Contacts of the strand formed by residues 530 - 536 (chain C) in PDB entry 3FCS
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 GLY 530 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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508C LEU 3.0 15.3 - - - -
509C GLN* 3.9 13.2 + - - +
510C LEU* 4.4 1.1 - - - -
523C LEU* 3.9 6.7 - - - -
528C GLN* 3.3 13.6 - - - +
529C ALA* 1.3 81.3 - - - +
531C THR* 1.3 71.1 + - - +
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Residues in contact with THR 531 (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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506C ALA 3.7 0.9 - - - +
507C GLU* 3.5 3.0 - - - +
508C LEU* 2.8 40.9 + - - +
509C GLN* 5.0 0.6 - - - +
523C LEU* 3.4 24.9 - - + +
526C SER* 4.3 11.2 - - - +
528C GLN* 5.4 0.7 - - + -
530C GLY* 1.3 83.3 - - - +
532C THR* 1.3 66.2 + - - +
533C LEU* 5.0 12.1 - - - +
548C THR* 6.1 0.5 - - - +
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Residues in contact with THR 532 (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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505C ASN* 4.0 20.2 - - + -
506C ALA 3.3 7.6 - - - +
507C GLU* 3.9 19.4 + - - +
531C THR* 1.3 77.5 + - - +
533C LEU* 1.3 79.8 + - - +
534C ASN* 4.4 9.2 + - - +
3570C NAG 4.1 9.4 - - + +
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Residues in contact with LEU 533 (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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489C MET* 3.3 37.7 - - + -
504C LEU 3.6 0.9 - - - +
505C ASN* 3.2 6.2 - - - -
506C ALA* 2.8 36.2 + - + +
508C LEU* 6.1 0.9 - - + -
531C THR* 5.0 13.2 - - - +
532C THR* 1.3 79.7 - - - +
534C ASN* 1.3 66.6 + - - +
535C LEU* 3.8 22.4 + - + -
546C HIS* 4.9 11.9 - - + -
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Residues in contact with ASN 534 (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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503C SER* 4.3 8.4 + - - +
504C LEU 3.7 5.4 - - - -
505C ASN* 2.7 28.1 + - - +
532C THR* 4.4 8.9 + - - +
533C LEU* 1.3 76.7 + - - +
535C LEU* 1.3 65.7 + - - +
536C ASP* 3.6 2.9 + - - +
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Residues in contact with LEU 535 (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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489C MET* 5.2 5.6 - - + +
491C VAL* 3.6 41.7 - - + +
503C SER* 3.1 15.2 + - - -
504C LEU* 2.9 25.7 + - + +
506C ALA* 4.2 14.6 - - + -
533C LEU* 4.1 21.3 - - + -
534C ASN* 1.3 71.6 - - - +
536C ASP* 1.3 60.4 + - - +
537C LEU* 3.3 13.5 + - + +
544C ILE* 4.5 20.6 - - + +
546C HIS* 3.8 28.9 - - + +
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Residues in contact with ASP 536 (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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501C LYS* 5.6 1.0 - - - -
502C LEU 3.5 8.9 + - - +
503C SER* 4.5 5.3 - - - +
534C ASN 3.6 4.7 + - - +
535C LEU* 1.3 69.1 - - - +
537C LEU* 1.3 56.2 + - - +
538C GLY* 3.2 20.5 + - - +
540C LYS* 3.5 18.2 - - - +
544C ILE* 3.1 21.0 - - + +
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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