Contacts of the strand formed by residues 538 - 546 (chain A) in PDB entry 3S3J
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 538 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496A THR* 4.0 2.4 - - - +
497A ASN* 2.9 27.4 + - - +
534A LEU* 4.0 8.9 - - - +
535A GLU* 2.8 38.8 + - - +
536A PRO 4.0 2.9 - - - -
537A PHE* 1.3 79.8 - - - +
539A GLU* 1.3 68.4 + - - +
540A LYS* 5.1 4.9 + - - -
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Residues in contact with GLU 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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494A HIS* 3.1 29.4 + - + -
495A ILE 3.1 14.4 - - - +
496A THR* 4.1 11.4 + - + +
534A LEU* 4.5 2.2 - - - -
538A SER* 1.3 82.1 - - - +
540A LYS* 1.3 70.5 + - - +
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Residues in contact with LYS 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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493A ALA 3.4 1.6 - - - +
494A HIS* 3.4 4.6 + - - -
495A ILE* 2.8 37.7 + - + +
532A LEU* 3.7 27.1 - - + -
533A ASN* 3.1 25.2 + - - +
534A LEU* 4.4 16.4 - - + +
535A GLU* 5.2 2.4 - - - +
538A SER* 5.1 4.6 + - - +
539A GLU* 1.3 81.0 + - - +
541A SER* 1.3 62.4 + - - +
542A VAL* 3.8 13.2 - - + -
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Residues in contact with SER 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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478A ARG* 4.5 8.6 + - - -
492A PHE* 3.9 27.3 - - - -
493A ALA 3.5 4.3 - - - -
494A HIS* 3.2 22.3 + - - +
540A LYS* 1.3 73.5 - - - +
542A VAL* 1.3 60.7 + - - +
543A PRO* 3.2 11.8 - - - +
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Residues in contact with VAL 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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492A PHE* 3.2 3.6 - - - -
493A ALA* 2.7 44.7 + - + +
495A ILE* 4.5 3.4 - - + -
507A LEU* 3.7 31.6 - - + -
509A LEU* 3.4 8.2 - - + +
527A LYS* 3.5 32.3 - - + -
529A LEU* 4.4 5.4 - - + -
532A LEU* 4.4 20.0 - - + -
540A LYS* 4.5 14.8 - - + -
541A SER* 1.3 71.7 - - - +
543A PRO* 1.3 63.9 - - + +
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Residues in contact with PRO 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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490A ASP* 4.7 11.4 - - - +
491A VAL 3.3 7.2 - - - +
492A PHE* 3.7 21.3 - - + -
509A LEU* 4.1 1.3 - - - -
527A LYS* 3.1 29.2 - - - +
541A SER 3.2 11.4 - - - +
542A VAL* 1.3 89.4 - - + +
544A LEU* 1.3 59.5 + - - +
545A CYS 5.4 0.2 - - - +
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Residues in contact with LEU 544 (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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490A ASP* 3.3 4.0 - - - -
491A VAL* 2.9 40.5 + - + +
509A LEU* 3.7 35.0 - - + +
510A CYS* 3.9 8.1 - - - -
511A ALA* 4.2 2.5 - - + +
525A GLY* 3.5 26.9 - - - +
526A THR 3.9 26.5 - - - +
527A LYS* 4.3 6.5 - - + -
543A PRO* 1.3 74.5 - - - +
545A CYS* 1.3 79.4 + - - +
546A ILE* 3.6 15.7 + - + -
563A VAL* 5.9 0.4 - - + -
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Residues in contact with CYS 545 (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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488A ASP* 4.6 6.1 - - - -
489A PHE 4.2 5.2 - - - -
490A ASP* 3.3 19.9 + - - +
524A CYS 4.8 3.1 - - - +
525A GLY* 4.8 2.1 - - - -
543A PRO* 4.3 0.6 - - - +
544A LEU* 1.3 87.8 - - + +
546A ILE* 1.3 65.8 + - - +
547A LEU* 3.6 36.2 + - + +
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Residues in contact with ILE 546 (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 SER 4.3 0.2 - - - +
488A ASP* 3.2 6.4 - - - +
489A PHE* 2.6 75.6 + - + +
491A VAL* 4.2 17.7 - - + -
511A ALA* 3.6 30.5 - - + -
524A CYS* 3.9 16.6 - - - +
544A LEU* 4.1 13.5 - - + -
545A CYS* 1.3 77.9 - - - +
547A LEU* 1.3 62.2 + - - +
551A TYR* 3.7 20.2 - - + -
561A ILE* 4.4 11.4 - - + -
563A VAL* 5.9 0.4 - - + -
582A LEU* 6.1 0.4 - - + -
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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