Contacts of the strand formed by residues 532 - 539 (chain A) in PDB entry 6BM0
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 CYS 532 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A LEU* 3.3 30.6 - - - +
530A PRO 3.2 3.4 + - - +
531A GLY* 1.3 77.0 + - - +
533A TYR* 1.3 59.7 + - - +
577A LEU* 3.7 32.8 - - + -
578A SER 3.9 8.3 - - - +
579A ARG* 3.8 18.6 - - + +
584A MET* 4.5 4.7 - - - -
990A PHE* 3.2 34.2 - - + -
994A GLY* 6.1 1.0 - - - -
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Residues in contact with TYR 533 (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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531A GLY 4.2 0.7 - - - -
532A CYS* 1.3 75.9 - - - +
534A ASP* 1.3 100.3 + - - +
578A SER* 3.5 23.9 + - - -
579A ARG 4.2 5.6 + - - -
580A GLU* 3.4 42.7 - - + +
605A PRO* 5.3 3.8 - - - +
926A GLY* 3.8 24.4 + - - -
928A VAL* 3.7 21.5 - - + +
973A ASP* 4.8 10.7 - - + +
974A SER* 3.1 25.8 + - - -
990A PHE* 3.5 7.3 - - - -
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Residues in contact with ASP 534 (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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533A TYR* 1.3 103.9 + - - +
535A MET* 1.3 64.4 + - - +
536A TRP* 3.5 31.2 - - + -
577A LEU* 3.5 15.2 - - - +
578A SER* 3.5 24.9 + - - -
606A THR 4.9 0.9 - - - +
607A VAL* 4.4 3.3 - - - +
926A GLY 5.8 0.3 - - - -
927A ARG 4.1 8.8 - - - +
928A VAL* 3.3 34.4 - - - +
929A ALA 5.6 0.2 - - - -
932A ARG* 3.6 9.1 + - - +
974A SER* 4.5 1.6 - - - -
990A PHE* 4.0 0.5 - - - -
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Residues in contact with MET 535 (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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534A ASP* 1.3 78.8 - - - +
536A TRP* 1.3 77.0 + - - +
575A LEU* 4.1 7.0 - - + -
576A ILE 3.3 7.9 - - - -
577A LEU* 3.7 13.0 - - + -
932A ARG* 3.6 18.3 + - - +
974A SER* 3.1 31.2 - - - +
975A PHE 3.7 16.9 - - - +
976A ALA* 3.9 8.7 - - + -
988A LEU* 3.5 47.3 - - + +
989A TYR 4.3 0.4 - - - -
990A PHE* 4.0 16.2 - - + -
996A LEU* 3.8 11.4 - - + -
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Residues in contact with TRP 536 (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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534A ASP* 3.5 33.9 - - + -
535A MET* 1.3 85.0 + - - +
537A THR* 1.3 64.4 + - - +
538A VAL* 4.2 0.4 - - + -
574A PHE 3.7 0.3 - - - +
575A LEU* 3.3 7.2 - - - +
576A ILE* 2.8 65.3 + - + +
578A SER* 3.9 8.1 - - - -
606A THR* 3.6 20.9 - - - -
607A VAL 2.8 35.2 - - - -
608A PHE* 3.1 27.8 - + + -
609A ALA* 3.2 33.2 - - + +
932A ARG* 5.8 4.5 - - - +
976A ALA* 4.5 4.5 - - - -
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Residues in contact with THR 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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536A TRP* 1.3 78.9 - - - +
538A VAL* 1.3 65.6 + - - +
572A HIS* 3.5 21.4 + - - -
574A PHE 3.3 7.6 - - - +
575A LEU* 3.7 19.1 - - + -
611A ASN* 4.9 0.9 - - - +
976A ALA* 3.7 17.8 - - + +
977A PRO* 2.4 35.3 + - - +
978A PHE* 4.2 9.2 - - + -
988A LEU* 4.0 11.2 - - + -
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Residues in contact with VAL 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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537A THR* 1.3 79.0 - - - +
539A ILE* 1.3 63.2 + - - +
572A HIS* 3.6 5.2 - - - +
573A GLY 2.9 21.0 + - - -
574A PHE* 3.2 31.8 + - + +
576A ILE* 4.1 12.8 - - + -
609A ALA 3.8 24.5 - - - +
610A GLY* 4.0 14.8 - - - +
611A ASN* 3.6 17.0 - - - +
618A ILE* 3.7 31.2 - - + -
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Residues in contact with ILE 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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538A VAL* 1.3 72.0 - - - +
540A ALA* 1.3 65.4 + - - +
541A PRO* 4.4 1.3 - - + +
570A ARG* 3.5 33.2 - - - +
571A ARG 3.4 22.0 - - - +
572A HIS* 3.6 29.6 - - + +
611A ASN* 3.0 26.6 + - - +
615A ASN* 3.4 55.7 - - + +
616A ARG 5.1 0.2 - - - +
618A ILE* 4.0 5.8 - - - +
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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