Contacts of the strand formed by residues 535 - 543 (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 GLN 535 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478A PHE 4.8 0.2 - - - +
480A LEU 3.1 30.5 + - - +
526A MET* 3.6 22.5 - - + +
527A THR 3.3 8.7 + - - +
528A ILE* 3.2 38.7 - - + +
529A SER* 4.8 8.6 + - - +
533A LEU 3.5 7.9 + - - +
534A MET* 1.3 73.4 - - - +
536A CYS* 1.3 60.3 + - - +
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Residues in contact with CYS 536 (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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477A ARG* 3.6 32.3 - - - +
478A PHE 3.1 21.5 - - - -
479A CYS* 2.0 44.2 - - + -
526A MET* 5.1 2.8 - - - +
534A MET* 3.8 5.4 + - + +
535A GLN* 1.3 75.7 - - - +
537A GLU* 1.3 64.9 + - - +
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Residues in contact with GLU 537 (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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477A ARG* 4.7 3.4 - - - -
478A PHE* 3.2 65.5 + - + -
522A HIS* 4.5 10.7 - - - -
524A LYS* 3.3 35.7 + - - +
526A MET* 5.3 10.6 - - + +
536A CYS* 1.3 79.1 - - - +
538A GLU* 1.3 70.7 + - - +
539A LEU* 5.0 7.4 - - - +
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Residues in contact with GLU 538 (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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451A TYR* 3.9 20.1 + - - +
475A ASN* 2.7 40.7 + - + +
476A VAL 3.6 9.0 - - - +
477A ARG* 4.3 13.1 - - + +
537A GLU* 1.3 83.0 - - - +
539A LEU* 1.3 73.3 + - - +
540A ILE* 5.9 0.4 - - + -
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Residues in contact with LEU 539 (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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475A ASN* 3.7 1.7 - - - -
476A VAL* 2.8 42.5 + - + +
478A PHE* 5.2 9.6 - - + -
514A PHE* 3.5 36.6 - - + -
516A TYR* 6.4 2.2 - - + -
517A SER* 6.1 0.4 - - - -
522A HIS* 4.0 31.6 - - + +
537A GLU* 5.0 9.2 - - - +
538A GLU* 1.3 82.7 - - - +
540A ILE* 1.3 67.4 + - - +
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Residues in contact with ILE 540 (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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462A CYS* 4.0 19.3 - - + -
473A CYS* 3.9 20.9 - - + -
474A PHE 3.5 11.7 - - - +
475A ASN* 3.5 27.6 - - - +
514A PHE* 3.8 8.4 - - - +
515A LEU* 2.9 50.8 + - + +
516A TYR 4.8 0.2 + - - -
538A GLU* 5.9 0.2 - - + -
539A LEU* 1.3 81.4 - - - +
541A ALA* 1.3 61.2 + - - +
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Residues in contact with ALA 541 (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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473A CYS* 3.5 2.2 - - - +
474A PHE* 2.7 59.2 + - + +
476A VAL* 4.2 9.4 - - + +
500A LEU* 3.8 28.9 - - + -
514A PHE* 4.0 16.4 - - + +
515A LEU 4.1 0.4 - - - +
539A LEU 4.1 2.0 + - - -
540A ILE* 1.3 74.4 - - - +
542A TYR* 1.3 57.2 + - - +
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Residues in contact with TYR 542 (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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464A LEU* 6.0 2.2 - - + -
471A VAL* 3.6 24.5 - - + -
472A SER 3.1 15.3 - - - +
473A CYS* 3.6 14.6 - - + +
474A PHE* 4.0 6.7 - - - -
512A ALA* 3.6 6.9 - - - +
513A LEU* 3.2 77.5 + - + +
514A PHE 3.6 5.6 - - - -
515A LEU* 3.9 26.7 - - + -
518A ARG* 5.5 4.6 + - - -
541A ALA* 1.3 75.1 - - - +
543A LEU* 1.3 86.0 + - - +
544A ARG* 4.2 9.1 + - + +
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Residues in contact with LEU 543 (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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455A LEU* 4.9 18.6 - - + -
456A ASN 4.4 15.5 - - - +
457A GLN* 4.2 19.5 - - - +
471A VAL* 4.9 2.3 - - - +
472A SER* 2.8 28.5 + - - +
474A PHE* 4.2 3.6 - - + -
511A ARG* 3.2 19.1 - - + +
512A ALA* 4.9 0.9 - - + +
542A TYR* 1.3 89.8 - - - +
544A ARG* 1.3 74.4 + - - +
545A ASP 4.0 0.2 + - - -
549A PHE* 3.7 20.2 - - + -
556A ILE* 3.8 24.9 - - + -
593A ILE* 4.7 16.8 - - + -
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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