Contacts of the helix formed by residues 462 - 477 (chain C) in PDB entry 6CP3
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 ARG 462 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458C ILE* 4.7 1.3 - - + -
459C GLU* 3.7 38.4 - - + +
460C LEU 2.9 0.6 + - - -
461C SER* 1.3 81.5 - - - +
463C ILE* 1.3 65.3 + - - +
464C GLY 3.0 4.0 + - - -
465C GLU* 2.7 54.0 + - + +
466C PHE* 3.1 9.1 + - + -
469C SER* 5.8 2.2 + - - -
510C PHE* 3.3 48.6 - - + -
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Residues in contact with ILE 463 (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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425C ARG* 4.4 16.8 - - + +
428C GLN* 4.6 7.0 - - + -
429C LEU* 3.8 33.8 - - + +
455C LEU* 4.4 14.6 - - + +
458C ILE* 3.7 32.8 - - + -
459C GLU 3.4 15.9 - - - +
460C LEU* 3.0 32.2 + - + +
461C SER 3.7 0.2 - - - -
462C ARG* 1.3 74.4 - - - +
464C GLY* 1.3 58.1 + - - +
466C PHE* 2.8 32.6 - - + +
467C GLU* 2.9 12.1 + - - +
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Residues in contact with GLY 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C GLN* 5.1 14.3 - - - +
429C LEU* 5.7 3.8 - - - -
431C LYS* 6.0 4.3 - - - -
460C LEU 4.8 0.2 + - - -
462C ARG 3.0 1.8 + - - -
463C ILE* 1.3 78.5 - - - +
465C GLU* 1.3 57.2 + - - -
467C GLU* 2.8 37.8 - - - +
468C SER* 3.7 1.0 + - - -
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Residues in contact with GLU 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C SER 5.4 1.3 - - - +
462C ARG* 2.7 54.9 + - - +
464C GLY* 1.3 71.1 - - - +
466C PHE* 1.3 60.2 + - - +
468C SER* 2.3 34.5 + - - +
469C SER* 2.8 16.1 + - - +
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Residues in contact with PHE 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C LEU* 6.5 0.4 - - + -
446C LEU* 6.3 1.3 - - + -
449C ALA* 6.2 0.4 - - + -
455C LEU* 3.6 28.5 - - + -
458C ILE* 3.6 22.9 - - + -
462C ARG* 3.1 9.0 + - + +
463C ILE* 2.8 29.2 - - + +
465C GLU* 1.3 75.2 - - - +
467C GLU* 1.3 54.7 + - - +
469C SER* 3.0 10.8 + - - -
470C PHE* 2.5 43.4 + + + +
506C PHE* 3.5 39.9 - + - -
507C VAL* 5.6 5.2 - - + -
510C PHE* 3.5 40.6 - + + -
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Residues in contact with GLU 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C LYS* 2.6 45.8 + - - +
429C LEU* 4.3 6.4 - - + +
431C LYS 4.3 2.4 - - - +
438C LEU* 3.5 13.5 - - - +
446C LEU* 3.5 39.7 - - + +
463C ILE 2.9 8.8 + - - +
464C GLY* 2.8 20.8 - - - +
466C PHE* 1.3 76.1 - - - +
468C SER* 1.3 49.3 + - - +
470C PHE* 3.0 6.2 + - - +
471C LEU* 2.7 44.4 + - + +
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Residues in contact with SER 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C GLY 3.7 0.6 + - - -
465C GLU* 2.3 36.7 + - - +
467C GLU* 1.3 77.9 - - - +
469C SER* 1.3 52.0 + - - +
471C LEU* 3.0 16.3 + - - +
472C SER* 2.6 39.0 + - - -
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Residues in contact with SER 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C ARG* 5.8 2.1 + - - -
465C GLU* 2.8 17.6 + - - +
466C PHE* 3.1 20.4 - - - -
468C SER* 1.3 77.6 + - - +
470C PHE* 1.3 55.9 + - - +
472C SER* 3.0 29.1 + - - -
473C TYR 3.1 5.2 + - - -
506C PHE* 3.3 26.1 - - - -
510C PHE* 6.2 2.0 - - - -
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Residues in contact with PHE 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C PRO* 3.7 24.5 - - + -
446C LEU* 4.3 18.8 - - + -
449C ALA* 5.4 5.2 - - + -
466C PHE* 2.5 27.0 + + + +
467C GLU* 3.4 10.1 - - - +
469C SER* 1.3 69.6 - - - +
471C LEU* 1.3 69.2 + - + +
473C TYR* 3.0 24.1 + + + +
474C LEU* 3.1 36.8 + - + +
499C LEU* 5.6 1.1 - - + -
502C ALA* 4.6 2.0 - - + -
503C THR* 4.1 36.3 - - + -
506C PHE* 3.4 41.2 - + + -
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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
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438C LEU* 4.8 17.9 - - + -
442C GLU* 4.5 32.3 - - + +
446C LEU* 5.0 6.1 - - + -
467C GLU* 2.7 33.7 + - + +
468C SER* 3.0 17.5 + - - +
470C PHE* 1.3 76.3 - - + +
472C SER* 1.3 54.5 + - - +
474C LEU* 3.0 11.8 + - + +
475C LYS* 2.5 62.2 + - + +
482C LEU* 6.2 2.2 - - + -
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Residues in contact with SER 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C SER* 2.6 22.9 + - - -
469C SER* 3.0 15.5 - - - -
471C LEU* 1.3 71.1 - - - +
473C TYR* 1.3 61.4 + - - +
475C LYS* 4.2 9.2 - - - +
476C SER* 3.6 18.7 + - - -
506C PHE* 5.6 0.9 - - - -
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Residues in contact with TYR 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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469C SER 3.1 4.4 + - - -
470C PHE* 3.0 16.4 + + + +
472C SER* 1.3 77.1 - - - +
474C LEU* 1.3 72.8 + - + +
476C SER* 2.9 7.8 + - - -
477C ASN* 2.9 53.0 + - - +
478C HIS* 3.4 34.7 + + - -
502C ALA* 3.6 24.7 + - + -
505C SER* 3.1 29.5 + - - -
506C PHE* 3.4 42.3 - + + -
509C THR* 5.8 1.3 - - - -
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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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445C PRO* 3.8 22.4 - - + -
470C PHE* 3.1 37.1 + - + +
471C LEU* 3.0 13.7 + - + +
473C TYR* 1.3 98.7 - - + +
475C LYS* 1.3 64.3 + - - +
476C SER 3.2 0.4 - - - -
477C ASN 4.4 0.4 - - - -
478C HIS* 3.7 29.6 - - + +
479C ASN* 3.9 14.6 + - - +
481C LEU* 5.0 6.3 - - + -
482C LEU* 3.4 36.4 - - + +
499C LEU* 5.3 3.6 - - + -
502C ALA* 4.8 6.5 - - + -
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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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442C GLU* 4.9 11.3 + - - -
471C LEU* 2.5 50.1 + - + +
472C SER* 4.6 8.3 - - - +
474C LEU* 1.3 74.3 - - - +
476C SER* 1.3 61.9 + - - +
479C ASN* 4.4 14.4 + - - +
482C LEU* 5.2 3.1 - - + -
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Residues in contact with SER 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C SER 3.6 12.4 + - - -
473C TYR 2.9 9.3 + - - -
474C LEU 4.6 0.2 - - - -
475C LYS* 1.3 83.6 - - - +
477C ASN* 1.3 76.2 + - - +
479C ASN* 4.4 6.1 + - - +
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Residues in contact with ASN 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 TYR* 2.9 53.2 + - + +
476C SER* 1.3 85.6 - - - +
478C HIS* 1.3 77.6 + - + +
479C ASN* 3.2 6.4 + - - +
480C GLU* 4.9 1.6 + - - +
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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