Contacts of the helix formed by residues 466 - 480 (chain C) in PDB entry 5MG3
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 ILE 466 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454C TRP* 5.9 8.1 - - + -
465C TYR* 1.4 99.1 - - + +
467C LEU* 1.3 72.7 + - + +
469C ILE* 3.2 12.1 + - + +
470C LEU* 3.1 30.2 + - + +
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Residues in contact with LEU 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C TRP* 5.6 9.0 - - + -
455C ILE* 3.6 30.3 - - + -
465C TYR* 3.6 15.0 - - + +
466C ILE* 1.3 81.2 - - + +
468C PRO* 1.4 73.0 - - + +
470C LEU* 3.2 17.4 + - + +
471C MET* 3.0 23.7 + - - +
511C SER* 3.9 31.9 - - - +
514C VAL* 3.6 11.5 - - + +
515C LEU* 4.5 18.4 - - + +
518C ILE* 3.7 28.0 - - + -
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Residues in contact with PRO 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C TYR* 3.7 19.1 - - + +
467C LEU* 1.4 96.3 - - + +
469C ILE* 1.4 61.7 + - + +
471C MET* 3.6 13.0 + - + +
472C GLY* 3.1 21.7 + - - -
503C THR* 4.3 9.2 - - + +
507C LEU* 3.8 43.5 - - + +
511C SER* 5.9 0.9 - - - +
514C VAL* 4.2 23.6 - - + -
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Residues in contact with ILE 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C TYR 3.3 27.1 - - - +
466C ILE* 3.2 8.2 + - + +
468C PRO* 1.4 78.7 - - + +
470C LEU* 1.3 63.7 + - - +
472C GLY* 3.2 2.3 + - - -
473C VAL* 3.0 34.0 + - + +
503C THR* 5.6 2.9 - - - -
507C LEU* 5.9 3.4 - - + -
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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
----------------------------------------------------------
454C TRP* 6.5 1.3 - - + -
466C ILE* 3.1 19.3 + - + +
467C LEU* 3.2 28.5 + - + +
469C ILE* 1.3 79.8 - - - +
471C MET* 1.3 49.2 + - - +
473C VAL* 3.8 9.9 - - + +
474C THR* 2.8 43.9 + - - +
518C ILE* 4.2 13.0 - - + -
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Residues in contact with MET 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C LEU 3.0 14.4 + - - +
468C PRO* 3.7 21.1 - - + +
470C LEU* 1.3 73.0 - - - +
472C GLY* 1.3 58.4 + - - +
474C THR* 4.1 7.0 - - - -
475C MET* 2.8 69.8 + - + +
502C PHE* 4.3 6.1 - - - -
503C THR* 3.8 19.1 - - - +
506C PHE* 3.7 36.8 - - + -
514C VAL* 3.7 19.3 - - + +
517C TYR* 4.2 14.4 - - + -
518C ILE* 4.4 9.8 - - + +
521C ASN* 5.7 0.7 - - - +
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Residues in contact with GLY 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C PRO 3.1 13.2 + - - -
469C ILE* 3.2 4.9 + - - -
471C MET* 1.3 79.0 - - - +
473C VAL* 1.4 53.6 + - - +
475C MET* 3.7 4.7 + - - +
476C PHE* 3.2 26.5 + - - +
499C PRO* 3.9 6.4 - - - +
503C THR* 3.2 27.6 - - - -
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Residues in contact with VAL 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C ILE* 3.0 25.5 + - + +
470C LEU* 3.8 11.2 - - + +
472C GLY* 1.4 72.1 - - - +
474C THR* 1.4 59.0 + - - +
476C PHE* 3.2 12.3 + - + +
477C PHE* 2.9 30.3 + - + +
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Residues in contact with THR 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C LEU* 2.8 35.5 + - - +
471C MET* 3.8 7.6 - - + +
473C VAL* 1.4 69.8 - - - +
475C MET* 1.4 62.3 + - - +
477C PHE* 3.6 7.4 + - - +
478C ILE* 3.3 24.6 + - - +
518C ILE* 4.1 26.2 - - + +
521C ASN* 3.6 32.1 - - + +
525C ILE* 3.8 17.5 - - + +
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Residues in contact with MET 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 MET* 2.8 51.0 + - + +
472C GLY* 3.8 5.4 - - - +
474C THR* 1.4 70.4 - - - +
476C PHE* 1.3 60.3 + - - +
478C ILE* 3.3 17.4 - - - +
479C GLN* 3.3 22.5 - - - +
498C MET* 5.9 0.8 - - + +
499C PRO* 4.0 18.2 - - + -
502C PHE* 3.6 39.3 - - + -
506C PHE* 4.2 4.7 - - + -
517C TYR* 3.8 29.2 - - + -
521C ASN* 3.4 18.6 - - - +
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Residues in contact with PHE 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 GLY 3.2 14.1 + - - +
473C VAL* 3.2 15.2 + - + +
475C MET* 1.3 73.4 - - - +
477C PHE* 1.3 65.0 + - - +
479C GLN* 3.5 13.1 + - + +
480C LYS* 3.4 53.1 + - + +
496C THR* 5.7 9.9 - - + -
499C PRO* 3.9 20.8 - - + +
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Residues in contact with PHE 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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473C VAL* 2.9 20.8 + - + +
474C THR* 3.7 8.3 - - - +
476C PHE* 1.3 73.3 - - - +
478C ILE* 1.3 57.6 + - - +
480C LYS* 3.0 25.9 + - + +
481C MET* 3.8 22.4 - - + -
525C ILE* 3.8 30.1 - - + -
528C GLN* 2.9 37.5 + - + -
529C GLN* 3.2 42.6 - - + -
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Residues in contact with ILE 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C TYR* 4.1 10.9 - - - -
474C THR 3.3 13.2 + - - +
475C MET* 3.3 22.4 - - - +
477C PHE* 1.3 76.3 - - - +
479C GLN* 1.4 69.0 + - - +
480C LYS 4.2 0.7 - - - +
521C ASN* 3.5 43.7 - - + +
524C THR* 4.1 21.9 - - + +
525C ILE* 3.8 29.8 - - + -
528C GLN* 3.7 12.9 - - - +
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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
----------------------------------------------------------
377C TYR* 2.7 33.7 + - - -
380C MET* 4.4 6.9 - - - +
475C MET 3.3 17.5 - - - +
476C PHE* 3.7 10.1 - - + +
477C PHE 3.3 0.6 - - - -
478C ILE* 1.4 88.3 - - - +
480C LYS* 1.3 60.7 + - + +
483C PRO* 4.0 11.6 - - - +
495C MET* 3.0 50.3 + - + +
496C THR* 6.0 2.7 - - + -
498C MET* 3.5 29.5 - - + +
499C PRO* 4.7 9.9 - - + -
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Residues in contact with LYS 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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377C TYR* 3.3 9.0 + - - -
476C PHE* 3.4 53.2 - - + +
477C PHE* 3.0 16.4 + - + +
478C ILE 4.2 0.5 - - - +
479C GLN* 1.3 83.1 - - + +
481C MET* 1.3 76.9 + - - +
483C PRO* 4.3 19.5 - - + +
485C THR* 6.0 3.8 - - - +
528C GLN* 3.3 16.3 - - - +
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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