Contacts of the helix formed by residues 509 - 524 (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 GLY 509 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358G VAL* 6.6 0.4 - - - -
504G ASN* 2.9 27.1 + - - -
508G GLU* 1.3 75.6 - - - +
510G LYS* 1.3 63.3 + - - +
511G LEU 3.2 3.4 - - - -
512G GLU* 3.0 27.9 + - - +
513G THR* 3.4 11.5 + - - +
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Residues in contact with LYS 510 (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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462G MET* 3.8 18.5 + - + +
463G ASN* 3.0 49.0 + - - +
467G TYR* 3.8 21.5 - - - +
507G SER* 3.2 22.9 + - - +
508G GLU* 3.3 8.2 - - - +
509G GLY* 1.3 76.9 - - - +
511G LEU* 1.3 59.4 + - - +
513G THR* 2.6 29.4 + - - -
514G TYR 3.5 2.4 + - - -
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Residues in contact with LEU 511 (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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458G ILE* 4.9 1.1 - - + -
462G MET* 3.8 25.7 - - + +
470G VAL* 4.0 26.7 - - + -
474G LEU* 5.3 9.4 - - + -
500G ILE* 3.9 26.0 - - + +
503G VAL* 3.8 23.1 - - + -
504G ASN* 4.0 13.7 - - + +
507G SER* 3.5 10.1 + - - +
509G GLY 3.2 0.8 + - - -
510G LYS* 1.3 77.8 - - - +
512G GLU* 1.3 63.8 + - - +
514G TYR* 3.3 6.6 + - + +
515G LEU* 3.0 51.9 + - + +
534G ILE* 5.8 0.9 - - + -
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Residues in contact with GLU 512 (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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356G SER* 4.2 3.7 - - - -
357G SER* 2.3 56.6 + - - +
504G ASN* 3.5 16.7 + - - +
509G GLY* 3.0 15.6 + - - +
511G LEU* 1.3 79.9 - - - +
513G THR* 1.3 65.5 + - - +
515G LEU* 3.2 10.9 + - - +
516G ASN* 2.9 41.0 + - - +
535G LEU* 5.0 4.3 - - + -
538G LEU* 4.8 9.6 - - + -
539G TRP* 4.0 7.3 - - - +
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Residues in contact with THR 513 (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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467G TYR* 4.7 5.5 + - - -
509G GLY 3.7 13.9 - - - +
510G LYS* 2.6 24.8 + - - +
512G GLU* 1.3 81.4 - - + +
514G TYR* 1.3 60.8 + - - +
516G ASN* 3.4 6.2 + - - +
517G LYS* 3.0 27.5 + - - +
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Residues in contact with TYR 514 (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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462G MET* 5.4 0.2 - - - -
467G TYR* 3.3 68.3 + + + -
468G SER* 5.0 2.8 + - - -
470G VAL* 4.4 15.3 - - + -
471G GLN* 5.8 0.5 + - - +
510G LYS 4.1 0.2 - - - +
511G LEU* 3.3 9.5 + - + +
513G THR* 1.3 80.8 + - - +
515G LEU* 1.3 67.3 + - + +
517G LYS* 3.3 25.0 + - + +
518G VAL* 3.2 45.1 + - + +
530G TRP* 3.8 33.8 - + - -
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Residues in contact with LEU 515 (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* 5.4 1.3 - - + -
500G ILE* 5.0 0.2 - - + -
504G ASN* 6.6 0.2 - - - -
511G LEU* 3.0 46.9 + - + +
512G GLU* 3.2 11.0 + - - +
514G TYR* 1.3 80.9 - - + +
516G ASN* 1.3 60.9 + - - +
518G VAL 3.8 0.2 + - - -
519G GLU* 3.2 23.7 + - - +
530G TRP* 4.4 15.5 - - + -
531G ALA* 3.9 24.2 - - + +
534G ILE* 3.7 33.4 - - + -
535G LEU* 3.3 31.0 - - + +
538G LEU* 4.7 10.1 - - + -
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Residues in contact with ASN 516 (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* 5.8 0.9 + - - -
356G SER* 6.3 1.4 - - - -
512G GLU* 2.9 37.4 + - - +
513G THR* 3.9 5.7 - - - +
514G TYR 3.3 0.2 - - - -
515G LEU* 1.3 73.9 - - - +
517G LYS* 1.3 64.0 + - - +
519G GLU* 3.7 7.3 - - - +
520G ALA* 3.2 21.7 + - - +
535G LEU* 3.6 19.3 - - - +
539G TRP* 5.5 4.5 + - - +
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Residues in contact with LYS 517 (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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45F GLN* 5.2 10.3 - - - +
513G THR 3.0 14.2 + - - +
514G TYR* 3.4 31.7 - - + +
515G LEU 3.3 0.4 - - - -
516G ASN* 1.3 74.5 - - - +
518G VAL* 1.3 67.9 + - - +
520G ALA* 3.0 17.8 + - - +
521G GLU* 3.2 36.2 + - + +
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Residues in contact with VAL 518 (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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514G TYR* 3.2 50.3 + - + +
515G LEU* 4.3 3.6 - - - +
517G LYS* 1.3 80.7 - - + +
519G GLU* 1.3 62.0 + - - +
521G GLU* 3.1 23.5 + - + +
522G ALA* 3.2 12.5 + - - +
529G SER* 3.8 11.2 + - - +
530G TRP* 3.8 27.1 - - + +
531G ALA* 4.5 5.6 - - + -
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Residues in contact with GLU 519 (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 27.1 + - - +
342G LEU* 5.6 2.6 - - - +
515G LEU 3.2 17.2 + - - +
516G ASN* 3.7 9.2 - - - +
518G VAL* 1.3 79.5 - - - +
520G ALA* 1.3 60.0 - - - +
522G ALA* 3.4 18.1 + - - +
523G LYS* 3.8 15.4 + - + +
529G SER* 3.9 5.7 + - - -
531G ALA* 3.4 15.5 - - - +
532G THR* 3.1 28.9 + - - +
535G LEU* 4.0 8.5 - - + -
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Residues in contact with ALA 520 (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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516G ASN 3.2 11.9 + - - +
517G LYS* 3.0 13.0 + - - +
519G GLU* 1.3 74.1 - - - +
521G GLU* 1.3 60.1 + - + +
522G ALA 3.0 8.1 + - - -
523G LYS* 3.5 16.8 + - - +
524G ALA* 3.5 13.0 + - - +
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Residues in contact with GLU 521 (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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517G LYS* 3.4 43.2 - - + +
518G VAL* 3.1 17.4 + - + +
520G ALA* 1.3 77.5 - - + +
522G ALA* 1.3 56.4 + - - +
524G ALA* 4.4 9.4 - - - -
525G ALA* 4.3 8.8 - - - +
527G GLU* 4.3 14.0 - - - +
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Residues in contact with ALA 522 (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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518G VAL 3.2 3.1 + - - +
519G GLU* 3.4 14.8 - - - +
520G ALA 3.0 0.8 - - - -
521G GLU* 1.3 80.2 - - - +
523G LYS* 1.3 63.9 + - + +
525G ALA 4.3 0.9 - - - -
526G ALA* 3.4 0.9 + - - -
527G GLU* 2.8 51.2 + - + +
528G PRO* 5.1 0.2 - - + -
529G SER* 3.6 28.3 - - - +
532G THR* 5.5 0.2 - - - +
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Residues in contact with LYS 523 (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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341G SER 6.0 2.0 - - - -
343G VAL 5.5 7.4 - - - -
344G GLU 5.2 10.4 + - - +
519G GLU* 3.9 15.9 - - + +
520G ALA* 3.5 9.1 + - - +
522G ALA* 1.3 79.0 - - + +
524G ALA* 1.3 65.8 + - - +
525G ALA 3.3 0.7 - - - -
526G ALA* 3.3 12.3 + - - +
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Residues in contact with ALA 524 (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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520G ALA 3.5 13.8 + - - +
521G GLU* 4.8 6.5 - - - -
522G ALA 3.5 0.2 - - - -
523G LYS* 1.3 81.2 - - - +
525G ALA* 1.3 58.8 + - + +
526G ALA* 3.3 1.7 + - - +
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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