Contacts of the helix formed by residues 530 - 539 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470G VAL* 4.8 1.8 - - + -
471G GLN* 3.6 66.2 + - + +
474G LEU* 4.3 15.3 - - + -
514G TYR* 3.8 37.2 - + - -
515G LEU* 4.4 9.4 - - + -
518G VAL* 3.8 19.6 - - + +
528G PRO 4.3 0.4 + - - -
529G SER* 1.3 74.3 + - - +
531G ALA* 1.3 79.2 + - + +
532G THR 3.1 8.8 + - - -
533G LYS* 3.9 12.0 + - - +
534G ILE* 3.7 20.6 + - + +
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Residues in contact with ALA 531 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515G LEU* 3.9 35.7 - - + +
518G VAL* 4.5 6.7 - - + -
519G GLU* 3.4 10.7 - - - +
529G SER* 3.1 11.2 + - - +
530G TRP* 1.3 97.5 - - + +
532G THR* 1.3 59.6 + - - -
534G ILE* 4.1 9.4 - - - -
535G LEU* 3.4 23.7 + - - +
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Residues in contact with THR 532 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338G ARG* 3.5 3.8 + - - +
342G LEU* 4.4 22.9 - - + -
519G GLU* 3.1 27.4 + - - +
522G ALA* 5.5 0.3 - - - +
529G SER* 3.3 28.8 + - - -
530G TRP 3.1 1.0 - - - -
531G ALA* 1.3 77.3 - - - +
533G LYS* 1.3 65.0 + - - +
535G LEU 3.5 0.2 + - - -
536G ASN* 2.8 38.8 + - - +
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Residues in contact with LYS 533 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478G GLU* 3.0 30.8 + - - +
493G GLU* 5.2 11.2 - - + +
496G PHE* 5.5 0.4 - - - -
529G SER 4.8 0.6 + - - -
530G TRP 3.9 9.0 + - - +
532G THR* 1.3 78.2 - - - +
534G ILE* 1.3 72.1 + - - +
536G ASN* 3.1 13.3 + - + +
537G LEU* 2.9 50.7 + - + +
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Residues in contact with ILE 534 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474G LEU* 4.4 21.1 - - + -
496G PHE* 4.3 22.0 - - + -
500G ILE* 3.7 31.4 - - + +
511G LEU* 5.8 0.2 - - + -
515G LEU* 3.7 31.2 - - + -
530G TRP* 3.7 22.2 + - + +
531G ALA* 4.1 11.9 - - - -
532G THR 3.2 0.8 - - - -
533G LYS* 1.3 86.0 - - - +
535G LEU* 1.3 53.1 + - - +
537G LEU* 3.0 10.0 + - + +
538G LEU* 2.8 31.5 + - - +
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Residues in contact with LEU 535 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338G ARG* 3.2 29.0 - - - +
512G GLU* 4.9 5.4 - - + +
515G LEU* 3.3 54.3 - - + +
516G ASN* 3.6 23.1 - - - +
519G GLU* 4.0 10.8 - - + -
531G ALA 3.4 16.8 + - - +
533G LYS 3.4 0.2 - - - -
534G ILE* 1.3 78.2 - - - +
536G ASN* 1.3 61.4 + - - +
538G LEU* 3.7 10.5 - - + -
539G TRP* 3.0 49.1 + - + +
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Residues in contact with ASN 536 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335G PHE* 3.2 33.7 - - + -
338G ARG* 2.6 39.4 + - - +
339G MET* 5.3 10.3 - - - +
342G LEU* 5.3 10.5 - - - +
532G THR* 2.8 25.0 + - - +
533G LYS* 3.1 15.9 + - + +
535G LEU* 1.3 78.2 - - - +
537G LEU* 1.3 62.9 + - + +
539G TRP 3.6 0.2 + - - -
540G ALA* 3.4 6.1 + - - +
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Residues in contact with LEU 537 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493G GLU* 3.9 43.5 - - + +
496G PHE* 4.1 29.2 - - + -
497G ALA* 3.5 24.1 - - + +
500G ILE* 3.8 22.0 - - + -
501G LYS* 3.9 4.2 - - - -
533G LYS* 2.9 33.8 + - + +
534G ILE* 3.0 9.2 + - + +
536G ASN* 1.3 77.8 - - + +
538G LEU* 1.3 64.5 + - - +
539G TRP 3.1 1.6 - - - -
540G ALA* 3.1 20.4 + - + +
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Residues in contact with LEU 538 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357G SER* 4.0 18.4 - - - +
362G GLU* 5.4 0.3 - - - +
500G ILE* 3.7 27.8 - - + +
501G LYS* 2.8 46.6 + - + +
504G ASN* 4.0 22.9 - - + +
512G GLU* 4.8 6.3 - - + -
515G LEU* 4.7 7.2 - - + -
534G ILE 2.8 15.7 + - - +
535G LEU* 3.7 19.7 - - + +
536G ASN 3.4 0.2 - - - -
537G LEU* 1.3 76.4 - - - +
539G TRP* 1.3 76.2 + - + +
540G ALA 3.4 0.2 - - - -
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Residues in contact with TRP 539 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331G ALA 4.2 3.8 - - - +
334G TRP* 3.8 43.3 - + + -
335G PHE* 3.3 26.3 - - + +
338G ARG* 3.8 33.6 - - + +
356G SER* 3.8 16.2 - - - -
357G SER* 3.1 48.7 + - - -
359G LEU* 5.8 1.6 - - + -
360G ASN* 4.8 11.7 - - - -
501G LYS* 4.2 0.4 - - - -
512G GLU* 4.0 5.8 + - - +
516G ASN* 5.5 4.8 + - - +
535G LEU* 3.0 38.3 + - + +
537G LEU 3.1 0.4 - - - -
538G LEU* 1.3 90.4 - - + +
540G ALA* 1.3 67.0 + - - +
541G PRO 3.6 0.3 - - - -
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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