Contacts of the strand formed by residues 536 - 545 (chain A) in PDB entry 4BGJ
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 536 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521A PHE* 3.5 3.2 - - - -
522A PHE* 2.9 38.2 + - + +
523A GLU* 5.1 6.1 - - + -
535A ARG* 1.3 77.1 - - + +
537A PRO* 1.4 71.5 - - + +
538A VAL* 4.0 6.6 - - + +
563A ARG* 5.3 11.0 - - + -
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Residues in contact with PRO 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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519A VAL* 4.6 2.2 - - + -
520A ASP 3.5 10.5 - - - +
521A PHE* 3.9 20.4 - - + -
535A ARG 3.9 6.7 - - - +
536A ILE* 1.4 85.9 - - + +
538A VAL* 1.3 65.1 + - - +
563A ARG* 4.5 9.4 - - - +
564A TYR 4.9 0.5 + - - -
595A LYS 3.5 24.7 - - - +
596A ASN* 4.3 9.4 - - - -
597A TYR* 4.4 11.9 - - - +
600A LEU* 3.6 21.0 - - + +
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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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519A VAL* 3.4 6.5 - - - +
520A ASP* 2.9 43.2 + - + +
521A PHE 4.3 11.0 - - - +
522A PHE* 4.3 13.7 - - + +
536A ILE* 4.0 8.3 - - + +
537A PRO* 1.3 80.6 - - - +
539A PHE* 1.3 63.2 + - - +
561A TYR* 3.8 31.0 - - + +
562A ARG 3.5 15.0 - - - +
563A ARG* 3.7 24.5 - - + -
600A LEU* 3.9 3.3 - - - +
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Residues in contact with PHE 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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516A ILE* 4.0 25.8 - - + -
518A TYR 4.3 2.2 - - - -
519A VAL* 4.0 10.8 - - + +
538A VAL* 1.3 71.9 - - - +
540A CYS* 1.3 60.6 + - - +
541A ILE* 3.7 2.8 + - + +
560A VAL 3.6 0.5 - - - +
561A TYR* 3.2 6.2 - - - -
562A ARG 2.8 38.4 + - - +
564A TYR* 3.9 11.7 - + + -
567A PHE* 3.4 29.8 - + + -
600A LEU* 3.4 55.2 - - + -
603A LYS* 4.5 4.7 - - + -
604A ARG* 3.9 14.6 - - - -
607A PHE* 3.6 32.5 - + - -
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Residues in contact with CYS 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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516A ILE* 3.4 9.8 - - - +
517A PRO* 3.2 21.7 - - - +
518A TYR* 3.2 56.7 + - + +
520A ASP* 4.8 1.6 - - + -
538A VAL 3.7 1.4 + - - -
539A PHE* 1.3 70.3 - - - +
541A ILE* 1.3 61.4 + - - +
542A ASP* 4.3 8.1 - - - -
559A SER* 4.2 17.5 - - - -
560A VAL 3.5 3.6 - - - -
561A TYR* 3.7 30.3 - - + -
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Residues in contact with ILE 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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514A ILE* 4.2 18.6 - - + -
515A SER 3.5 9.2 - - - +
516A ILE* 4.3 14.8 - - + -
539A PHE* 4.2 6.5 - - + +
540A CYS* 1.3 73.7 - - - +
542A ASP* 1.3 70.2 + - - +
543A VAL* 3.7 14.3 + - + +
559A SER* 3.2 3.7 - - - -
560A VAL* 2.6 48.8 + - + +
562A ARG* 3.7 33.4 - - + -
567A PHE* 4.2 4.0 - - + -
611A LEU* 4.2 9.6 - - + -
629A PHE* 4.1 16.6 - - + +
630A LEU* 4.2 12.6 - - + -
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Residues in contact with ASP 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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513A LYS 4.1 0.2 - - - +
514A ILE* 3.2 9.5 - - - +
515A SER* 2.8 45.1 + - - +
517A PRO* 3.5 23.9 - - - +
518A TYR* 5.5 1.0 + - - -
540A CYS* 3.9 7.3 + - - -
541A ILE* 1.3 71.5 - - - +
543A VAL* 1.3 59.9 + - - +
558A TRP 3.7 4.2 - - - +
559A SER* 2.8 26.7 + - - -
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Residues in contact with VAL 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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512A TRP* 3.9 22.0 - - + -
513A LYS 3.8 1.8 - - - -
514A ILE* 4.1 17.0 - - + -
541A ILE* 3.9 16.2 - - + +
542A ASP* 1.3 80.4 - - - +
544A GLU* 1.3 69.3 + - - +
545A ARG 4.3 0.2 - - - -
557A HIS* 3.2 8.4 - - - +
558A TRP* 2.9 65.9 + - + +
560A VAL* 4.1 6.1 - - + -
630A LEU* 3.6 21.8 - - + +
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Residues in contact with GLU 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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512A TRP* 3.2 8.7 - - - +
513A LYS* 2.8 50.6 + - + +
543A VAL* 1.3 73.4 - - - +
545A ARG* 1.3 61.1 + - - +
546A ASN* 3.3 25.3 + - - +
555A PRO* 4.4 12.6 - - + +
556A GLU 3.5 4.7 - - - +
557A HIS* 4.1 16.2 - - + -
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Residues in contact with ARG 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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507A ARG* 4.1 20.6 - - - +
511A ALA 4.2 1.1 - - - -
512A TRP* 3.3 43.3 - - + +
544A GLU* 1.3 73.2 - - - +
546A ASN* 1.3 59.3 + - - +
547A ASP* 2.9 36.0 + - - +
548A ARG* 3.0 44.0 + - - +
555A PRO* 3.4 17.3 - - - +
556A GLU* 2.8 46.7 + - + +
558A TRP* 4.1 19.6 - - + -
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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