Contacts of the helix formed by residues 560 - 568 (chain C) in PDB entry 5JHQ
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 THR 560 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527C HIS* 3.5 1.8 - - - -
551C VAL 4.6 0.2 - - - -
552C ASN* 3.9 35.9 + - + +
553C GLU 3.4 3.1 - - - +
554C LYS* 4.8 5.6 - - + +
558C PHE 3.7 5.1 + - - +
559C MET* 1.3 78.0 - - - +
561C PRO* 1.4 76.7 - - - +
562C LEU* 3.4 15.2 + - - +
563C HIS* 3.1 35.4 + - + +
564C VAL* 3.3 12.6 + - - +
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Residues in contact with PRO 561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C THR* 5.1 0.9 - - + -
526C LEU* 3.7 39.9 - - + +
527C HIS* 3.4 26.5 - - + +
530C VAL* 3.6 21.9 - - + +
550C ASN 4.8 2.0 - - - +
551C VAL* 3.4 16.8 - - + +
553C GLU 3.4 7.9 - - - +
560C THR* 1.4 88.1 - - - +
562C LEU* 1.3 57.1 + - - +
564C VAL* 3.1 3.5 + - + +
565C ALA* 2.9 31.3 + - - +
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Residues in contact with LEU 562 (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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551C VAL 5.3 0.6 + - - -
552C ASN* 6.2 1.3 - - - +
560C THR* 3.2 11.1 + - - +
561C PRO* 1.3 78.9 - - - +
563C HIS* 1.3 59.6 + - + +
565C ALA* 3.9 7.1 - - + -
566C ALA* 2.9 36.2 + - + +
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Residues in contact with HIS 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558C PHE 4.8 4.8 + - - -
559C MET* 3.7 29.3 - - + +
560C THR* 3.1 46.3 + - - +
562C LEU* 1.3 78.8 - - + +
564C VAL* 1.3 66.0 + - - +
566C ALA* 3.8 4.3 - - - +
567C GLU* 3.0 29.6 + - - +
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Residues in contact with VAL 564 (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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523C GLU* 5.1 6.7 - - - +
527C HIS* 3.9 21.8 - - + +
530C VAL* 3.8 11.4 - - + -
531C ALA* 3.7 24.0 - - + -
555C ASN* 5.4 2.0 - - - +
559C MET* 4.3 23.6 - - + -
560C THR 3.6 12.6 - - - +
561C PRO 3.1 7.3 + - - +
563C HIS* 1.3 79.4 - - - +
565C ALA* 1.3 61.9 - - - +
567C GLU* 3.6 12.2 - - - +
568C ARG* 3.5 37.3 - - - +
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Residues in contact with ALA 565 (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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530C VAL* 4.1 28.0 - - + +
561C PRO 2.9 16.8 + - - +
562C LEU* 3.9 9.0 - - + +
564C VAL* 1.3 77.3 - - - +
566C ALA* 1.3 62.5 + - - +
568C ARG* 3.3 2.6 + - - -
569C ALA* 3.1 3.8 + - - -
570C HIS* 3.1 44.8 + - - +
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Residues in contact with ALA 566 (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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562C LEU* 2.9 25.5 + - + +
563C HIS* 3.3 5.6 + - - +
565C ALA* 1.3 77.6 - - - +
567C GLU* 1.3 60.6 + - - +
568C ARG 3.3 0.7 + - - -
569C ALA* 3.4 11.2 + - - +
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Residues in contact with GLU 567 (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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559C MET* 3.6 33.0 - - - +
563C HIS 3.0 18.7 + - - +
564C VAL* 3.6 11.1 - - - +
566C ALA* 1.3 76.8 - - - +
568C ARG* 1.3 76.2 + - + +
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Residues in contact with ARG 568 (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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530C VAL 4.9 0.2 - - - -
531C ALA* 3.7 38.3 + - - +
533C LEU* 6.3 0.4 - - - +
559C MET* 6.0 0.6 - - - +
564C VAL* 3.5 31.5 + - - +
565C ALA 3.3 3.0 + - - +
566C ALA 3.2 0.6 - - - -
567C GLU* 1.3 99.3 + - + +
569C ALA* 1.3 67.7 + - - +
570C HIS* 3.4 29.3 + - + +
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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