Contacts of the strand formed by residues 384 - 393 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378E PHE 3.2 11.9 - - - +
379E LYS* 3.5 37.3 - - + +
380E GLY 5.1 1.6 - - - +
383E CYS* 1.3 79.0 - - - +
385E THR* 1.3 76.1 + - - +
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Residues in contact with THR 385 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344E ASP* 5.9 5.8 - - + +
346E LEU* 4.1 20.7 - - + +
376E LEU* 4.4 7.1 - - - +
377E ASP* 3.6 0.7 - - - +
378E PHE* 2.9 34.5 + - - +
383E CYS* 5.1 7.1 - - + -
384E GLU* 1.3 87.2 - - - +
386E SER* 1.3 63.7 + - - +
387E VAL* 3.8 20.8 - - + +
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Residues in contact with SER 386 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376E LEU 3.2 5.8 - - - -
377E ASP* 3.5 25.7 + - - -
385E THR* 1.3 75.5 - - - +
387E VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 387 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343E GLU* 4.1 11.9 - - + +
374E VAL 3.8 1.0 - - - +
375E ASP* 3.2 5.9 - - - +
376E LEU* 2.9 41.5 + - + +
377E ASP* 4.5 0.8 + - - +
385E THR* 3.8 26.9 - - + +
386E SER* 1.3 79.3 + - - +
388E SER* 1.3 63.9 + - - +
389E ASN* 3.1 28.7 - - - +
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Residues in contact with SER 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373E THR* 3.9 10.2 - - - +
374E VAL 3.6 3.8 - - - -
375E ASP* 2.9 23.0 + - - -
387E VAL* 1.3 78.2 - - - +
389E ASN* 1.3 63.8 + - - +
390E ASP* 4.8 4.3 + - - -
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Residues in contact with ASN 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E LYS* 5.4 9.1 - - - +
341E TYR 4.5 2.2 + - - -
342E LEU* 4.0 22.6 - - - +
343E GLU* 3.4 21.2 + - - +
373E THR* 3.4 4.0 - - - +
374E VAL* 2.9 39.0 + - + +
376E LEU* 6.1 2.2 - - - +
387E VAL* 3.1 27.9 - - - +
388E SER* 1.3 74.3 + - - +
390E ASP* 1.3 65.8 + - - +
391E TYR* 3.4 34.3 + - + +
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Residues in contact with ASP 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E LYS* 2.9 37.0 - - + +
372E PHE 3.5 5.4 - - - +
373E THR* 2.9 27.2 + - - +
388E SER* 4.8 3.8 + - - -
389E ASN* 1.3 77.8 - - - +
391E TYR* 1.3 65.5 + - - +
392E LYS* 6.2 1.6 - - + -
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Residues in contact with TYR 391 (chain E).
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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255E MET 3.5 23.1 - - - -
256E LYS* 3.0 14.6 - - + +
257E GLU 4.6 0.4 - - - -
258E PRO* 4.2 17.3 - - + -
340E PHE* 3.7 26.8 - + + +
341E TYR 2.4 40.0 + - - -
342E LEU* 4.2 5.2 - - - +
371E ASP* 3.7 0.7 - - - +
372E PHE* 3.0 41.5 + - + +
374E VAL* 3.9 22.0 - - + +
389E ASN* 3.4 43.4 + - + -
390E ASP* 1.3 77.8 - - - +
392E LYS* 1.3 69.4 + - - +
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Residues in contact with LYS 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E LYS* 2.8 15.0 + - + +
257E GLU* 3.6 10.2 - - - +
258E PRO* 3.4 15.4 - - - +
363E ASN* 3.4 19.8 - - - +
369E ASP* 5.9 4.1 - - + +
370E LEU 3.3 6.3 - - - +
371E ASP* 3.3 27.6 + - - +
372E PHE* 5.1 0.4 - - - -
390E ASP* 6.2 2.0 - - + -
391E TYR* 1.3 78.5 - - - +
393E MET* 1.3 62.6 + - - +
394E ARG 3.5 4.5 + - - +
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Residues in contact with MET 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E TYR* 3.9 20.4 - - + +
190E CYS* 4.0 25.1 - - - -
193E TYR* 3.4 49.6 - - + -
258E PRO* 3.7 25.4 - - + +
260E VAL* 4.4 8.5 - - + -
338E THR* 4.2 12.6 - - - -
369E ASP* 3.6 14.8 - - - +
370E LEU* 2.8 24.4 + - + +
372E PHE* 3.8 13.4 - - + -
392E LYS* 1.3 69.8 - - - +
394E ARG* 1.3 85.3 + - + +
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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