Contacts of the strand formed by residues 467 - 474 (chain E) in PDB entry 1D00
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 SER 467 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410E PHE* 3.7 4.9 - - - -
411E PHE* 2.9 34.1 + - - +
447E PHE* 3.9 2.9 - - - -
450E ASP* 6.0 0.2 - - - +
453E SER* 5.1 0.7 + - - -
455E SER* 3.6 24.6 - - - -
456E PHE* 4.0 15.0 - - - -
465E ILE 3.7 0.4 + - - -
466E ALA* 1.3 75.1 - - - +
468E GLY* 1.3 58.7 + - - +
250M PRO* 3.0 23.7 + - - +
251M VAL 3.2 16.7 + - - -
252M GLN* 3.7 5.9 + - - +
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Residues in contact with GLY 468 (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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409E LEU 3.9 6.7 - - - -
410E PHE* 3.4 4.4 - - - -
432E LEU* 5.2 0.4 - - - -
447E PHE* 3.7 17.9 - - - -
467E SER* 1.3 77.5 + - - +
469E CYS* 1.3 64.6 + - - -
470E PRO* 3.6 5.5 - - - +
249M ACE 4.6 1.4 - - - +
250M PRO* 3.5 7.5 - - - +
251M VAL* 2.7 35.2 + - - +
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Residues in contact with CYS 469 (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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409E LEU 2.9 32.0 + - - +
410E PHE* 4.4 2.6 - - - -
432E LEU* 4.2 20.2 - - - -
445E ASP* 3.6 34.1 - - - +
447E PHE* 4.3 13.5 - - - -
468E GLY* 1.3 76.2 - - - -
470E PRO* 1.3 67.1 - - - +
471E LEU 3.1 1.6 - - - -
472E PHE* 3.1 28.6 + - + +
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Residues in contact with PRO 470 (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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399E ASP* 4.0 13.0 - - - +
400E GLY* 5.6 0.2 - - - -
401E THR* 3.3 24.7 - - - +
402E GLY* 3.6 10.9 - - - -
406E HIS* 3.6 5.0 - - - +
408E SER* 2.6 30.7 + - - +
410E PHE* 4.2 13.5 - - + -
468E GLY 3.6 9.4 - - - +
469E CYS* 1.3 82.4 - - - +
471E LEU* 1.3 59.8 + - + +
472E PHE 3.4 0.8 + - - -
251M VAL* 3.7 35.0 - - + -
252M GLN 5.1 0.7 - - - +
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Residues in contact with LEU 471 (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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401E THR* 3.4 39.5 - - - +
402E GLY* 3.4 15.5 - - - +
406E HIS* 3.4 37.3 + - + +
445E ASP* 6.0 0.4 - - - -
469E CYS* 3.1 2.4 - - - -
470E PRO* 1.3 78.8 - - + +
472E PHE* 1.3 64.9 + - - +
473E CYS* 3.3 3.8 + - - -
474E PRO* 5.2 0.9 - - - +
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Residues in contact with PHE 472 (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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407E LEU* 3.4 21.3 + - + +
409E LEU* 3.9 31.2 - - + +
432E LEU* 3.4 37.2 - - + -
433E MET* 3.8 3.6 - - - -
434E LEU* 3.7 37.5 - - + -
443E VAL* 3.9 22.9 - - + +
445E ASP* 4.1 21.5 - - + +
469E CYS* 3.1 33.2 + - + +
470E PRO 3.4 1.2 - - - -
471E LEU* 1.3 78.4 - - - +
473E CYS* 1.3 68.2 + - + +
474E PRO* 4.5 1.6 - - - +
492E ILE* 4.9 2.2 - - + -
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Residues in contact with CYS 473 (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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406E HIS* 3.3 5.1 - - - -
407E LEU* 2.7 43.4 + - + +
434E LEU* 3.8 26.2 - - + -
443E VAL* 4.2 18.4 - - + -
471E LEU 3.3 0.8 + - - -
472E PHE* 1.3 95.1 - - + +
474E PRO* 1.3 84.7 - - - +
477E LYS* 4.3 7.6 - - - -
478E MET* 3.8 11.4 - - - -
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Residues in contact with PRO 474 (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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405E THR 3.7 7.6 - - - +
406E HIS* 3.9 20.6 - - + +
407E LEU* 5.7 0.4 - - - -
443E VAL* 6.1 0.4 - - + -
471E LEU 5.2 0.7 - - - +
472E PHE 4.5 1.8 - - - +
473E CYS* 1.3 95.5 - - - +
475E VAL* 1.3 65.6 + - - +
476E SER* 4.1 14.6 - - - +
477E LYS* 3.1 32.5 + - + +
478E MET* 4.0 2.6 + - - +
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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