Contacts of the helix formed by residues 463 - 470 (chain C) in PDB entry 3GJN
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 463 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461C ASN* 2.6 21.6 + - - +
462C ASN* 1.3 80.5 - - - +
464C TRP* 1.3 66.6 + - - +
465C LEU 3.3 2.2 - - - -
466C ASN* 3.1 45.3 + - + +
467C ASN* 5.7 0.2 - - - +
512C GLN* 3.5 4.0 - - + -
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Residues in contact with TRP 464 (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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460C VAL* 3.4 32.5 - - + +
461C ASN* 3.1 17.6 + - - +
463C LYS* 1.3 77.5 - - - +
465C LEU* 1.3 84.8 + - + +
466C ASN 3.3 2.9 + - - -
467C ASN* 3.7 9.5 + - - +
474C SER* 3.2 24.9 + - - -
475C PRO* 3.0 25.4 + - + -
477C PRO* 3.7 24.2 - - + -
499C PHE* 4.0 10.1 - + - -
500C TRP* 3.9 17.9 - + - -
503C VAL* 3.8 25.8 - - + -
509C LEU* 3.8 15.0 - - + -
512C GLN* 2.9 15.9 + - - +
513C PHE* 4.0 17.5 - + - -
563C VAL* 3.9 12.1 - - + -
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Residues in contact with LEU 465 (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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463C LYS 3.1 1.2 + - - -
464C TRP* 1.3 116.8 - - + +
466C ASN* 1.3 65.5 + - - +
467C ASN 3.0 2.2 - - - -
468C ALA* 3.1 17.3 + - + +
474C SER* 3.7 11.0 - - - -
500C TRP* 4.8 0.9 - - + -
512C GLN* 4.5 1.6 + - - -
513C PHE* 3.3 29.4 - - + -
527C PRO* 4.5 2.7 - - + -
541C PHE* 3.7 45.1 - - + -
563C VAL* 3.8 19.7 - - + -
1055D TRP* 5.6 4.0 - - + -
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Residues in contact with ASN 466 (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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463C LYS* 3.1 46.1 + - + +
465C LEU* 1.3 76.4 - - - +
467C ASN* 1.3 62.8 + - - +
468C ALA 3.0 1.5 + - - -
469C GLY* 4.3 3.3 + - - -
470C LYS* 4.8 3.8 - - - +
530C ARG* 5.5 8.1 - - - +
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Residues in contact with ASN 467 (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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461C ASN* 5.1 5.9 - - - +
463C LYS 4.6 0.5 + - - +
464C TRP 3.7 7.0 + - - +
465C LEU 3.0 0.8 - - - -
466C ASN* 1.3 80.6 - - - +
468C ALA* 1.3 56.3 + - - +
469C GLY 3.0 9.2 + - - -
470C LYS* 3.2 42.6 + - - +
473C GLY* 3.7 17.1 + - - +
474C SER* 3.3 16.4 - - - +
475C PRO* 5.5 5.4 - - + +
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Residues in contact with ALA 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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465C LEU* 3.1 19.2 + - + +
466C ASN 3.0 4.0 - - - -
467C ASN* 1.3 76.8 - - - +
469C GLY* 1.3 55.9 + - - +
470C LYS 3.4 1.1 - - - -
473C GLY* 4.1 4.3 - - - -
474C SER* 3.6 11.0 + - - +
541C PHE* 3.8 25.4 - - + -
563C VAL 3.7 19.5 - - - +
564C VAL* 3.2 12.6 - - - +
565C THR* 2.8 29.8 + - + -
568C ARG* 3.9 1.7 - - - +
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Residues in contact with GLY 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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466C ASN 4.3 3.3 + - - -
467C ASN 3.0 1.4 + - - -
468C ALA* 1.3 79.4 - - - +
470C LYS* 1.3 61.7 + - - +
533C ASP* 5.7 1.1 - - - -
565C THR* 3.9 19.9 - - - +
568C ARG* 3.7 17.0 - - - +
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Residues in contact with LYS 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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466C ASN 4.8 2.9 - - - +
467C ASN* 3.2 42.5 - - - +
469C GLY* 1.3 82.4 - - - +
471C ASP* 1.3 77.7 + - + +
473C GLY* 2.7 35.2 + - - -
568C ARG* 3.8 6.0 - - - +
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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