Contacts of the helix formed by residues 530 - 539 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470C VAL* 4.2 2.5 - - + -
471C GLN* 3.0 68.3 + - + +
474C LEU* 4.1 10.3 - - + -
475C ASP* 5.5 1.8 - - - -
514C TYR* 3.3 44.4 + + - -
515C LEU* 4.2 10.8 - - + -
518C VAL* 3.7 18.2 - - + +
529C SER* 1.3 78.7 + - - +
531C ALA* 1.3 60.5 + - + +
532C THR 3.0 9.4 + - - -
533C LYS* 3.5 10.7 + - - +
534C ILE* 3.4 37.9 + - + +
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Residues in contact with ALA 531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515C LEU* 3.6 35.7 - - + +
518C VAL* 3.8 22.7 - - + -
519C GLU* 3.8 8.2 - - + +
529C SER* 3.2 2.8 + - - +
530C TRP* 1.3 86.5 - - + +
532C THR* 1.3 61.7 + - - +
534C ILE* 4.0 7.6 - - - -
535C LEU* 3.3 29.1 + - - +
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Residues in contact with THR 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C ARG* 3.2 6.1 + - - +
342C LEU* 5.6 8.7 - - + -
519C GLU* 3.4 21.2 + - - +
528C PRO* 5.2 0.9 - - - +
529C SER* 2.7 33.3 + - - -
530C TRP 3.0 0.4 - - - -
531C ALA* 1.3 78.3 - - - +
533C LYS* 1.3 62.8 + - - +
536C ASN* 2.8 40.7 + - - +
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Residues in contact with LYS 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478C GLU* 3.0 39.3 + - - +
493C GLU* 5.6 6.3 - - - +
496C PHE* 3.9 18.8 - - - -
530C TRP* 3.5 7.1 + - - +
531C ALA 3.5 0.2 - - - -
532C THR* 1.3 78.6 - - + +
534C ILE* 1.3 72.6 + - - +
536C ASN* 3.1 25.8 + - + +
537C LEU* 3.3 20.1 - - + +
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Residues in contact with ILE 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474C LEU* 3.8 24.9 - - + -
475C ASP* 5.7 2.5 - - - +
496C PHE* 3.8 34.3 - - + -
500C ILE* 3.7 25.4 - - + +
515C LEU* 3.6 29.6 - - + -
530C TRP* 3.4 36.3 + - + +
531C ALA* 4.4 1.1 - - - -
532C THR 3.4 0.4 - - - -
533C LYS* 1.3 86.5 - - - +
535C LEU* 1.3 61.0 + - - +
537C LEU* 3.3 9.9 + - + -
538C LEU* 3.3 12.0 + - - +
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Residues in contact with LEU 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C ARG* 3.2 23.7 + - - +
512C GLU* 5.2 3.1 - - + +
515C LEU* 3.6 44.6 - - + +
516C ASN* 3.3 26.0 - - - +
519C GLU* 3.3 24.9 - - - +
531C ALA 3.3 16.5 + - - +
533C LYS 3.3 0.4 - - - -
534C ILE* 1.3 74.1 - - - +
536C ASN* 1.3 62.9 + - - +
537C LEU 3.1 2.8 + - - -
538C LEU* 3.5 19.7 + - + -
539C TRP* 3.4 35.7 + - - +
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Residues in contact with ASN 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C PHE* 3.4 27.6 - - - -
338C ARG* 2.3 43.7 + - - +
339C MET* 4.0 26.3 - - + +
342C LEU* 5.4 6.7 - - - +
532C THR* 2.8 21.4 + - - +
533C LYS* 3.1 21.3 + - + +
535C LEU* 1.3 75.9 - - - +
537C LEU* 1.3 66.4 + - + +
539C TRP* 4.5 1.1 - - - -
540C ALA* 4.0 1.6 + - - +
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Residues in contact with LEU 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493C GLU* 4.1 39.9 - - + +
496C PHE* 3.5 42.8 - - + -
497C ALA* 3.4 28.0 - - + +
500C ILE* 3.9 9.4 - - + -
501C LYS* 3.8 4.3 - - - -
533C LYS* 3.3 24.9 - - + +
534C ILE 3.3 6.0 + - - +
535C LEU 3.1 0.4 - - - -
536C ASN* 1.3 85.7 - - + +
538C LEU* 1.3 62.9 + - - +
539C TRP 3.3 2.2 - - - -
540C ALA* 3.2 20.6 - - + +
544C TRP* 5.6 2.2 - - + -
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Residues in contact with LEU 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359C LEU* 3.6 25.4 - - + +
362C GLU* 5.1 0.7 - - - +
500C ILE* 3.7 16.3 - - + +
501C LYS* 2.8 52.7 + - + -
504C ASN* 3.6 34.5 - - + +
511C LEU* 5.5 0.4 - - + -
512C GLU* 4.5 11.2 - - + +
515C LEU* 4.3 11.4 - - + -
534C ILE 3.3 12.6 + - - +
535C LEU* 3.5 24.2 + - + +
537C LEU* 1.3 80.5 - - - +
539C TRP* 1.3 61.7 + - + +
540C ALA 3.2 0.2 - - - -
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Residues in contact with TRP 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C ALA 4.1 5.5 - - - +
334C TRP* 4.2 45.0 - + + +
335C PHE* 3.2 30.5 + - + +
338C ARG* 3.8 28.2 - - + +
358C VAL* 3.8 42.6 - - + -
359C LEU* 3.7 23.7 - - + +
501C LYS* 4.7 0.2 - - - -
512C GLU* 3.9 19.4 - - + +
516C ASN* 5.3 5.4 + - - -
535C LEU* 3.4 39.3 + - + +
538C LEU* 1.3 78.1 - - + +
540C ALA* 1.3 66.3 + - - +
541C PRO 3.6 0.7 - - - -
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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