Contacts of the strand formed by residues 566 - 570 (chain C) in PDB entry 2FH2
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 ALA 566 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541C VAL* 3.0 30.4 + - + +
565C ASP* 1.3 74.3 - - - +
567C PHE* 1.3 67.5 + - - +
577C LEU* 4.4 6.1 - - + -
578C TRP 3.4 10.5 - - - +
579C VAL* 4.8 2.7 - - - -
580C GLY 4.4 0.4 - - - +
583C ALA* 3.9 8.9 - - + +
587C GLU* 3.7 33.1 + - + +
588C LYS* 4.4 4.3 - - + +
591C ALA* 4.3 11.0 - - + -
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Residues in contact with PHE 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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538C LEU* 3.8 24.0 - - + -
539C PHE 3.2 15.0 - - - -
540C GLN* 3.4 38.6 - - + -
541C VAL* 4.8 0.2 - - - -
554C VAL* 4.5 3.4 - - + -
560C ALA 3.2 28.9 - - - -
561C LEU* 3.7 20.0 - - + -
562C ASN* 3.4 31.6 - - + -
565C ASP* 4.0 3.8 - - + -
566C ALA* 1.3 88.6 - - - +
568C VAL* 1.3 63.3 + - - +
569C LEU 4.2 0.4 + - - -
576C TYR 3.8 0.5 - - - +
577C LEU* 3.6 5.3 - - - +
578C TRP* 2.8 63.6 + + + +
614C PHE* 6.0 0.4 - - + -
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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
----------------------------------------------------------
537C ARG 3.7 0.9 - - - +
538C LEU* 3.3 6.1 - - - +
539C PHE* 2.8 38.6 + - + +
541C VAL* 4.7 1.3 - - + +
567C PHE* 1.3 76.8 - - - +
569C LEU* 1.3 67.7 + - - +
570C LYS* 4.2 0.9 - - + +
576C TYR 3.5 4.3 - - - +
577C LEU* 4.6 1.1 - - + -
591C ALA* 3.6 38.6 - - + +
594C LEU* 3.9 25.8 - - + -
595C LEU* 3.5 34.8 - - + -
598C LEU* 4.4 12.8 - - + -
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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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536C THR* 4.3 17.5 - - + -
537C ARG 3.3 16.4 - - - +
538C LEU* 4.2 10.5 - - + -
556C PRO* 4.7 0.2 - - + -
567C PHE 4.2 0.4 - - - -
568C VAL* 1.3 76.3 - - - +
570C LYS* 1.3 59.8 + - - +
571C THR* 4.6 5.2 - - - +
575C ALA* 3.2 5.4 - - - +
576C TYR* 2.9 60.0 + - + -
614C PHE* 3.8 31.4 - - + +
617C ALA* 4.1 9.6 - - + +
618C LEU* 3.7 36.1 - - + -
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Residues in contact with LYS 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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535C SER 3.6 5.5 - - - +
536C THR* 3.4 6.1 - - - +
537C ARG* 2.9 48.4 + - + +
539C PHE* 5.9 0.6 - - + -
568C VAL* 4.2 2.1 - - + +
569C LEU* 1.3 72.7 - - - +
571C THR* 1.3 87.0 + - - +
572C PRO* 4.7 7.6 + - - -
574C ALA 3.9 5.6 - - - +
575C ALA* 4.5 2.2 - - + +
598C LEU* 3.8 47.8 + - + +
599C ARG 5.2 2.2 + - - -
600C ALA* 4.3 22.6 - - + +
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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