Contacts of the helix formed by residues 468 - 480 (chain C) in PDB entry 5G04
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 MET 468 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437C VAL* 5.5 3.4 - - + -
464C ASP* 3.6 1.6 + - - -
465C VAL* 4.5 12.4 - - + +
466C GLU* 3.0 18.3 + - + +
467C LYS* 1.3 74.1 - - - +
469C ALA* 1.3 62.4 + - - +
470C LEU 3.3 1.2 + - - -
471C VAL* 3.4 31.9 + - + -
472C LYS* 3.6 34.1 + - - +
493C TYR* 4.4 9.9 - - + +
509C GLU* 4.1 18.8 - - - +
82R HIS* 4.8 11.0 - - + -
83R ARG* 4.8 11.0 - - + -
84R SER* 5.1 5.8 - - - +
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Residues in contact with ALA 469 (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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433C SER* 5.1 1.1 - - - +
437C VAL* 3.8 27.6 - - + +
456C TYR* 4.0 15.4 - - + +
459C ALA* 3.8 20.2 - - + -
460C TYR* 4.3 9.2 - - + +
464C ASP* 4.1 8.9 + - - +
465C VAL* 5.7 0.6 - - - +
467C LYS 2.8 8.9 + - - +
468C MET* 1.3 73.4 - - - +
470C LEU* 1.3 55.8 + - + +
472C LYS* 3.4 8.8 + - - +
473C LEU* 3.0 27.3 + - - +
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Residues in contact with LEU 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C TRP* 4.7 4.5 - - + -
460C TYR* 3.4 55.0 - - + -
464C ASP* 5.0 0.9 - - - +
467C LYS* 3.6 9.0 + - + +
468C MET 3.4 0.6 - - - -
469C ALA* 1.3 74.9 - - - +
471C VAL* 1.3 67.9 + - - +
473C LEU* 3.1 9.9 + - + -
474C ALA* 2.9 20.1 + - - +
489C CYS* 3.2 37.1 - - - +
492C LYS* 4.1 10.8 - - + +
493C TYR* 3.6 43.7 - - + +
496C ASP* 5.1 3.8 - - + -
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Residues in contact with VAL 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C MET* 3.4 24.8 + - + +
470C LEU* 1.3 75.6 - - - +
472C LYS* 1.3 55.2 + - + +
474C ALA* 3.2 7.7 + - - +
475C LYS* 2.8 52.3 + - + +
490C TYR* 4.5 10.5 - - + -
493C TYR* 3.5 50.2 - - + +
509C GLU* 4.0 25.4 - - - +
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Residues in contact with LYS 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C VAL* 3.9 18.4 - - + -
441C GLU* 4.3 11.9 + - - +
456C TYR* 3.6 27.0 + - + +
468C MET* 3.6 37.4 + - - +
469C ALA* 3.4 6.0 + - - +
470C LEU 3.1 0.4 - - - -
471C VAL* 1.3 79.1 - - + +
473C LEU* 1.3 64.6 + - - +
475C LYS* 3.3 8.9 + - + +
476C LEU* 3.2 23.4 + - - +
83R ARG* 3.7 30.5 - - - +
84R SER 5.4 0.4 - - - +
85R ALA* 4.5 21.0 - - - +
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Residues in contact with LEU 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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453C LYS* 3.6 35.4 - - + +
456C TYR* 3.7 17.3 - - + +
457C TRP* 3.7 41.5 - - + +
460C TYR* 5.7 0.2 - - + -
469C ALA 3.0 13.8 + - - +
470C LEU* 3.5 11.4 - - + +
472C LYS* 1.3 74.8 - - - +
474C ALA* 1.3 60.4 + - - +
476C LEU* 3.3 7.8 + - - +
477C HIS* 3.2 52.2 + - + -
489C CYS* 3.8 19.7 - - - -
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Residues in contact with ALA 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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470C LEU 2.9 15.4 + - - +
471C VAL 3.5 5.6 - - - +
472C LYS 3.1 0.2 - - - -
473C LEU* 1.3 74.1 - - - +
475C LYS* 1.3 61.4 + - - +
477C HIS* 3.2 9.2 + - - +
478C GLU* 3.0 30.0 + - - +
486C ALA* 4.0 3.0 - - - +
489C CYS* 3.7 24.7 - - + -
490C TYR* 3.6 34.5 - - + -
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Residues in contact with LYS 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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471C VAL* 2.8 31.1 + - + +
472C LYS* 3.3 8.0 + - + +
474C ALA* 1.3 77.2 - - - +
476C LEU* 1.3 55.6 + - - +
478C GLU* 3.0 40.4 + - - +
479C GLN* 2.9 25.4 + - - +
490C TYR* 2.9 30.1 + - + +
509C GLU* 5.9 1.8 - - - +
511C THR* 5.6 8.1 + - - +
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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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444C GLU* 3.8 20.4 - - + -
449C LEU* 3.0 38.6 - - + +
452C ALA* 3.7 30.1 - - + -
453C LYS* 4.1 19.5 - - + -
456C TYR* 3.7 19.7 - - + -
472C LYS 3.2 9.4 + - - +
473C LEU 3.5 9.6 - - - +
474C ALA 3.2 0.4 - - - -
475C LYS* 1.3 74.1 - - - +
477C HIS* 1.3 58.8 + - - +
479C GLN* 3.2 16.8 + - + +
480C LEU* 2.9 32.1 + - - +
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Residues in contact with HIS 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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453C LYS* 3.6 27.0 + - + -
473C LEU* 3.2 48.5 + - + +
474C ALA* 3.2 6.9 + - - +
476C LEU* 1.3 75.3 - - - +
478C GLU* 1.3 58.2 + - - +
480C LEU* 2.9 26.2 + - + +
482C GLU* 3.4 39.7 + - + +
485C GLN* 4.1 23.4 + - + +
486C ALA* 3.3 26.2 - - + +
489C CYS* 5.0 2.1 - - + +
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Residues in contact with GLU 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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474C ALA 3.0 15.8 + - - +
475C LYS* 3.0 33.6 + - - +
477C HIS* 1.3 77.9 - - - +
479C GLN* 1.3 58.4 + - - +
480C LEU 3.4 6.5 - - - +
482C GLU 5.0 1.8 - - - -
486C ALA* 4.2 8.5 - - + -
490C TYR* 3.3 21.2 + - + +
511C THR 5.8 0.3 - - - -
512C ALA* 5.2 0.9 - - - -
515C TYR* 3.0 47.4 - - + +
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Residues in contact with GLN 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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444C GLU* 4.5 12.9 + - - +
447C ASN* 4.1 22.8 + - - +
449C LEU* 4.2 19.9 - - + +
475C LYS 2.9 12.7 + - - +
476C LEU* 3.2 25.3 + - + +
478C GLU* 1.3 75.7 - - - +
480C LEU* 1.3 62.6 + - - +
481C THR* 5.6 1.4 - - - +
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Residues in contact with LEU 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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449C LEU* 3.9 30.5 - - + -
450C VAL 5.7 0.2 - - - +
453C LYS* 3.7 37.5 - - + +
476C LEU 2.9 22.4 + - - +
477C HIS* 2.9 22.1 + - + +
478C GLU 3.4 7.6 - - - +
479C GLN* 1.3 79.3 - - - +
481C THR* 1.3 65.0 + - - +
482C GLU* 3.1 15.2 + - + +
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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