Contacts of the helix formed by residues 467 - 481 (chain C) in PDB entry 2A19
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 LYS 467 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406C HIS* 4.0 27.8 - - + +
411C ILE* 3.4 29.4 - - + -
466C GLY* 1.3 74.1 - - - -
468C GLU* 1.3 68.6 + - + +
469C VAL* 3.0 10.3 - - - +
470C ASP* 2.9 24.8 + - - +
471C LEU* 3.5 12.9 - - + +
528C ASN* 5.6 8.5 - - - +
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Residues in contact with GLU 468 (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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466C GLY* 3.4 18.3 + - - -
467C LYS* 1.3 109.5 + - + +
469C VAL* 1.3 62.0 + - + +
470C ASP 3.1 0.2 - - - -
471C LEU* 3.5 15.8 + - + +
472C TYR* 3.1 25.3 + - - +
523C PRO* 3.6 49.6 - - + +
524C GLU* 4.7 1.6 - - - +
526C ARG* 5.4 2.8 - - + +
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Residues in contact with VAL 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C ILE* 4.5 11.2 - - + -
413C ARG* 4.9 16.4 - - + +
466C GLY 3.8 21.5 - - - +
467C LYS* 4.0 5.4 - - - -
468C GLU* 1.3 80.3 - - + +
470C ASP* 1.3 71.3 + - - +
472C TYR* 3.6 6.9 - - - +
473C ALA* 3.4 22.3 + - - +
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Residues in contact with ASP 470 (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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402C VAL* 4.2 2.5 - - + +
405C ILE* 5.2 0.3 - - - +
406C HIS* 3.4 25.8 + - + +
411C ILE* 3.7 8.8 - - - +
412C ASN* 2.4 47.6 + - - +
413C ARG* 4.1 3.5 + - - +
415C LEU* 3.4 19.3 - - + +
467C LYS 2.9 13.7 + - - +
469C VAL* 1.3 86.5 - - - +
471C LEU* 1.3 59.3 + - - +
472C TYR 3.2 1.6 - - - -
473C ALA* 3.2 6.1 + - - +
474C LEU* 2.9 31.9 + - - +
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Residues in contact with LEU 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C HIS* 4.0 13.5 - - + +
467C LYS* 3.5 21.8 - - + +
468C GLU* 3.5 15.7 + - + +
470C ASP* 1.3 74.1 - - - +
472C TYR* 1.3 59.8 + - - +
474C LEU* 3.2 14.4 + - + +
475C GLY* 2.9 26.3 + - - -
518C LEU* 4.0 10.6 - - + +
526C ARG* 4.6 14.4 - - + +
527C PRO 3.2 23.3 - - - +
528C ASN* 4.0 13.7 - - - +
529C THR* 3.5 43.5 - - + +
532C ILE* 4.1 4.5 - - + +
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Residues in contact with TYR 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C GLU 3.1 18.7 + - - +
469C VAL* 3.6 10.8 - - - +
471C LEU* 1.3 76.8 - - - +
473C ALA* 1.3 61.3 + - - +
475C GLY* 3.4 3.1 + - - -
476C LEU* 3.2 29.0 + - + +
518C LEU 4.3 17.6 + - - +
519C LEU* 4.8 6.4 - - + +
526C ARG* 5.4 0.4 - - - +
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Residues in contact with ALA 473 (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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413C ARG 6.1 0.9 - - - +
415C LEU* 3.8 35.9 - - + +
469C VAL 3.4 10.8 + - - +
470C ASP* 3.2 10.4 + - - +
472C TYR* 1.3 77.1 - - - +
474C LEU* 1.3 65.9 + - - +
476C LEU* 3.0 27.2 - - - +
477C ILE* 3.0 13.0 + - + +
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Residues in contact with LEU 474 (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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395C PHE* 3.4 22.6 - - + -
398C ILE* 4.2 9.9 - - + -
399C THR* 3.5 28.5 - - - +
402C VAL* 3.8 28.7 - - + -
415C LEU* 5.2 1.6 - - + -
470C ASP 2.9 18.7 + - - +
471C LEU* 3.2 20.2 + - + +
473C ALA* 1.3 76.3 - - - +
475C GLY* 1.3 61.8 + - - +
477C ILE* 3.1 10.9 + - + +
478C LEU* 3.0 21.3 + - - +
529C THR* 3.8 28.7 - - + -
532C ILE* 4.2 11.0 - - + -
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Residues in contact with GLY 475 (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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395C PHE* 5.6 0.2 - - - -
471C LEU 2.9 14.2 + - - -
472C TYR 3.4 4.2 + - - -
473C ALA 3.3 0.2 - - - -
474C LEU* 1.3 74.5 - - - +
476C LEU* 1.3 64.3 - - - +
478C LEU* 3.6 5.3 + - - +
479C ALA* 3.5 4.2 + - - +
515C LEU* 3.4 26.0 - - - +
518C LEU* 3.9 20.8 - - - +
519C LEU* 4.0 10.6 - - - +
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Residues in contact with LEU 476 (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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472C TYR* 3.2 20.4 + - + +
473C ALA* 3.0 15.9 + - - +
475C GLY* 1.3 77.8 - - - +
477C ILE* 1.3 67.2 + - + +
479C ALA* 3.0 13.9 + - - +
480C GLU* 3.3 10.9 + - - +
519C LEU* 3.8 24.0 - - + -
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Residues in contact with ILE 477 (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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374C LEU* 4.7 8.5 - - + -
395C PHE* 4.4 9.6 - - + -
398C ILE* 4.4 22.0 - - + -
415C LEU* 4.8 15.5 - - + +
416C LYS* 4.8 4.5 - - - +
417C PRO* 4.7 19.5 - - + -
420C ILE* 4.3 18.6 - - + -
473C ALA 3.0 19.1 + - - +
474C LEU* 3.1 16.4 + - + +
476C LEU* 1.3 75.8 - - + +
478C LEU* 1.3 53.3 + - - +
480C GLU* 3.0 13.2 + - + +
481C LEU* 2.8 52.5 + - + +
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Residues in contact with LEU 478 (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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392C LEU* 4.1 15.0 - - + -
395C PHE* 3.5 48.4 - - + -
474C LEU 3.0 10.3 + - - +
475C GLY* 3.8 7.4 - - - +
476C LEU 3.2 0.2 + - - -
477C ILE* 1.3 75.6 - - - +
479C ALA* 1.3 62.9 + - - +
481C LEU* 3.0 25.6 - - + +
482C LEU* 3.1 33.4 + - + +
511C GLU* 5.5 1.3 - - - +
514C LEU* 3.8 32.5 - - + -
515C LEU* 3.9 15.9 - - + -
536C LEU* 6.2 0.2 - - + -
539C TRP* 5.3 7.9 - - + -
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Residues in contact with ALA 479 (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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475C GLY 3.5 2.8 + - - +
476C LEU* 3.0 11.4 + - - +
478C LEU* 1.3 76.8 - - - +
480C GLU* 1.3 59.2 + - - +
482C LEU* 2.8 36.4 + - - +
507C PHE* 5.3 3.8 - - + -
515C LEU* 3.8 26.7 - - + -
519C LEU* 5.7 3.8 - - + -
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Residues in contact with GLU 480 (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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417C PRO* 3.5 30.0 - - + +
476C LEU* 3.3 8.0 + - - +
477C ILE* 3.0 12.9 + - - +
479C ALA* 1.3 78.3 - - - +
481C LEU* 1.3 55.7 + - - +
482C LEU 3.1 6.3 + - - +
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Residues in contact with LEU 481 (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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374C LEU* 4.3 20.9 - - + -
391C ALA* 3.5 33.0 - - + +
392C LEU* 4.7 6.3 - - + +
394C LEU* 4.8 9.2 - - + -
395C PHE* 4.4 19.3 - - + +
398C ILE* 4.3 11.2 - - + -
477C ILE* 2.8 32.5 + - + +
478C LEU* 3.0 11.6 + - + +
480C GLU* 1.3 75.2 - - - +
482C LEU* 1.3 62.6 + - - +
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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