Contacts of the helix formed by residues 565 - 572 (chain C) in PDB entry 5J87
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 PRO 565 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563C TRP 3.8 6.3 - - - +
564C SER* 1.3 90.4 - - - +
566C PRO* 1.3 75.5 - - + +
567C GLU* 3.1 23.4 + - - +
568C VAL* 3.3 23.0 + - + -
569C LEU* 3.3 11.0 + - - +
578C SER* 3.4 27.1 - - - +
581C TRP* 3.5 11.4 - - + -
610C ILE* 4.9 0.7 - - - -
641C ARG* 3.3 27.8 - - - +
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Residues in contact with PRO 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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564C SER 4.5 0.2 - - - +
565C PRO* 1.3 88.1 - - + +
567C GLU* 1.3 62.4 + - - +
569C LEU* 3.8 2.8 + - - +
570C MET* 3.3 39.6 + - + +
581C TRP* 3.3 35.0 - - + -
610C ILE* 4.0 28.3 - - + +
611C ALA* 5.9 2.5 - - - -
615C ARG* 5.1 2.5 - - - +
635C HIS 4.8 0.7 - - - +
636C GLU* 4.1 18.2 - - + +
641C ARG* 3.8 6.7 - - - +
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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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565C PRO* 3.3 26.1 - - + +
566C PRO* 1.3 78.6 - - - +
568C VAL* 1.3 60.3 + - - +
569C LEU 3.3 0.2 - - - -
570C MET* 4.4 0.7 - - - +
571C TYR* 2.5 46.0 + - + +
572C SER 3.2 3.6 + - - -
573C LYS* 3.5 29.0 + - + +
575C SER* 4.8 3.1 + - - +
578C SER* 4.2 8.8 + - - -
636C GLU 4.4 2.4 - - - +
638C ALA* 3.8 19.7 + - + +
641C ARG* 3.1 25.5 + - - -
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Residues in contact with VAL 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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554C SER* 4.6 4.6 + - - +
559C PHE* 3.9 20.2 - - + -
564C SER* 4.0 7.4 - - - +
565C PRO* 3.3 18.4 + - + +
567C GLU* 1.3 74.0 - - - +
569C LEU* 1.3 67.4 + - - +
572C SER* 2.9 26.4 + - - +
573C LYS 3.5 22.9 - - - +
574C PHE* 3.8 35.7 - - + -
578C SER* 3.7 26.0 - - - +
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Residues in contact with LEU 569 (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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554C SER* 4.7 16.0 - - - +
559C PHE* 4.1 21.3 - - + -
561C VAL* 3.9 24.0 - - + +
564C SER* 3.8 25.8 - - - +
565C PRO 3.3 8.5 + - - +
566C PRO 3.9 4.3 - - - +
568C VAL* 1.3 79.8 - - - +
570C MET* 1.3 61.3 + - + +
607C ALA* 3.9 27.6 - - + +
610C ILE* 3.6 36.1 - - + -
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Residues in contact with MET 570 (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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566C PRO* 3.3 24.5 + - + +
567C GLU* 5.7 0.2 - - - -
568C VAL 3.1 0.2 - - - -
569C LEU* 1.3 85.8 - - + +
571C TYR* 1.3 103.2 + - + +
572C SER* 3.6 2.0 + - - -
610C ILE* 6.2 1.8 - - + -
611C ALA* 4.9 16.6 - - + -
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Residues in contact with TYR 571 (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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567C GLU* 2.5 25.3 + - + +
570C MET* 1.3 113.1 - - + +
572C SER* 1.3 71.0 + - - +
573C LYS* 2.9 13.3 + - + +
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Residues in contact with SER 572 (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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554C SER* 3.5 20.1 + - - -
568C VAL* 2.9 19.6 + - - +
570C MET 3.6 1.2 + - - -
571C TYR* 1.3 79.9 - - - +
573C LYS* 1.3 58.3 + - - +
574C PHE* 3.3 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