Contacts of the helix formed by residues 523 - 534 (chain E) in PDB entry 4DHZ
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 523 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522E THR* 1.3 73.3 - - - +
524E GLU* 1.3 55.7 + - - +
526E VAL* 2.8 9.0 + - + +
527E LYS* 2.8 49.5 + - - +
543E LEU* 4.4 9.9 - - + -
550E LEU* 3.8 46.9 - - + +
551E GLU 3.2 24.7 - - - +
552E ASP* 3.5 9.6 - - - +
554E ARG* 3.0 19.3 + - + +
555E THR 4.2 9.0 - - - +
556E LEU* 3.8 24.7 - - + -
559E TYR* 4.6 2.5 - - + -
561E ILE* 5.5 0.2 - - + -
567E LEU* 5.9 0.7 - - + -
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Residues in contact with GLU 524 (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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522E THR* 3.7 19.1 - - + +
523E ILE* 1.3 78.8 - - - +
525E ASN* 1.3 55.6 + - + +
526E VAL 3.0 0.2 - - - -
527E LYS* 3.5 12.0 - - + +
528E ALA* 2.7 35.2 + - - +
552E ASP* 3.6 35.1 + - - +
553E GLY* 4.9 2.8 - - - -
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Residues in contact with ASN 525 (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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521E ASP* 3.0 36.6 + - - +
522E THR* 3.6 27.4 + - - +
524E GLU* 1.3 82.4 - - + +
526E VAL* 1.3 57.6 + - - +
528E ALA* 4.1 8.1 - - - +
529E LYS* 3.4 30.5 + - - +
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Residues in contact with VAL 526 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503E ILE* 5.3 7.4 - - + -
515E LEU* 5.8 2.5 - - + -
517E VAL* 3.8 28.3 - - + -
521E ASP* 4.5 5.6 - - + -
522E THR 3.5 13.6 + - - +
523E ILE* 2.8 9.6 + - + +
525E ASN* 1.3 79.6 - - - +
527E LYS* 1.3 61.0 + - - +
528E ALA 3.0 5.2 - - - -
529E LYS* 3.3 8.2 + - + +
530E ILE* 3.2 35.6 + - + +
543E LEU* 3.9 23.6 - - + -
556E LEU* 4.0 18.6 - - + -
567E LEU* 5.2 6.7 - - + -
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Residues in contact with LYS 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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523E ILE* 2.8 27.0 + - + +
524E GLU* 3.2 10.1 + - + +
526E VAL* 1.3 71.0 - - - +
528E ALA* 1.3 58.9 + - - +
530E ILE* 3.9 7.9 - - - -
531E GLN* 3.4 25.1 + - - +
538E PRO* 4.0 23.7 + - + +
541E GLN* 2.8 55.8 + - + +
542E ARG* 3.7 5.1 - - - +
543E LEU* 3.6 39.4 - - + +
549E GLN* 4.2 8.7 - - - +
550E LEU 4.9 2.2 + - - -
552E ASP* 4.3 18.3 + - - +
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Residues in contact with ALA 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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524E GLU 2.7 16.7 + - - +
525E ASN* 4.1 10.8 - - - +
526E VAL 3.0 0.2 - - - -
527E LYS* 1.3 75.1 - - - +
529E LYS* 1.3 67.5 + - + +
530E ILE 2.9 3.1 + - - -
531E GLN* 3.0 9.1 + - - +
532E ASP* 2.9 33.1 + - - +
538E PRO* 5.6 2.2 - - - -
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Residues in contact with LYS 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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515E LEU* 4.4 19.0 - - + +
516E GLU 2.7 29.2 + - - +
517E VAL* 3.6 21.0 - - + +
518E GLU* 4.8 1.6 - - - +
521E ASP* 3.7 13.9 + - - -
525E ASN* 3.4 25.2 + - - +
526E VAL* 3.3 10.7 + - - +
528E ALA* 1.3 77.3 - - - +
530E ILE* 1.3 56.8 + - + +
532E ASP* 3.4 10.0 - - - +
533E LYS* 3.0 26.9 + - - +
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Residues in contact with ILE 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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505E VAL* 5.0 8.7 - - + -
513E ILE* 5.3 5.4 - - + -
515E LEU* 3.6 37.0 - - + -
526E VAL* 3.4 22.2 - - + +
527E LYS* 3.8 7.4 - - - +
528E ALA 3.1 1.0 - - - -
529E LYS* 1.3 73.9 - - + +
531E GLN* 1.3 56.6 + - - +
532E ASP 2.9 5.8 - - - -
533E LYS* 3.6 4.7 - - + +
534E GLU* 2.8 40.0 + - + +
541E GLN* 3.1 28.9 - - - +
543E LEU* 4.8 15.9 - - + -
569E LEU* 4.2 21.8 - - + -
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Residues in contact with GLN 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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527E LYS 3.4 14.8 - - - +
528E ALA* 3.0 18.9 + - - +
530E ILE* 1.3 79.9 - - - +
532E ASP* 1.3 74.4 + - - +
534E GLU 3.4 10.5 - - - -
535E GLY* 3.3 19.3 - - - -
536E ILE* 2.8 36.0 - - - +
537E PRO* 4.1 0.7 - - - +
538E PRO* 3.4 26.4 - - + +
541E GLN* 3.8 7.2 - - - +
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Residues in contact with ASP 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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528E ALA* 2.9 24.3 + - - +
529E LYS* 3.4 9.4 + - - +
530E ILE 2.9 0.2 - - - -
531E GLN* 1.3 112.0 + - - +
533E LYS* 1.3 57.2 + - - +
534E GLU 3.3 4.3 - - - -
535E GLY 4.9 1.4 + - - -
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Residues in contact with LYS 533 (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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513E ILE* 3.3 39.3 - - + +
514E THR 4.0 18.4 + - - +
515E LEU* 4.9 9.4 - - + -
529E LYS 3.0 16.6 + - - +
530E ILE* 3.3 5.6 + - + +
532E ASP* 1.3 75.5 - - - +
534E GLU* 1.3 70.0 + - - +
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Residues in contact with GLU 534 (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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513E ILE* 5.4 17.3 - - + -
530E ILE* 2.8 20.3 + - + +
531E GLN* 3.4 3.5 - - - -
532E ASP 3.3 0.6 - - - -
533E LYS* 1.3 86.3 - - + +
535E GLY* 1.3 66.8 + - - +
536E ILE* 2.9 37.1 + - + +
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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