Contacts of the strand formed by residues 530 - 538 (chain I) in PDB entry 5FUR
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 LYS 530 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528I VAL* 5.2 0.2 - - - +
529I VAL* 1.3 89.8 - - + +
531I PHE* 1.3 69.1 + - - +
532I TYR* 4.0 2.5 - - - +
550I GLN* 3.5 1.4 - - - +
551I ASP* 3.0 52.8 + - + +
639I LYS* 3.2 30.5 - - + +
641I GLU* 3.0 44.7 + - + +
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Residues in contact with PHE 531 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528I VAL* 3.2 28.0 - - + -
530I LYS* 1.3 78.1 - - - +
532I TYR* 1.3 63.4 + - - +
533I GLY 3.4 0.9 + - - -
548I ILE* 4.6 4.9 - - + -
549I LYS 3.6 6.1 - - - +
550I GLN* 4.2 28.0 - - + -
560I TYR 5.6 0.7 - - - -
561I VAL 6.1 0.2 - - - -
562I GLY* 4.6 10.5 - - - -
564I LEU* 3.1 30.7 - - + -
581I ILE* 5.3 3.6 - - + -
636I VAL* 3.3 23.6 - - + -
638I ARG* 2.6 55.0 - - + +
639I LYS 2.8 9.5 + - - -
640I VAL* 3.8 4.6 - - + +
641I GLU 3.1 22.5 + - - -
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Residues in contact with TYR 532 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530I LYS* 4.0 4.3 + - - +
531I PHE* 1.3 71.9 - - - +
533I GLY* 1.3 70.7 + - - +
534I SER* 3.8 26.2 + - - -
547I GLU* 4.6 6.3 - - - -
548I ILE* 3.3 10.0 - - - +
549I LYS* 2.8 68.5 + - + +
550I GLN* 4.5 1.0 - - - +
551I ASP* 6.0 4.2 - - + +
641I GLU* 3.4 40.6 - - + +
643I GLU* 6.1 0.5 - - - -
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Residues in contact with GLY 533 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531I PHE 3.4 2.8 + - - -
532I TYR* 1.3 84.3 - - - +
534I SER* 1.4 63.4 + - - -
535I PHE* 5.7 0.5 - - - -
548I ILE* 3.6 16.6 - - - -
640I VAL* 5.5 1.8 - - - +
641I GLU 3.0 23.2 + - - +
642I PHE* 4.2 21.8 - - - -
643I GLU* 4.8 3.1 + - - +
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Residues in contact with SER 534 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532I TYR* 3.8 23.5 + - - -
533I GLY* 1.4 75.9 - - - -
535I PHE* 1.3 72.1 + - - +
546I LEU* 3.3 10.7 - - - +
547I GLU* 2.9 48.8 + - - -
642I PHE* 5.4 1.3 - - - -
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Residues in contact with PHE 535 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533I GLY 5.7 0.4 - - - -
534I SER* 1.3 87.6 + - - +
536I ALA* 1.3 70.5 + - - +
545I GLU 3.7 3.4 - - - -
546I LEU* 4.5 2.9 - - + -
547I GLU* 6.4 0.2 - - - -
625I LEU* 4.6 17.7 - - + -
628I ILE* 4.7 15.7 - - + -
642I PHE* 4.7 22.7 - + + -
643I GLU* 4.9 24.9 - - + -
644I GLN* 5.3 11.2 - - + -
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Residues in contact with ALA 536 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535I PHE* 1.3 82.5 - - - +
537I PHE* 1.3 63.7 + - - +
538I ASN* 5.1 7.6 - - - +
544I LEU* 2.8 19.9 - - - +
545I GLU* 2.8 40.2 + - + +
625I LEU* 4.0 4.5 - - - -
628I ILE* 5.5 0.4 - - - +
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Residues in contact with PHE 537 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536I ALA* 1.3 73.4 - - - +
538I ASN* 1.3 77.8 + - - +
539I ARG* 3.8 1.6 + - - -
542I ASN* 4.2 15.0 - - + -
543I VAL 3.4 20.0 - - - -
544I LEU* 3.1 29.4 - - + -
594I SER* 6.1 2.9 - - - -
622I ASP* 4.2 12.3 - - + +
625I LEU* 2.9 52.9 - - + +
626I LEU* 3.4 52.3 - - + -
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Residues in contact with ASN 538 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536I ALA* 5.1 7.6 - - - +
537I PHE* 1.3 81.4 + - - +
539I ARG* 1.3 68.0 - - - +
540I LYS* 4.7 4.3 - - + +
541I ARG* 4.9 19.1 - - + +
542I ASN* 3.4 18.4 + - - -
543I VAL* 3.2 15.4 + - - +
545I GLU* 3.9 29.9 + - - +
622I ASP* 4.4 0.7 - - - -
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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