Contacts of the helix formed by residues 530 - 539 (chain E) in PDB entry 4KYI
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 TRP 530 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470E VAL* 4.4 4.9 - - + -
471E GLN* 3.4 62.9 + - + +
474E LEU* 4.3 10.5 - - + -
514E TYR* 3.6 38.4 - + - -
515E LEU* 3.5 27.1 - - + -
518E VAL* 4.0 20.1 - - + +
529E SER* 1.3 76.3 + - - +
531E ALA* 1.3 68.6 + - + +
532E THR 3.2 0.9 + - - -
533E LYS* 3.7 9.9 + - - +
534E ILE* 3.4 30.7 + - + +
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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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515E LEU* 3.8 29.8 - - + +
518E VAL* 3.8 19.3 - - + -
519E GLU* 4.3 6.1 - - + +
529E SER* 3.1 12.5 + - - +
530E TRP* 1.3 90.3 - - + +
532E THR* 1.3 63.7 + - - +
533E LYS 3.4 0.2 - - - -
534E ILE* 3.2 4.8 + - - +
535E LEU* 3.0 29.6 + - - +
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Residues in contact with THR 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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338E ARG* 3.6 5.4 + - - +
342E LEU* 4.6 18.8 - - + -
519E GLU* 3.9 30.0 + - - +
529E SER* 3.4 23.2 + - - -
530E TRP 3.2 1.0 - - - -
531E ALA* 1.3 79.6 - - - +
533E LYS* 1.3 59.6 + - - +
536E ASN* 2.9 41.1 + - - +
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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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478E GLU* 3.1 33.3 + - - -
492E LYS* 4.6 5.5 - - - +
493E GLU* 4.6 14.6 - - - +
496E PHE* 4.6 12.1 - - - -
529E SER 4.8 0.4 + - - -
530E TRP 3.7 6.9 + - - +
531E ALA 3.4 0.4 - - - -
532E THR* 1.3 77.1 - - - +
534E ILE* 1.3 69.5 + - - +
536E ASN* 3.3 12.6 + - + +
537E LEU* 3.2 34.5 + - + +
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Residues in contact with ILE 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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474E LEU* 4.2 17.5 - - + -
475E ASP* 5.9 2.7 - - - +
478E GLU* 5.7 0.2 - - - +
496E PHE* 3.8 32.3 - - + -
500E ILE* 3.6 25.5 - - + +
511E LEU* 5.4 0.2 - - + -
515E LEU* 3.6 27.1 - - + -
530E TRP* 3.4 34.1 - - + +
531E ALA* 3.2 7.1 + - - +
533E LYS* 1.3 86.3 - - - +
535E LEU* 1.3 56.9 + - - +
537E LEU* 3.3 4.4 + - + +
538E LEU* 2.9 25.8 + - - +
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Residues in contact with LEU 535 (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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338E ARG* 3.2 31.7 + - - +
512E GLU* 4.3 16.4 - - + -
515E LEU* 3.6 45.8 - - + +
516E ASN* 3.3 28.0 - - - +
519E GLU* 3.9 14.1 - - + +
531E ALA 3.0 15.9 + - - +
534E ILE* 1.3 76.9 - - - +
536E ASN* 1.3 58.0 + - - +
538E LEU* 3.7 10.8 - - + -
539E TRP* 3.0 41.3 + - + +
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Residues in contact with ASN 536 (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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335E PHE* 3.5 15.8 - - + -
338E ARG* 2.9 40.6 + - - +
339E MET* 3.8 27.9 - - + +
342E LEU* 5.0 4.9 - - - +
532E THR* 2.9 32.8 + - - +
533E LYS* 3.3 14.8 + - + +
534E ILE 3.2 0.8 - - - -
535E LEU* 1.3 77.8 - - - +
537E LEU* 1.3 63.8 + - + +
539E TRP 3.7 0.5 + - - -
540E ALA* 3.3 19.1 + - - +
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Residues in contact with LEU 537 (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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493E GLU* 3.3 49.1 - - + +
496E PHE* 3.5 43.7 - - + -
497E ALA* 3.3 32.0 - - + +
500E ILE* 4.0 9.2 - - + -
501E LYS* 3.8 5.7 - - - -
533E LYS* 3.2 23.6 + - + +
534E ILE 3.3 6.0 + - - +
536E ASN* 1.3 77.5 - - + +
538E LEU* 1.3 62.7 + - - +
539E TRP 3.3 0.7 - - - -
540E ALA* 3.3 12.4 - - + +
544E TRP* 5.3 5.4 - - + -
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Residues in contact with LEU 538 (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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357E SER* 3.9 22.7 + - - +
362E GLU* 4.5 3.7 - - - +
500E ILE* 3.9 17.5 - - + -
501E LYS* 3.2 48.4 + - + -
504E ASN* 3.9 21.5 - - + +
511E LEU* 5.6 0.7 - - + -
512E GLU* 4.0 22.9 - - + -
515E LEU* 5.1 4.5 - - + -
534E ILE 2.9 18.0 + - - +
535E LEU* 3.8 12.1 - - + +
536E ASN 3.3 0.2 - - - -
537E LEU* 1.3 79.5 - - - +
539E TRP* 1.3 71.1 + - + +
540E ALA 3.3 0.4 - - - -
602E GOL 6.0 0.4 - - - -
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Residues in contact with TRP 539 (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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331E ALA 4.7 1.7 - - - +
334E TRP* 3.8 51.6 - + + +
335E PHE* 3.2 25.7 + - - +
338E ARG* 4.1 35.0 - - + +
355E THR* 4.5 4.5 - - - -
356E SER 3.2 37.5 - - - -
357E SER* 3.7 11.0 - - - -
359E LEU* 5.3 0.4 - - + -
360E ASN* 4.3 14.8 - - - -
512E GLU* 3.4 27.8 + - - -
516E ASN* 5.2 2.8 + - - +
535E LEU* 3.0 35.6 + - + +
536E ASN 3.8 1.6 - - - +
537E LEU 3.3 0.4 - - - -
538E LEU* 1.3 86.4 - - + +
540E ALA* 1.3 63.9 + - - +
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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