Contacts of the strand formed by residues 384 - 393 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A PHE 3.2 11.2 - - - +
379A LYS* 3.6 34.9 - - + +
380A GLY 4.9 2.0 - - - +
383A CYS* 1.3 81.6 - - - +
385A THR* 1.3 73.7 + - - +
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Residues in contact with THR 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A ASP* 5.8 6.1 - - + +
346A LEU* 4.1 20.6 - - + +
376A LEU* 4.3 7.0 - - - +
377A ASP* 3.6 0.5 - - - +
378A PHE* 2.9 35.4 + - - +
383A CYS* 4.9 7.6 - - + -
384A GLU* 1.3 85.8 - - - +
386A SER* 1.3 63.6 + - - +
387A VAL* 3.8 19.8 - - + +
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Residues in contact with SER 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A LEU 3.2 6.5 - - - -
377A ASP* 3.6 26.3 + - - -
385A THR* 1.3 77.4 - - - +
387A VAL* 1.3 62.7 + - - +
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Residues in contact with VAL 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A GLU* 4.3 10.5 - - + +
374A VAL 4.5 0.7 - - - -
375A ASP* 3.3 5.4 - - - +
376A LEU* 2.9 40.6 + - + +
377A ASP* 4.6 1.1 + - - +
385A THR* 3.8 27.1 - - + +
386A SER* 1.3 80.7 + - - +
388A SER* 1.3 66.5 + - - +
389A ASN* 3.1 35.0 - - - +
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Residues in contact with SER 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A THR* 3.8 9.2 - - - +
374A VAL 3.6 4.5 - - - -
375A ASP* 2.7 24.7 + - - -
387A VAL* 1.3 78.1 - - - +
389A ASN* 1.3 64.4 + - - +
390A ASP* 4.4 3.3 + - - +
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Residues in contact with ASN 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LYS* 5.3 8.0 - - - +
341A TYR 4.5 0.2 + - - -
342A LEU* 4.2 23.8 - - - +
343A GLU* 3.5 21.5 + - - +
373A THR* 3.4 1.6 - - - +
374A VAL* 3.0 37.1 + - + +
376A LEU* 6.3 1.2 - - - +
387A VAL* 3.1 30.4 - - - +
388A SER* 1.3 75.9 - - - +
390A ASP* 1.3 68.9 + - - +
391A TYR* 3.5 33.1 + - + +
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Residues in contact with ASP 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LYS* 2.9 37.0 - - + +
372A PHE 3.5 5.4 - - - +
373A THR* 2.9 28.0 + - - +
388A SER* 4.4 3.2 + - - -
389A ASN* 1.3 76.8 - - - +
391A TYR* 1.3 70.3 + - - +
392A LYS* 6.3 1.1 - - + -
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Residues in contact with TYR 391 (chain A).
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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255A MET 3.6 23.6 - - - -
256A LYS* 3.0 13.2 - - + +
257A GLU 4.6 0.7 - - - -
258A PRO* 4.2 15.7 - - + -
340A PHE* 3.8 32.7 + + + +
341A TYR 2.4 34.2 + - - -
342A LEU* 4.2 5.5 - - - +
370A LEU 4.5 0.2 - - - -
371A ASP* 3.7 0.7 - - - +
372A PHE* 2.9 45.1 + - + +
374A VAL* 3.8 27.1 - - + +
389A ASN* 3.5 39.3 + - + -
390A ASP* 1.3 78.7 - - - +
392A LYS* 1.3 68.6 + - - +
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Residues in contact with LYS 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LYS* 2.8 17.6 + - + +
257A GLU* 3.6 8.3 - - - +
258A PRO* 3.3 16.0 - - - +
363A ASN* 3.4 29.9 - - - +
369A ASP* 6.1 3.1 - - + +
370A LEU 3.4 4.5 - - - +
371A ASP* 3.6 16.0 + - - +
372A PHE* 5.2 0.2 - - - -
390A ASP* 6.3 1.1 - - + -
391A TYR* 1.3 79.9 - - - +
393A MET* 1.3 62.6 + - - +
394A ARG 3.5 4.2 + - - +
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Residues in contact with MET 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A TYR* 3.9 17.5 - - + -
190A CYS* 4.1 25.8 - - - -
193A TYR* 3.4 53.1 - - + -
258A PRO* 3.7 24.7 - - + +
260A VAL* 4.5 7.4 - - + -
338A THR* 4.2 12.6 - - - -
369A ASP* 3.5 14.2 - - - +
370A LEU* 3.0 22.7 + - + +
372A PHE* 3.9 13.2 - - + -
392A LYS* 1.3 71.0 - - - +
394A ARG* 1.3 85.7 + - + +
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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