Contacts of the helix formed by residues 509 - 525 (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 GLY 509 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360C ASN* 4.5 13.4 + - - -
504C ASN* 2.9 25.4 + - - -
508C GLU* 1.3 75.5 - - - +
510C LYS* 1.3 63.9 + - - +
511C LEU 3.2 2.9 - - - -
512C GLU* 3.1 21.3 + - - +
513C THR* 3.3 16.8 + - - +
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Residues in contact with LYS 510 (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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462C MET* 4.1 19.9 + - + +
463C ASN* 3.1 49.7 + - - +
467C TYR* 3.7 22.1 - - - +
507C SER* 3.2 24.3 + - - +
508C GLU* 3.3 5.1 - - + +
509C GLY* 1.3 77.6 - - - +
511C LEU* 1.3 59.5 + - - +
513C THR* 2.7 26.5 + - - -
514C TYR 3.4 4.0 + - - -
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Residues in contact with LEU 511 (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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458C ILE* 4.9 1.8 - - + -
462C MET* 4.0 24.0 - - + -
470C VAL* 3.8 28.9 - - + -
474C LEU* 5.1 11.0 - - + -
500C ILE* 4.1 31.2 - - + +
503C VAL* 3.8 22.9 - - + -
504C ASN* 4.0 12.6 - - + +
507C SER* 3.7 7.7 + - - +
509C GLY 3.2 0.8 - - - -
510C LYS* 1.3 77.0 - - - +
512C GLU* 1.3 59.7 + - - +
514C TYR* 3.4 5.4 + - + +
515C LEU* 3.0 47.6 + - + +
538C LEU* 5.5 0.7 - - + -
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Residues in contact with GLU 512 (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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358C VAL* 3.3 43.3 - - - +
359C LEU* 4.4 8.9 - - + +
360C ASN* 4.8 2.8 + - - -
504C ASN* 3.6 19.4 + - - +
509C GLY* 3.1 15.6 + - - +
511C LEU* 1.3 76.9 - - - +
513C THR* 1.3 66.2 + - - +
515C LEU* 3.4 3.7 + - - +
516C ASN* 3.3 38.6 + - - +
535C LEU* 5.5 2.5 - - + -
538C LEU* 4.5 15.9 - - + -
539C TRP* 3.9 14.6 - - + +
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Residues in contact with THR 513 (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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467C TYR* 4.6 5.9 + - - -
509C GLY 3.5 14.4 - - - +
510C LYS* 2.7 24.7 + - - -
512C GLU* 1.3 79.4 - - + +
514C TYR* 1.3 65.9 + - - +
516C ASN* 3.7 5.1 + - - +
517C LYS* 3.4 21.5 + - - +
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Residues in contact with TYR 514 (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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467C TYR* 3.4 65.0 + + + -
468C SER 5.2 1.7 + - - -
470C VAL* 4.1 15.6 - - + +
471C GLN* 5.2 1.2 + - - +
510C LYS 3.4 1.9 + - - +
511C LEU* 3.7 9.9 - - + +
512C GLU 3.3 0.6 - - - -
513C THR* 1.3 82.7 + - - +
515C LEU* 1.3 73.9 + - + +
517C LYS* 3.3 14.4 + - + +
518C VAL* 3.1 41.1 + - + +
530C TRP* 3.3 41.4 - + - -
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Residues in contact with LEU 515 (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* 5.3 0.2 - - + -
511C LEU* 3.0 41.5 + - + +
512C GLU 3.9 2.9 - - - +
513C THR 3.4 0.2 - - - -
514C TYR* 1.3 81.4 - - + +
516C ASN* 1.3 61.2 + - - +
518C VAL* 3.7 0.8 + - - -
519C GLU* 3.3 22.3 + - - +
530C TRP* 4.2 19.3 - - + -
531C ALA* 3.6 27.4 - - + +
534C ILE* 3.6 36.8 - - + -
535C LEU* 3.6 32.7 - - + +
538C LEU* 4.3 12.6 - - + -
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Residues in contact with ASN 516 (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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512C GLU* 3.3 31.9 + - - +
513C THR* 4.1 5.1 - - - +
515C LEU* 1.3 73.0 - - - +
517C LYS* 1.3 55.1 + - - +
519C GLU* 3.2 4.8 + - - +
520C ALA* 2.8 38.0 + - - +
535C LEU* 3.3 27.5 - - - +
539C TRP* 5.3 5.3 + - - +
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Residues in contact with LYS 517 (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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45B GLN* 4.9 12.7 + - - +
513C THR 3.4 12.2 + - - +
514C TYR* 3.3 17.4 + - + +
516C ASN* 1.3 78.6 - - - +
518C VAL* 1.3 66.1 + - + +
520C ALA* 3.3 7.0 + - - +
521C GLU* 3.1 52.9 + - + +
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Residues in contact with VAL 518 (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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514C TYR* 3.1 52.8 + - + +
515C LEU 3.8 5.4 - - - +
517C LYS* 1.3 79.9 - - + +
519C GLU* 1.3 63.0 + - - +
521C GLU* 3.3 10.4 + - - +
522C ALA* 3.2 19.8 + - + +
529C SER* 3.2 23.3 - - - +
530C TRP* 3.7 18.2 - - + +
531C ALA* 3.8 7.9 - - + -
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Residues in contact with GLU 519 (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* 2.6 33.9 + - - -
515C LEU 3.3 13.1 + - - +
516C ASN* 3.2 5.6 + - - +
518C VAL* 1.3 79.2 - - - +
520C ALA* 1.3 59.5 + - - +
522C ALA* 3.2 8.8 + - + +
523C LYS* 2.9 37.7 + - + +
529C SER* 4.6 5.4 - - - -
531C ALA* 4.2 8.5 - - + +
532C THR* 3.4 29.5 + - - +
535C LEU* 3.3 16.8 - - - +
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Residues in contact with ALA 520 (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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516C ASN 2.8 18.6 + - - +
517C LYS* 3.6 7.6 - - - +
519C GLU* 1.3 77.2 - - - +
521C GLU* 1.3 62.1 + - + +
523C LYS* 3.3 30.4 + - + +
524C ALA* 3.4 9.4 + - - +
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Residues in contact with GLU 521 (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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517C LYS* 3.1 47.8 + - + +
518C VAL* 3.7 9.6 - - - +
519C GLU 3.3 0.2 - - - -
520C ALA* 1.3 76.8 - - + +
522C ALA* 1.3 56.9 + - - +
523C LYS 3.3 0.2 - - - -
524C ALA* 4.0 4.3 + - - +
525C ALA* 3.2 27.4 + - - +
527C GLU* 5.0 0.3 - - - +
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Residues in contact with ALA 522 (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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518C VAL* 3.2 13.2 + - + +
519C GLU* 3.4 10.8 - - + +
520C ALA 3.1 0.6 - - - -
521C GLU* 1.3 77.3 - - - +
523C LYS* 1.3 62.1 + - - +
525C ALA* 4.0 1.1 - - - -
526C ALA* 3.2 1.6 + - - -
527C GLU* 3.0 56.0 + - + +
528C PRO 4.7 0.2 - - - +
529C SER* 3.6 22.7 - - - -
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Residues in contact with LYS 523 (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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519C GLU* 2.9 25.2 + - + +
520C ALA* 3.3 19.0 + - + +
522C ALA* 1.3 75.7 - - - +
524C ALA* 1.3 65.2 + - - +
526C ALA* 3.1 14.6 + - - +
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Residues in contact with ALA 524 (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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520C ALA 3.4 10.0 + - - +
521C GLU* 4.4 4.9 - - - +
523C LYS* 1.3 81.0 - - - +
525C ALA* 1.3 58.7 + - - +
526C ALA* 3.0 7.3 + - - +
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Residues in contact with ALA 525 (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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521C GLU 3.2 19.1 + - - +
522C ALA 4.4 0.2 - - - +
523C LYS 3.3 0.6 - - - -
524C ALA* 1.3 75.3 - - - +
526C ALA* 1.3 70.1 + - - +
527C GLU* 3.3 32.2 + - + +
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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