Contacts of the strand formed by residues 537 - 544 (chain A) in PDB entry 4BHZ
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 537 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532A GLY 3.7 11.6 - - - +
536A SER* 1.4 86.2 + - - +
538A LYS* 1.3 59.5 + - - +
539A VAL* 5.5 1.3 - - - +
553A LYS* 4.5 5.4 - - - -
554A TYR 3.2 12.1 - - - -
555A VAL* 3.9 16.2 - - - -
1795A 7PE 3.3 29.6 + - - -
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Residues in contact with LYS 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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530A GLN* 4.9 9.9 - - + +
532A GLY 4.2 6.1 - - - -
537A SER* 1.3 72.1 - - - +
539A VAL* 1.3 58.6 + - - +
540A PHE* 3.6 29.2 - - + -
552A ILE 3.8 0.7 - - - +
553A LYS* 3.7 1.0 - - - +
554A TYR* 2.7 50.2 + - + +
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Residues in contact with VAL 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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530A GLN* 3.4 7.4 - - - +
531A ILE* 2.6 35.0 + - + -
532A GLY* 3.3 25.5 + - - +
537A SER 5.5 2.0 - - - -
538A LYS* 1.3 76.7 - - - +
540A PHE* 1.3 61.5 + - - +
551A ALA* 4.6 3.4 - - + -
552A ILE 3.4 13.2 - - - +
553A LYS* 3.8 15.5 - - + -
1795A 7PE 3.5 24.2 - - - +
1797A Z0B 3.9 41.3 - - + +
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Residues in contact with PHE 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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518A MET* 3.7 23.8 - - + -
527A ILE* 4.0 25.1 - - + -
529A LYS 3.4 6.1 - - - +
530A GLN* 3.7 32.1 - - + -
531A ILE* 3.9 7.2 - - - +
538A LYS* 3.6 30.7 - - + -
539A VAL* 1.3 74.4 - - - +
541A GLN* 1.3 60.6 + - - +
542A VAL* 4.1 15.7 - - + +
551A ALA* 3.2 7.4 - - - +
552A ILE 2.8 42.0 + - - +
554A TYR* 4.1 15.0 - + + -
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Residues in contact with GLN 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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527A ILE* 3.8 0.7 - - - +
528A LEU* 2.7 46.1 + - + +
529A LYS* 2.7 40.9 + - + +
531A ILE* 3.8 13.1 - - + +
540A PHE* 1.3 73.0 - - - +
542A VAL* 1.3 56.8 + - - +
549A ILE* 3.7 29.7 - - + +
550A TYR 3.6 4.9 - - - +
604A CYS* 3.6 19.5 - - - -
1798A EDO 3.4 28.9 + - - -
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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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518A MET* 4.6 1.6 - - + -
525A TYR* 3.8 18.4 - - + -
526A SER 3.2 14.4 - - - +
527A ILE* 4.0 16.4 - - + -
528A LEU* 4.4 3.4 - - - +
540A PHE* 4.1 17.3 - - + +
541A GLN* 1.3 80.4 - - - +
543A LEU* 1.4 60.5 + - - +
549A ILE* 3.3 9.2 - - - +
550A TYR* 2.8 48.3 + - + +
552A ILE* 3.6 40.8 - - + +
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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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525A TYR* 3.4 6.2 - - - -
526A SER* 2.8 44.2 + - - +
528A LEU* 3.8 30.3 - - + -
542A VAL* 1.4 74.0 - - - +
544A ASN* 1.4 65.0 + - - +
547A LYS* 3.4 33.4 - - + +
548A GLN 3.2 12.8 - - - +
549A ILE* 3.9 15.7 - - + +
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Residues in contact with ASN 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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523A ARG* 6.2 1.6 - - + -
524A ILE 3.8 9.9 - - - +
525A TYR* 3.7 26.8 + - + -
526A SER* 5.3 2.1 + - - -
543A LEU* 1.4 76.7 - - - +
545A GLU* 1.4 60.2 + - - +
546A LYS* 3.1 11.3 + - - +
547A LYS* 3.0 22.9 + - - -
548A GLN* 2.8 58.2 + - - +
550A TYR* 3.4 19.3 + - + -
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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