Contacts of the helix formed by residues 545 - 550 (chain C) in PDB entry 2JGN
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 ASN 545 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420C TRP* 3.7 21.3 - - + -
421C VAL 2.9 25.9 + - - +
422C GLU* 4.2 9.0 - - - +
423C GLU* 3.1 35.9 + - - +
426C LYS* 3.6 7.1 - - - +
544C PHE* 1.3 91.9 - - - +
546C GLU* 1.3 58.7 + - - +
547C ARG* 3.0 31.5 + - - +
548C ASN* 2.9 27.6 + - - -
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Residues in contact with GLU 546 (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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563A LYS* 4.0 16.0 - - - -
420C TRP* 3.6 18.9 - - + -
422C GLU* 5.6 2.9 - - - +
545C ASN* 1.3 73.5 + - + +
547C ARG* 1.3 62.1 + - - +
548C ASN 2.9 7.4 + - - -
549C ILE* 3.0 40.4 + - + +
573C MET* 3.5 19.5 - - - +
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Residues in contact with ARG 547 (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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423C GLU* 3.5 37.6 - - + +
426C LYS* 6.2 0.2 - - - +
448C GLU* 6.0 2.0 - - - -
545C ASN* 3.0 17.0 + - - +
546C GLU* 1.3 78.4 - - - +
548C ASN* 1.3 66.8 + - - +
549C ILE 3.4 1.5 + - - -
550C ASN* 4.1 11.3 + - - +
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Residues in contact with ASN 548 (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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426C LYS* 5.0 4.4 + - - +
517C LEU* 3.5 39.7 + - + +
518C PRO 5.0 2.8 + - - -
543C PHE 4.0 3.1 - - - +
544C PHE* 3.4 35.3 - - + -
545C ASN* 2.9 35.6 + - - +
546C GLU 2.9 1.4 - - - -
547C ARG* 1.3 86.2 + - - +
549C ILE* 1.4 65.0 + - - +
550C ASN* 3.1 9.9 + - - +
551C ILE* 3.0 18.3 + - + +
552C THR 3.6 0.2 + - - -
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Residues in contact with ILE 549 (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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544C PHE* 4.6 1.3 - - - -
545C ASN 4.1 0.4 + - - -
546C GLU* 3.0 52.3 + - + +
547C ARG 3.4 1.4 - - - -
548C ASN* 1.4 77.0 - - - +
550C ASN* 1.3 62.6 + - - +
552C THR* 2.6 31.3 + - - +
553C LYS 5.0 0.2 + - - -
573C MET* 4.0 10.8 - - + -
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Residues in contact with ASN 550 (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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518C PRO 4.9 1.2 - - - +
519C SER* 3.8 35.2 + - - +
547C ARG 4.1 8.7 + - - +
548C ASN* 3.4 15.3 + - - +
549C ILE* 1.3 80.8 - - - +
551C ILE* 1.3 77.0 + - - +
552C THR 3.8 0.2 + - - -
553C LYS 5.1 1.4 + - - -
554C ASP* 5.3 4.7 + - - +
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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