Contacts of the strand formed by residues 482 - 487 (chain E) in PDB entry 3E20
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 THR 482 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476E LYS* 3.9 34.8 - - + -
477E TYR 3.7 5.8 - - - +
478E LYS* 2.9 20.9 - - + +
481E GLY* 1.3 72.4 - - - -
483E ILE* 1.3 62.9 + - - +
484E LEU* 4.0 4.3 - - + -
532E LEU 3.6 0.3 - - - +
533E ARG* 3.4 7.0 - - - +
534E VAL* 3.1 48.6 + - + +
538E ASP* 2.8 30.4 + - - +
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Residues in contact with ILE 483 (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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480A LEU* 4.6 10.5 - - + -
475E SER 3.8 0.2 - - - +
476E LYS* 3.3 4.2 - - - -
477E TYR* 2.8 78.3 + - + +
478E LYS 6.4 0.2 - - - -
479E ASP* 5.9 2.9 - - + +
481E GLY 4.9 3.8 - - - +
482E THR* 1.3 73.1 - - - +
484E LEU* 1.3 66.7 + - - +
485E GLU 3.9 0.4 + - - +
514E TYR* 5.3 1.3 - - + -
531E ARG* 4.0 22.7 - - + -
532E LEU 3.2 15.0 - - - +
533E ARG* 3.7 45.1 - - + +
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Residues in contact with LEU 484 (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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471E MET* 4.8 3.8 - - + +
473E ILE* 4.3 10.5 - - + -
475E SER 3.5 3.4 - - - +
476E LYS* 3.6 32.1 - - + -
482E THR* 4.0 6.3 + - + -
483E ILE* 1.3 74.1 - - - +
485E GLU* 1.3 57.2 + - - +
508E LEU* 4.0 9.6 - - + -
531E ARG 3.6 0.2 - - - -
532E LEU* 2.7 43.5 + - + +
534E VAL* 3.7 35.4 - - + -
538E ASP* 6.1 0.7 - - + -
541E VAL* 3.9 20.9 - - + -
547E LEU* 3.9 35.4 - - + -
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Residues in contact with GLU 485 (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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471E MET* 4.2 3.6 - - - -
473E ILE* 3.9 0.5 - - - +
474E ALA* 2.9 43.0 + - - +
475E SER* 2.8 35.5 + - - +
477E TYR* 5.2 4.3 - - + -
483E ILE* 3.9 4.0 + - + +
484E LEU* 1.3 75.0 - - - +
486E GLY* 1.3 68.9 + - - +
529E GLN* 3.9 19.0 + - - +
530E VAL 3.5 11.1 - - - +
531E ARG* 3.5 26.2 - - + +
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Residues in contact with GLY 486 (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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471E MET* 3.8 15.7 - - - +
472E PRO 3.8 15.3 - - - -
474E ALA* 4.1 4.5 - - - -
485E GLU* 1.3 81.9 - - - +
487E LYS* 1.3 59.4 + - - -
529E GLN* 3.2 13.4 + - - -
530E VAL 3.0 28.8 + - - +
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Residues in contact with LYS 487 (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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471E MET* 3.6 9.8 - - - +
472E PRO* 3.8 8.0 + - - +
486E GLY* 1.3 73.7 - - - -
488E ILE* 1.3 69.4 + - - +
489E GLU* 3.1 36.7 + - - +
527E GLY* 3.6 25.7 + - - +
528E ASP 3.5 11.9 - - - +
529E GLN* 3.4 30.5 - - - +
639J TYR* 4.4 22.8 - - - -
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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