Contacts of the helix formed by residues 571 - 582 (chain C) in PDB entry 2FGJ
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 SER 571 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569C GLY 4.3 0.4 + - - -
570C MET* 1.3 87.0 - - - +
572C VAL* 1.3 66.4 + - - +
573C GLU* 2.8 26.4 + - - -
574C LYS* 3.3 23.7 + - - +
575C VAL* 3.7 3.8 - - - +
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Residues in contact with VAL 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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560C ILE* 4.2 20.9 - - + -
570C MET 4.6 1.8 - - - +
571C SER* 1.3 75.0 - - - +
573C GLU* 1.3 63.3 + - - +
575C VAL* 3.1 19.0 + - + +
576C ILE* 3.1 30.6 + - + +
595C TYR* 5.9 5.6 - - + -
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Residues in contact with GLU 573 (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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571C SER* 2.8 35.0 + - - -
572C VAL* 1.3 72.8 + - - +
574C LYS* 1.3 77.5 + - - +
576C ILE* 3.6 13.1 + - + +
577C TYR* 3.0 30.0 + - - +
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Residues in contact with LYS 574 (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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570C MET* 3.8 24.7 - - + -
571C SER* 3.3 28.3 - - - +
572C VAL 3.2 0.4 - - - -
573C GLU* 1.3 93.0 + - - +
575C VAL* 1.3 61.2 + - - +
577C TYR* 3.6 8.8 + - - +
578C ALA* 3.2 21.7 + - - +
621C VAL* 4.7 1.7 - - - +
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Residues in contact with VAL 575 (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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560C ILE* 3.9 31.4 - - + -
563C ILE* 3.8 36.0 - - + +
564C SER* 4.0 3.8 - - - +
570C MET* 3.6 27.8 - - + +
571C SER 3.7 9.0 - - - +
572C VAL* 3.3 10.8 - - + +
574C LYS* 1.3 73.2 - - - +
576C ILE* 1.3 61.6 + - + +
578C ALA* 3.0 9.7 + - - +
579C ALA* 2.8 26.0 + - - +
595C TYR* 4.3 12.3 - - + -
621C VAL* 4.7 3.8 - - - -
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Residues in contact with ILE 576 (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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572C VAL* 3.1 31.2 + - + +
573C GLU* 3.8 11.7 - - + +
575C VAL* 1.3 78.6 - - + +
577C TYR* 1.3 50.8 + - - +
579C ALA* 2.8 5.9 + - - +
580C LYS* 2.6 54.9 + - + +
585C HIS* 3.5 32.5 - - + +
595C TYR* 3.9 23.8 - - + +
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Residues in contact with TYR 577 (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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573C GLU 3.0 18.8 + - - +
574C LYS* 3.8 9.4 - - - +
576C ILE* 1.3 78.1 - - - +
578C ALA* 1.3 59.1 + - - +
580C LYS* 3.6 12.0 + - + +
581C LEU* 3.2 55.6 + - + +
650C LYS* 3.7 35.1 + - + +
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Residues in contact with ALA 578 (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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574C LYS 3.2 13.4 + - - +
575C VAL 3.0 9.7 + - - +
577C TYR* 1.3 79.5 - - + +
579C ALA* 1.3 62.8 + - - +
581C LEU* 3.4 8.0 + - - +
582C ALA* 3.3 22.7 + - - +
617C ALA* 3.7 17.5 - - + +
620C LEU* 3.8 15.7 - - + +
621C VAL* 3.9 22.9 - - + -
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Residues in contact with ALA 579 (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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563C ILE* 4.9 2.2 - - + -
575C VAL 2.8 10.0 + - - +
576C ILE 2.8 4.6 + - - +
578C ALA* 1.3 76.3 - - - +
580C LYS* 1.3 60.9 + - - +
582C ALA 3.4 0.7 + - - -
583C GLY 3.2 2.9 + - - -
584C ALA* 2.7 39.5 + - + +
585C HIS 3.0 12.2 + - - +
588C ILE* 4.4 2.5 - - + -
595C TYR* 3.2 34.8 - - + +
617C ALA* 4.2 12.3 - - + +
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Residues in contact with LYS 580 (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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576C ILE* 2.6 42.8 + - + +
577C TYR* 3.7 13.0 - - + +
579C ALA* 1.3 73.4 - - - +
581C LEU* 1.3 63.2 + - + +
583C GLY* 3.7 8.2 + - - +
584C ALA 5.1 0.2 - - - +
585C HIS* 3.6 34.3 + - + -
643C VAL* 4.6 2.9 - - - +
647C ASN* 3.6 9.5 + - - -
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Residues in contact with LEU 581 (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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577C TYR* 3.2 55.3 + - + +
578C ALA* 3.7 7.4 - - - +
579C ALA 3.2 0.4 - - - -
580C LYS* 1.3 80.1 - - + +
582C ALA* 1.3 61.1 + - - +
583C GLY 3.3 0.7 - - - -
620C LEU* 4.0 17.9 - - + -
644C ILE* 4.0 10.0 - - - +
647C ASN* 2.9 33.2 + - + +
650C LYS* 4.0 28.0 - - + -
651C ILE* 3.9 31.6 - - + +
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Residues in contact with ALA 582 (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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578C ALA 3.3 15.7 + - - +
579C ALA 3.4 4.7 + - - +
581C LEU* 1.3 77.3 - - - +
583C GLY* 1.3 61.6 + - - +
584C ALA* 4.3 2.2 - - + -
613C ARG* 3.3 44.7 + - - +
616C ILE* 3.8 20.4 - - + -
617C ALA* 3.9 5.6 - - + +
640C SER 4.9 0.7 - - - +
644C ILE* 3.4 20.7 - - - +
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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