Contacts of the strand formed by residues 595 - 602 (chain A) in PDB entry 5FZ9
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 ASN 595 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488A TYR 4.8 0.7 - - - +
489A VAL* 3.5 9.5 - - - +
490A GLY* 3.0 42.5 + - - +
511A LEU* 4.1 12.1 - - + +
513A TRP* 3.5 20.2 - - - +
514A GLY* 4.1 0.9 - - - -
515A GLU 3.1 27.2 + - - +
516A PRO 3.6 10.1 + - - -
517A LYS* 4.3 4.5 + - - +
591A ASN* 2.9 26.3 + - - +
593A GLY 3.6 7.7 + - - +
594A PHE* 1.3 79.8 - - - +
596A PHE* 1.3 64.3 + - - +
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Residues in contact with PHE 596 (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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74A PHE* 3.5 24.0 - + - -
379A LEU* 5.1 4.9 - - + -
434A PHE* 3.4 35.2 - + - -
435A GLY 4.8 2.2 - - - -
437A GLY* 4.3 6.3 - - - -
487A LEU* 4.1 26.0 - - + -
488A TYR 3.4 4.9 - - - -
489A VAL* 4.0 20.9 - - + -
511A LEU* 3.4 4.8 - - - +
512A HIS* 2.8 62.3 + + + +
513A TRP* 3.1 33.6 + + + -
595A ASN* 1.3 81.0 + - - +
597A ALA* 1.3 63.2 + - - +
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Residues in contact with ALA 597 (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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487A LEU* 3.6 5.5 - - - +
488A TYR* 2.8 42.0 + - + +
509A ASN* 3.8 17.9 - - - +
510A TYR 3.3 11.9 - - - +
511A LEU* 3.9 7.9 - - + -
512A HIS* 4.4 3.1 - - - +
517A LYS* 3.9 25.4 - - - +
596A PHE* 1.3 78.1 - - - +
598A GLU* 1.3 59.9 + - - +
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Residues in contact with GLU 598 (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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436A SER* 2.7 25.0 + - - -
437A GLY 3.0 15.8 + - - -
438A PHE* 3.6 15.4 - - + -
461A LEU* 3.4 13.5 - - + +
462A ASN* 4.3 0.9 + - - -
485A PRO* 3.4 26.8 - - + +
486A TRP 3.3 13.0 - - - +
487A LEU* 3.6 14.4 - - + +
488A TYR* 5.1 0.2 - - - -
509A ASN* 3.5 1.6 - - - -
510A TYR 2.7 37.9 + - - +
512A HIS* 2.9 29.3 + - + +
597A ALA* 1.3 75.3 - - - +
599A ALA* 1.3 62.6 + - - +
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Residues in contact with ALA 599 (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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461A LEU* 4.0 3.4 - - - -
485A PRO* 3.3 4.5 - - - +
486A TRP 2.9 32.0 + - - -
488A TYR* 3.9 7.6 - - + -
507A SER* 5.9 0.7 - - - -
508A ILE 3.2 12.6 - - - +
509A ASN* 3.7 22.0 - - + +
598A GLU* 1.3 75.8 - - - +
600A VAL* 1.3 63.0 + - - +
1756A DMS 3.7 26.4 - - + +
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Residues in contact with VAL 600 (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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461A LEU* 4.0 30.7 - - + +
464A MET* 4.9 5.2 - - + -
465A PRO* 4.4 10.5 - - + -
482A MET 4.9 0.4 - - - +
483A LYS 3.9 14.6 - - - +
484A LEU 3.8 28.3 - - - +
485A PRO* 3.9 4.0 - - + -
507A SER* 3.5 1.2 - - - -
508A ILE* 3.1 47.8 + - + +
599A ALA* 1.3 75.1 - - - +
601A ASN* 1.3 73.6 + - - +
602A PHE* 4.2 0.4 - - + -
1756A DMS 3.7 8.9 - - - +
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Residues in contact with ASN 601 (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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465A PRO* 5.0 6.2 - - - +
472A LEU* 5.7 2.1 - - + +
481A GLY 4.1 9.9 - - - +
482A MET* 3.7 36.2 + - + +
484A LEU 5.4 0.4 + - - -
501A GLU* 3.2 28.5 + - - +
502A ASP* 5.7 2.4 - - - +
505A SER* 3.2 22.8 + - - +
506A TYR 3.5 8.0 + - - -
507A SER* 4.1 0.2 - - - -
600A VAL* 1.3 89.5 - - - +
602A PHE* 1.3 66.1 + - - +
1756A DMS 3.3 29.0 - - - +
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Residues in contact with PHE 602 (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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46A PHE* 4.3 13.7 - + + -
49A ILE* 3.6 30.3 - - + -
464A MET* 4.2 25.1 - - + +
465A PRO* 5.3 3.8 - - + -
470A SER* 5.3 4.3 - - - +
472A LEU* 5.2 5.6 - - - -
505A SER* 3.6 0.2 - - - -
506A TYR* 3.0 71.0 + + + +
507A SER 4.0 5.6 - - - -
508A ILE* 3.9 35.4 - - + -
580A ILE* 4.7 3.1 - - + -
600A VAL* 4.2 2.2 - - + -
601A ASN* 1.3 79.8 - - - +
603A CYS* 1.3 71.4 + - - +
604A THR* 3.8 22.9 - - + -
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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