Contacts of the strand formed by residues 414 - 420 (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 ILE 414 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411C SER* 3.1 36.5 + - - +
412C GLU 4.2 2.2 - - - -
413C ASN* 1.3 82.5 - - - +
415C THR* 1.3 72.7 + - - +
416C GLN* 3.3 18.6 + - + +
528C ILE* 3.4 22.9 - - + +
529C GLY* 4.0 13.7 - - - +
531C THR* 3.7 39.3 - - + +
538C GLY* 3.7 4.5 - - - -
540C ALA* 3.9 14.4 - - + +
564C GLN* 3.4 6.1 + - - -
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Residues in contact with THR 415 (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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412C GLU 5.3 1.0 + - - -
413C ASN 3.9 1.4 - - - -
414C ILE* 1.3 70.7 - - - +
416C GLN* 1.3 56.0 + - - +
417C LYS* 3.3 31.6 - - + +
537C LEU* 4.4 20.0 - - - +
538C GLY 2.9 17.6 + - - -
539C LEU* 3.4 15.4 - - + +
540C ALA 2.8 31.5 + - - +
564C GLN* 3.5 9.8 + - - +
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Residues in contact with GLN 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C SER* 2.8 43.9 + - - -
414C ILE* 3.3 12.5 + - + +
415C THR* 1.3 73.4 - - - +
417C LYS* 1.3 68.8 + - - +
418C VAL* 3.9 3.4 + - + -
524C TYR* 2.7 31.5 + - - +
528C ILE* 3.3 15.8 - - + +
540C ALA* 3.3 7.2 - - + +
558C LEU* 3.2 20.8 - - - +
559C LEU* 3.7 14.9 - - + +
562C ALA* 4.2 1.0 - - - +
564C GLN* 2.9 35.9 + - - +
565C GLU* 4.6 12.5 + - - +
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Residues in contact with LYS 417 (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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535A GLY 3.3 28.0 - - - +
536A ASN* 4.3 17.0 - - - -
537A LEU 5.6 0.4 - - - +
415C THR* 3.3 25.0 - - + +
416C GLN* 1.3 79.2 - - - +
418C VAL* 1.3 63.2 + - - +
419C VAL* 4.7 1.6 - - + -
539C LEU* 4.4 18.4 - - + +
540C ALA 2.8 12.0 + - - +
541C THR* 3.3 13.0 - - + +
542C SER 2.9 23.4 + - - -
565C GLU* 4.0 24.3 + - + +
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Residues in contact with VAL 418 (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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537A LEU* 4.3 3.6 - - - +
416C GLN 3.9 1.2 + - - +
417C LYS* 1.3 76.6 - - - +
419C VAL* 1.3 67.9 + - - +
524C TYR* 4.5 8.5 - - - +
542C SER* 3.5 20.2 - - - +
544C PHE* 3.9 13.9 - - + -
555C LEU* 4.0 22.4 - - + -
559C LEU* 3.9 33.9 - - + -
565C GLU 5.6 1.6 + - - -
567C PRO* 3.3 29.4 - - + +
569C TRP* 3.8 23.6 - - + -
570C LEU* 5.3 1.1 - - + -
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Residues in contact with VAL 419 (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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413A ASN* 3.6 18.8 - - - +
535A GLY* 3.9 28.0 - - - +
536A ASN* 4.1 12.1 - - - +
537A LEU* 4.2 5.6 - - + -
417C LYS* 4.7 0.9 - - + +
418C VAL* 1.3 83.6 - - - +
420C TRP* 1.3 58.3 + - - +
421C VAL* 3.8 4.9 - - + -
429C PHE* 3.7 29.2 - - + -
541C THR* 4.4 9.0 - - + -
542C SER 2.9 16.5 + - - +
543C PHE* 3.4 10.0 - - + -
544C PHE* 2.7 32.2 + - - +
569C TRP* 3.9 5.8 - - - -
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Residues in contact with TRP 420 (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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412A GLU* 3.7 36.7 + - + -
413A ASN* 2.9 37.5 + - - +
563A LYS* 3.7 25.4 - - - -
419C VAL* 1.3 70.7 - - - +
421C VAL* 1.3 69.2 + - - +
422C GLU* 3.0 32.5 + - + +
429C PHE* 4.6 1.9 - - - -
544C PHE* 3.3 26.5 - + - -
545C ASN* 3.7 13.0 - - + -
546C GLU* 3.6 44.2 - - + -
569C TRP* 3.6 32.2 - + - +
573C MET* 3.6 24.2 - - + -
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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