Contacts of the strand formed by residues 526 - 532 (chain E) in PDB entry 3CB4
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 ILE 526 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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550D LEU* 3.8 29.4 - - + -
487E ILE* 5.0 5.8 - - + -
488E ASN* 3.4 15.5 - - - +
519E ILE* 3.8 16.2 - - + -
520E PRO 4.6 1.8 - - - +
522E GLN* 3.4 43.1 - - + +
524E PHE* 3.5 13.0 - - + +
525E ASP* 1.3 79.1 - - - +
527E ALA* 1.3 62.9 + - - +
528E ILE* 3.6 17.7 + - + -
540E SER 3.9 0.3 - - - +
541E THR* 3.5 3.7 + - - -
542E VAL* 3.0 42.7 + - + +
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Residues in contact with ALA 527 (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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486E LEU 3.8 1.4 - - - +
487E ILE* 3.2 3.3 - - - -
488E ASN* 2.7 42.4 + - - +
489E GLY 4.7 0.8 + - - +
525E ASP 4.2 1.0 - - - -
526E ILE* 1.3 70.4 - - - +
528E ILE* 1.3 61.7 + - - +
529E GLN* 5.2 4.8 - - - +
539E ARG* 5.1 16.8 - - + +
540E SER 3.8 5.8 - - - +
541E THR* 4.4 10.5 - - - +
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Residues in contact with ILE 528 (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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485E VAL* 4.9 3.1 - - + -
487E ILE* 3.7 27.8 - - + -
511E LEU 5.6 0.2 - - - -
512E VAL* 4.0 25.0 - - + +
515E MET* 4.0 40.6 - - + -
516E LYS* 4.3 9.0 - - + +
519E ILE* 4.3 10.1 - - + -
526E ILE* 4.3 8.3 - - + +
527E ALA* 1.3 76.0 - - - +
529E GLN* 1.3 68.0 + - - +
539E ARG* 3.4 3.3 - - - +
540E SER 2.9 37.8 + - - +
542E VAL* 3.9 27.6 - - + -
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Residues in contact with GLN 529 (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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484E ASP 3.8 0.3 - - - +
485E VAL* 3.4 8.4 - - - +
486E LEU* 2.9 81.1 + - + +
489E GLY* 6.0 2.0 - - - +
512E VAL* 4.3 3.1 - - - -
527E ALA* 5.2 5.5 - - - +
528E ILE* 1.3 78.1 - - - +
530E ALA* 1.3 61.2 + - - +
531E ALA* 4.5 2.8 - - - +
536E ILE* 3.1 33.9 - - + +
538E ALA 3.3 9.6 - - - +
539E ARG* 3.1 38.8 - - + +
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Residues in contact with ALA 530 (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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483E VAL* 3.8 18.8 - - + -
484E ASP 3.5 4.9 - - - -
485E VAL* 4.7 4.5 - - + +
508E GLY* 3.7 29.2 - - - +
511E LEU* 5.0 4.5 - - + -
512E VAL* 3.8 8.4 - - + +
529E GLN* 1.3 72.8 - - - +
531E ALA* 1.3 61.4 + - - +
536E ILE* 3.8 3.3 - - - +
537E ILE* 2.9 25.9 + - + -
538E ALA* 2.7 15.6 + - + +
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Residues in contact with ALA 531 (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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483E VAL* 3.4 6.8 - - - -
484E ASP* 2.9 38.3 + - + +
486E LEU* 4.7 10.5 - - + -
529E GLN* 4.2 7.2 - - - +
530E ALA* 1.3 76.5 - - - +
532E ILE* 1.3 64.0 + - - +
533E GLY 4.0 12.8 - - - +
534E THR 5.1 1.1 - - - +
535E HIS 3.3 19.3 - - - +
536E ILE* 4.0 10.5 - - + -
537E ILE* 4.0 2.5 - - - +
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Residues in contact with ILE 532 (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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393E VAL* 6.5 1.3 - - + -
481E VAL* 4.8 18.2 - - + -
482E ARG 3.8 19.5 - - - +
483E VAL* 4.1 5.6 - - + -
504E SER* 4.1 24.0 - - - +
505E GLN 5.5 0.2 - - - +
531E ALA* 1.3 76.3 - - - +
533E GLY* 1.3 65.1 + - - +
534E THR 3.5 0.3 + - - -
535E HIS* 2.9 31.0 + - + +
537E ILE* 3.9 34.5 - - + +
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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