Contacts of the strand formed by residues 521 - 529 (chain A) in PDB entry 5FFO
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 521 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497A GLU* 6.5 0.2 - - - -
498A LEU 3.2 14.6 - - - -
499A LEU* 3.6 19.5 - - - -
514A PHE* 4.1 0.7 - - - -
517A SER* 3.8 4.2 + - - -
519A SER* 2.7 31.6 + - - +
520A PRO* 1.3 78.3 - - - +
522A HIS* 1.3 62.1 + - - +
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Residues in contact with HIS 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A PHE* 5.9 4.7 - + - -
496A VAL 3.9 3.5 - - - +
497A GLU* 4.0 1.5 - - - -
498A LEU* 3.4 31.5 + - + +
514A PHE* 3.7 27.9 - - + -
517A SER* 4.3 19.5 - - - +
521A SER* 1.3 77.2 - - - +
523A SER* 1.3 78.4 + - - +
524A LYS* 3.8 20.4 - - + +
537A GLU* 4.5 9.6 - - - -
539A LEU* 4.0 29.1 - - + +
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Residues in contact with SER 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496A VAL 3.8 4.3 - - - -
497A GLU* 3.4 26.6 + - - -
522A HIS* 1.3 86.8 + - - +
524A LYS* 1.3 69.3 + - - +
525A ASN* 4.8 5.9 + - - -
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Residues in contact with LYS 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A PHE* 5.7 7.2 - - + -
496A VAL* 3.2 38.4 + - + +
497A GLU* 5.4 0.2 - - - +
522A HIS* 3.8 18.2 - - + +
523A SER* 1.3 80.5 + - - +
525A ASN* 1.3 86.7 + - - +
526A MET* 3.7 12.4 + - + +
537A GLU* 3.3 32.6 + - - +
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Residues in contact with ASN 525 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494A PHE 3.7 4.0 - - - +
495A GLN* 4.0 22.2 - - + +
523A SER* 4.8 6.2 + - - -
524A LYS* 1.3 95.5 - - - +
526A MET* 1.3 60.0 + - - +
527A THR 4.1 1.5 + - - -
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Residues in contact with MET 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A PHE* 4.9 15.3 - - + -
480A LEU* 3.9 22.7 - - + -
492A LEU 3.6 0.9 - - - +
493A ASN* 3.4 1.9 - - - +
494A PHE* 2.4 55.3 + - + +
496A VAL* 4.6 8.5 - - + -
524A LYS* 4.6 16.4 - - + +
525A ASN* 1.3 73.2 - - - +
527A THR* 1.3 63.5 + - - +
528A ILE* 3.7 25.8 + - + -
535A GLN* 3.6 35.9 - - + +
536A CYS* 4.8 6.1 - - - +
537A GLU* 5.3 8.1 - - + +
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Residues in contact with THR 527 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491A LYS* 4.1 30.7 - - + -
492A LEU 3.7 3.8 - - - +
493A ASN* 2.7 33.4 + - - +
525A ASN 4.1 2.0 + - - -
526A MET* 1.3 72.6 - - - +
528A ILE* 1.3 63.5 + - - +
535A GLN* 3.3 14.2 + - - +
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Residues in contact with ILE 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A LEU* 4.4 16.8 - - + +
481A LYS* 4.4 3.8 - - - -
482A ALA* 3.9 28.0 - - + +
490A ARG 3.7 0.3 - - - +
491A LYS* 3.8 1.3 - - - -
492A LEU* 2.9 34.8 + - + +
494A PHE* 3.4 34.1 - - + -
526A MET* 3.7 35.7 - - + +
527A THR* 1.3 79.3 - - - +
529A SER* 1.3 67.4 + - - +
530A ARG 5.2 0.2 - - - +
535A GLN* 3.2 24.0 - - + +
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Residues in contact with SER 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A ALA 4.5 2.1 + - - +
490A ARG* 3.4 13.7 - - - -
491A LYS* 3.5 30.2 + - - +
528A ILE* 1.3 79.1 - - - +
530A ARG* 1.3 68.5 + - - +
531A GLY 3.8 0.9 + - - -
532A GLY* 4.1 12.8 + - - -
533A LEU 4.3 12.8 + - - +
535A GLN* 4.2 9.9 + - - +
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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