Contacts of the helix formed by residues 558 - 564 (chain B) 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 558 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557B ARG* 1.3 80.5 - - - +
559B ILE* 1.3 59.9 + - - +
560B ILE* 3.3 4.9 - - - +
561B ASP* 2.9 33.7 + - - +
562B ASN* 2.9 29.8 + - - +
595B TYR 4.2 2.0 - - - -
596B ASN* 3.7 21.8 - - - -
597B THR 3.2 14.8 - - - -
598B ILE* 4.0 5.3 - - - +
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Residues in contact with ILE 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558B SER* 1.3 69.7 - - - +
560B ILE* 1.3 62.0 + - - +
562B ASN* 2.8 23.3 + - + +
563B ILE* 2.9 33.2 + - + +
587B PHE* 5.6 0.2 - - + -
588B ILE* 3.3 29.8 - - + -
591B LEU* 3.7 30.7 - - + -
595B TYR* 3.5 7.5 + - + +
597B THR* 3.0 22.2 + - - +
599B VAL* 3.3 30.1 - - + -
606B LEU* 4.9 5.6 - - + -
614B ILE* 4.1 21.5 - - + -
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Residues in contact with ILE 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B SER* 3.3 11.9 - - - +
559B ILE* 1.3 73.1 - - - +
561B ASP* 1.3 65.4 + - - +
563B ILE* 3.6 1.9 + - - +
564B SER* 2.8 39.1 + - - +
570B MET 5.9 1.3 - - - +
572B VAL* 4.1 38.1 - - + -
575B VAL* 4.2 27.6 - - + -
595B TYR* 2.8 36.3 + - + +
596B ASN* 3.4 19.5 - - - +
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Residues in contact with ASP 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557B ARG* 3.7 32.0 + - - -
558B SER* 2.9 28.1 + - - +
559B ILE 3.1 0.6 - - - -
560B ILE* 1.3 86.1 - - - +
562B ASN* 1.3 61.4 + - - +
564B SER* 3.5 21.4 + - - +
565B LEU* 4.1 3.1 + - - +
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Residues in contact with ASN 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554B LEU* 4.0 23.6 - - + +
555B LEU* 3.1 51.4 + - - +
557B ARG* 3.0 19.1 - - - +
558B SER 2.9 18.9 + - - +
559B ILE* 2.8 11.9 + - - +
561B ASP* 1.3 75.9 - - - +
563B ILE* 1.3 63.0 + - - +
564B SER 3.7 0.2 + - - -
565B LEU* 4.0 8.2 + - - +
599B VAL* 4.1 8.1 - - - +
614B ILE* 4.6 6.7 - - + -
618B ARG* 3.4 19.8 + - - +
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Residues in contact with ILE 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B ILE* 2.9 35.2 + - + +
560B ILE 4.0 4.0 - - - +
562B ASN* 1.3 74.8 - - - +
564B SER* 1.3 56.7 + - - +
565B LEU 3.1 7.5 + - - -
575B VAL* 4.2 27.6 - - + +
578B ALA* 5.0 0.2 - - + -
579B ALA* 4.5 12.3 - - + -
595B TYR* 4.6 2.9 - - + -
614B ILE* 4.0 24.5 - - + +
617B ALA* 3.8 18.4 - - + -
618B ARG* 3.6 27.2 - - - +
621B VAL* 3.3 38.4 - - + +
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Residues in contact with SER 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B ILE* 2.8 26.5 + - - +
561B ASP* 3.5 11.9 + - - +
562B ASN 3.4 0.4 - - - -
563B ILE* 1.3 73.0 - - - +
565B LEU* 1.3 63.5 + - - +
566B ALA 3.6 1.8 - - - -
567B ASN 3.8 8.1 - - - -
568B PRO* 3.6 20.9 - - - +
569B GLY 5.2 1.6 - - - -
570B MET* 3.2 33.9 + - - +
575B VAL* 3.5 9.0 - - - +
621B VAL* 4.2 1.1 - - - -
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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