3.6 33.2 + - + +
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Residues in contact with ASP 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256F LYS* 2.9 37.8 - - + +
372F PHE 3.6 5.6 - - - +
373F THR* 2.9 27.4 + - - +
388F SER* 4.8 4.0 + - - -
389F ASN* 1.3 76.0 - - - +
391F TYR* 1.3 66.1 + - - +
392F LYS* 6.3 1.3 - - + -
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Residues in contact with TYR 391 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255F MET 3.6 24.9 - - - -
256F LYS* 3.2 13.5 - - + +
258F PRO* 4.2 16.4 - - + -
340F PHE* 3.8 34.2 + + + +
341F TYR 2.5 33.2 + - - -
342F LEU* 4.2 5.9 - - - +
371F ASP* 3.6 0.9 - - - +
372F PHE* 2.8 42.0 + - + +
374F VAL* 3.9 22.9 - - + +
389F ASN* 3.6 42.0 + - + -
390F ASP* 1.3 78.6 - - - +
392F LYS* 1.3 70.6 + - - +
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Residues in contact with LYS 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256F LYS* 2.9 16.1 + - + +
257F GLU* 3.7 10.6 - - - +
258F PRO* 3.4 14.0 - - - +
363F ASN* 3.3 30.5 - - - +
369F ASP* 6.2 2.0 - - + +
370F LEU 3.4 4.5 - - - +
371F ASP* 3.6 15.8 + - - +
372F PHE* 5.3 0.2 - - - -
390F ASP* 6.3 1.6 - - + -
391F TYR* 1.3 81.4 - - - +
393F MET* 1.3 62.6 + - - +
394F ARG 3.4 4.2 + - - +
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Residues in contact with MET 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F TYR* 3.9 18.4 - - + -
190F CYS* 4.0 26.0 - - - -
193F TYR* 3.4 53.0 - - + -
258F PRO* 3.8 26.0 - - + +
260F VAL* 4.4 8.3 - - + -
338F THR* 4.2 12.8 - - - -
369F ASP* 3.7 12.9 - - - +
370F LEU* 2.9 23.0 + - + +
372F PHE* 3.9 12.1 - - + -
392F LYS* 1.3 70.4 - - - +
394F ARG* 1.3 84.7 + - + +
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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