Contacts of the strand formed by residues 384 - 393 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378H PHE 3.2 10.8 - - - +
379H LYS* 3.4 37.8 - - + +
380H GLY 5.0 1.3 - - - +
383H CYS* 1.3 79.8 - - - +
385H THR* 1.3 73.1 + - - +
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Residues in contact with THR 385 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344H ASP* 5.8 7.9 - - + +
346H LEU* 3.9 23.8 - - + +
376H LEU* 3.9 6.3 - - - +
377H ASP* 3.5 0.5 - - - -
378H PHE* 2.8 35.5 + - - +
383H CYS* 5.4 4.5 - - + -
384H GLU* 1.3 83.4 - - - +
386H SER* 1.3 63.6 + - - +
387H VAL* 3.9 19.1 - - + +
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Residues in contact with SER 386 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376H LEU 3.2 6.3 - - - -
377H ASP* 3.3 30.5 + - - -
385H THR* 1.3 75.6 - - - +
387H VAL* 1.3 61.8 + - - +
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Residues in contact with VAL 387 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343H GLU* 4.2 9.9 - - + +
374H VAL 3.9 0.8 - - - +
375H ASP* 3.2 4.7 - - - +
376H LEU* 2.8 45.1 + - + +
377H ASP* 4.7 1.1 + - - +
385H THR* 3.9 24.9 - - + +
386H SER* 1.3 80.9 + - - +
388H SER* 1.3 64.5 + - - +
389H ASN* 3.2 31.0 - - - +
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Residues in contact with SER 388 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373H THR* 3.9 10.2 - - - +
374H VAL 3.6 3.6 - - - -
375H ASP* 2.8 23.1 + - - -
387H VAL* 1.3 77.2 - - - +
389H ASN* 1.3 65.7 + - - +
390H ASP* 4.3 3.2 + - - +
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Residues in contact with ASN 389 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256H LYS* 5.4 8.5 - - - +
341H TYR 4.6 0.2 + - - -
342H LEU* 4.1 23.6 - - - +
343H GLU* 3.3 21.9 + - - +
373H THR* 3.2 4.5 - - - +
374H VAL* 2.9 40.8 + - - +
376H LEU* 6.2 1.4 - - - +
387H VAL* 3.2 29.1 - - - +
388H SER* 1.3 75.1 + - - +
390H ASP* 1.3 65.1 + - - +
391H TYR* 3.4 34.9 + - + +
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Residues in contact with ASP 390 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256H LYS* 3.0 36.4 - - + +
372H PHE 3.6 6.1 - - - +
373H THR* 2.8 29.7 + - - +
388H SER* 4.3 3.4 + - - -
389H ASN* 1.3 76.2 - - - +
391H TYR* 1.3 67.9 + - - +
392H LYS* 6.2 2.2 - - + -
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Residues in contact with TYR 391 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255H MET 3.5 23.3 - - - -
256H LYS* 3.0 13.0 - - + +
258H PRO* 4.2 17.5 - - + -
340H PHE* 3.8 27.9 + + + +
341H TYR 2.6 40.8 + - - -
342H LEU* 4.1 5.2 - - - +
371H ASP* 3.5 2.8 - - - +
372H PHE* 2.7 43.7 + - + +
374H VAL* 3.9 22.6 - - + +
389H ASN* 3.4 42.9 + - + -
390H ASP* 1.3 77.9 - - - +
392H LYS* 1.3 65.6 + - - +
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Residues in contact with LYS 392 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256H LYS* 2.8 15.6 + - + +
257H GLU* 3.7 8.0 - - - +
258H PRO* 3.3 16.0 - - - +
363H ASN* 3.3 30.1 - - - +
369H ASP* 6.0 4.0 - - + +
370H LEU 3.3 4.9 - - - +
371H ASP* 3.5 17.7 + - - +
390H ASP* 6.2 3.1 - - + -
391H TYR* 1.3 78.1 - - - +
393H MET* 1.3 63.1 + - - +
394H ARG 3.6 3.3 + - - +
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Residues in contact with MET 393 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189H TYR* 3.9 20.0 - - + -
190H CYS* 4.1 24.9 - - - -
193H TYR* 3.4 53.7 - - + -
258H PRO* 3.7 26.2 - - + +
260H VAL* 4.5 7.9 - - + -
338H THR* 4.3 12.8 - - - -
369H ASP* 3.7 13.2 - - - +
370H LEU* 2.8 22.2 + - + +
372H PHE* 3.9 13.0 - - + -
392H LYS* 1.3 69.8 - - - +
394H ARG* 1.3 83.0 - - + +
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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