Contacts of the strand formed by residues 524 - 533 (chain A) in PDB entry 4BI2
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 ILE 524 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A SER* 3.3 25.4 - - - +
518A MET 3.5 7.0 - - - +
519A SER* 3.6 21.1 - - - +
522A GLY 3.5 19.3 - - - +
523A ARG* 1.4 70.1 - - - +
525A TYR* 1.3 62.7 + - - +
526A SER* 4.2 3.0 + - - +
543A LEU 3.7 0.5 - - - +
544A ASN* 3.4 17.8 - - - -
545A GLU* 3.1 37.2 + - + +
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Residues in contact with TYR 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A SER* 3.5 2.8 - - - -
518A MET* 2.7 43.2 + - + +
520A VAL* 4.0 24.2 + - + -
523A ARG* 3.6 38.8 - - + +
524A ILE* 1.3 73.6 - - - +
526A SER* 1.3 61.3 + - - +
542A VAL* 3.7 24.5 - - + -
543A LEU 3.2 3.6 - - - -
544A ASN* 3.6 28.5 + - + +
550A TYR* 3.8 18.6 - + - -
552A ILE* 3.4 24.7 - - + -
590A ASP* 5.4 5.2 + - - +
601A VAL* 3.8 23.7 - - + +
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Residues in contact with SER 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A GLN 3.7 9.0 - - - -
517A SER* 4.3 6.5 + - - -
524A ILE* 5.3 2.4 + - - +
525A TYR* 1.3 71.3 - - - +
527A ILE* 1.3 64.4 + - - +
528A LEU* 3.5 8.0 + - - +
542A VAL* 3.2 6.4 - - - -
543A LEU* 2.8 42.7 + - - +
544A ASN 5.1 2.6 + - - -
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Residues in contact with ILE 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A GLN* 2.9 35.6 + - + +
517A SER 3.6 34.8 - - - +
518A MET* 3.6 34.8 - - + -
526A SER* 1.3 71.7 - - - +
528A LEU* 1.4 64.4 + - - +
529A LYS* 3.9 14.1 - - - +
540A PHE* 3.8 31.2 - - + -
541A GLN 3.9 2.5 - - - -
542A VAL* 4.1 8.1 - - + -
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Residues in contact with LEU 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A SER* 3.6 18.8 - - - +
527A ILE* 1.4 76.0 - - - +
529A LYS* 1.3 62.4 + - + +
541A GLN* 2.8 39.5 + - - +
542A VAL 4.5 2.0 - - - +
543A LEU* 3.6 37.2 - - + +
549A ILE* 3.8 21.3 - - + -
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Residues in contact with LYS 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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527A ILE* 3.8 7.8 - - - +
528A LEU* 1.3 79.3 - - + +
530A GLN* 1.3 61.9 + - - +
531A ILE* 5.1 3.8 - - + -
540A PHE* 3.4 5.7 - - - +
541A GLN* 2.8 68.9 + - + +
1795A EDO 3.2 35.9 + - - -
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Residues in contact with GLN 530 (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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529A LYS* 1.3 76.1 - - - +
531A ILE* 1.3 65.6 + - - +
532A GLY 4.2 7.0 - - - +
533A SER* 4.2 16.6 - - - -
538A LYS* 3.6 24.2 - - - +
539A VAL 3.6 13.5 - - - +
540A PHE* 3.5 26.3 - - + -
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Residues in contact with ILE 531 (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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529A LYS* 3.9 4.7 + - + -
530A GLN* 1.3 74.9 - - - +
532A GLY* 1.3 58.9 + - - +
539A VAL* 2.7 19.1 + - + +
540A PHE 4.1 4.9 - - - +
541A GLN* 3.8 28.7 - - + +
551A ALA* 4.3 5.8 - - + -
604A CYS* 3.6 31.2 - - - -
1795A EDO 4.0 17.3 - - - +
1797A ZO8 3.4 53.2 - - + +
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Residues in contact with GLY 532 (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* 4.2 6.3 - - - +
531A ILE* 1.3 84.0 - - - +
533A SER* 1.3 58.7 + - - -
534A GLY 4.3 0.4 - - - -
538A LYS* 3.5 1.6 - - - -
539A VAL* 2.6 43.9 + - - +
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Residues in contact with SER 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A GLN* 4.2 16.4 - - - -
532A GLY* 1.3 73.4 - - - -
534A GLY* 1.3 63.5 - - - +
535A GLY* 4.6 4.9 - - - -
537A SER 3.2 12.8 - - - -
538A LYS* 4.6 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