Contacts of the strand formed by residues 384 - 393 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378I PHE 3.2 11.4 - - - +
379I LYS* 3.6 35.9 - - + +
380I GLY 5.0 1.8 - - - +
383I CYS* 1.3 80.5 - - - +
385I THR* 1.3 75.8 + - - +
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Residues in contact with THR 385 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344I ASP* 5.8 7.4 - - + +
346I LEU* 4.2 21.2 - - + +
376I LEU* 4.3 5.9 - - - +
377I ASP* 3.7 0.3 - - - -
378I PHE* 2.9 35.0 + - - +
383I CYS* 5.2 4.6 - - + -
384I GLU* 1.3 87.8 - - - +
386I SER* 1.3 63.9 + - - +
387I VAL* 3.7 20.5 - - + +
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Residues in contact with SER 386 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376I LEU 3.2 6.3 - - - -
377I ASP* 3.4 27.2 + - - -
385I THR* 1.3 75.3 - - - +
387I VAL* 1.3 62.2 + - - +
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Residues in contact with VAL 387 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343I GLU* 4.3 8.7 - - + +
346I LEU* 6.4 0.4 - - + -
374I VAL 4.5 0.7 - - - -
375I ASP* 3.2 4.9 - - - +
376I LEU* 2.7 43.9 + - + +
377I ASP* 4.4 1.1 + - - +
385I THR* 3.7 26.7 - - + +
386I SER* 1.3 79.9 - - - +
388I SER* 1.3 63.9 + - - +
389I ASN* 3.3 29.8 - - - +
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Residues in contact with SER 388 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373I THR* 3.8 9.4 - - - +
374I VAL 3.5 3.6 - - - -
375I ASP* 2.3 28.2 + - - -
387I VAL* 1.3 77.9 - - - +
389I ASN* 1.3 66.1 + - - +
390I ASP* 4.4 3.0 + - - -
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Residues in contact with ASN 389 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256I LYS* 5.3 8.7 - - - +
341I TYR 4.5 0.6 + - - -
342I LEU* 4.2 23.2 - - - +
343I GLU* 3.2 28.9 + - - +
373I THR* 3.4 4.4 - - - +
374I VAL* 2.9 36.5 + - + +
376I LEU* 6.3 1.0 - - - +
387I VAL* 3.3 22.5 - - - +
388I SER* 1.3 76.4 + - - +
390I ASP* 1.3 64.7 + - - +
391I TYR* 3.5 33.2 + - + +
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Residues in contact with ASP 390 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256I LYS* 2.9 36.9 - - + +
372I PHE 3.5 4.9 - - - +
373I THR* 2.9 27.7 + - - +
388I SER* 5.0 3.4 + - - -
389I ASN* 1.3 76.5 - - - +
391I TYR* 1.3 68.1 + - - +
392I LYS* 6.4 1.1 - - + -
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Residues in contact with TYR 391 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255I MET 3.4 24.0 - - - -
256I LYS* 3.0 13.9 - - + +
257I GLU 4.6 0.7 - - - -
258I PRO* 4.2 16.4 - - + -
340I PHE* 3.8 27.6 - + + +
341I TYR 2.5 39.3 + - - -
342I LEU* 4.2 6.1 - - - +
371I ASP* 3.7 0.9 - - - +
372I PHE* 2.9 44.6 + - + +
374I VAL* 3.9 22.7 - - + +
389I ASN* 3.5 42.1 + - + -
390I ASP* 1.3 77.6 - - - +
392I LYS* 1.3 68.5 + - - +
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Residues in contact with LYS 392 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256I LYS* 2.8 12.5 + - + +
257I GLU* 3.7 10.2 - - - +
258I PRO* 3.3 15.3 - - - +
363I ASN* 3.3 31.1 - - - +
369I ASP* 5.9 3.9 + - + +
370I LEU 3.3 4.3 - - - +
371I ASP* 3.4 18.5 + - - +
372I PHE* 5.2 0.2 - - - -
390I ASP* 6.4 1.1 - - + -
391I TYR* 1.3 77.0 - - - +
393I MET* 1.3 65.0 + - - +
394I ARG 3.5 3.4 + - - +
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Residues in contact with MET 393 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189I TYR* 3.9 17.9 - - + -
190I CYS* 4.0 26.9 - - - -
193I TYR* 3.2 56.3 - - + -
258I PRO* 3.7 25.8 - - + +
260I VAL* 4.5 7.6 - - + -
338I THR* 4.2 11.7 - - - -
369I ASP* 3.6 15.3 - - - +
370I LEU* 2.9 22.5 + - + +
372I PHE* 3.8 13.7 - - + -
392I LYS* 1.3 70.4 - - - +
394I ARG* 1.3 81.9 - - + +
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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