Contacts of the strand formed by residues 542 - 549 (chain A) in PDB entry 4PBX
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 LYS 542 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540A ILE* 3.4 8.6 - - - +
541A ILE* 1.3 97.6 - - + +
543A TYR* 1.3 59.9 + - - +
559A THR* 3.6 31.0 + - + -
560A PHE* 3.4 14.4 - - - +
561A ASP* 2.8 31.9 + - - +
562A PRO* 4.6 1.8 - - - -
584A ARG* 2.9 38.8 + - + +
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Residues in contact with TYR 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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515A PRO* 4.6 6.5 - - + -
532A TRP* 3.3 31.6 + + - -
535A PRO* 3.7 28.9 - - + +
540A ILE* 4.2 12.3 - - + +
542A LYS* 1.3 73.7 - - - +
544A GLU* 1.3 59.4 + - - +
545A LEU 4.0 0.4 - - - -
558A ARG 3.8 1.4 - - - +
559A THR* 3.3 10.9 - - - +
560A PHE* 2.9 54.0 + + + -
562A PRO* 3.7 29.8 - - + -
563A THR 3.4 20.7 + - - -
581A LEU* 4.1 19.7 - - + -
582A ALA 3.6 14.1 - - - -
583A ALA* 4.0 17.7 - - + +
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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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542A LYS 4.1 0.6 + - - +
543A TYR* 1.3 72.0 - - - +
545A LEU* 1.3 63.8 + - - +
546A LEU* 3.9 21.5 - - + +
557A GLY* 4.7 1.6 - - - -
558A ARG 3.9 6.0 + - - -
559A THR* 2.9 29.3 + - - +
581A LEU* 3.6 5.8 - - - +
582A ALA* 2.7 39.8 + - + +
584A ARG* 4.8 13.1 + - + +
589A LEU* 3.8 25.6 - - + -
592A PHE* 3.8 20.3 - - + -
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Residues in contact with LEU 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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518A LEU* 6.2 0.4 - - + -
530A LEU* 3.8 25.6 - - + -
543A TYR 4.0 0.4 - - - -
544A GLU* 1.3 74.3 - - - +
546A LEU* 1.3 78.0 + - - +
547A PHE* 4.2 22.4 - - + -
556A VAL 4.0 0.2 - - - +
557A GLY* 3.3 4.5 - - - -
558A ARG* 2.9 45.2 + - + +
560A PHE* 3.9 14.4 - - + -
566A TYR* 3.8 35.7 - - + -
568A VAL* 4.4 2.2 - - + -
579A PHE* 4.4 10.3 - - + -
580A ARG 3.7 12.1 - - - +
581A LEU* 4.2 12.1 - - + -
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Residues in contact with LEU 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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544A GLU* 3.9 13.7 + - + +
545A LEU* 1.3 83.9 - - - +
547A PHE* 1.3 64.4 + - - +
555A GLU* 4.1 23.6 - - + +
556A VAL 3.3 5.4 - - - +
557A GLY* 3.8 16.8 - - - +
579A PHE* 3.6 0.7 - - - -
580A ARG* 3.0 73.4 + - + +
592A PHE* 3.6 19.7 - - + -
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Residues in contact with PHE 547 (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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545A LEU* 4.2 17.7 - - + -
546A LEU* 1.3 77.2 - - - +
548A ARG* 1.3 65.4 + - - +
555A GLU* 3.4 5.1 - - - +
556A VAL* 2.7 79.3 + - + +
558A ARG* 4.1 27.8 - - + -
568A VAL* 3.9 24.9 - - + -
571A LEU* 4.3 13.5 - - + -
577A TYR* 4.3 13.7 - + - -
578A ALA 3.1 16.4 - - - +
579A PHE* 3.4 28.0 - + + -
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Residues in contact with ARG 548 (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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547A PHE* 1.3 77.3 - - - +
549A GLU* 1.3 61.6 + - - +
550A GLY 3.3 10.6 + - - +
551A ASP* 3.5 27.6 + - - +
552A HIS* 5.2 1.6 - - - +
553A GLY 3.5 19.3 + - - +
554A ARG 3.4 18.6 - - - +
555A GLU* 3.5 39.9 + - - +
556A VAL* 5.5 0.7 - - - -
577A TYR* 3.5 9.3 - - - -
578A ALA* 3.1 33.7 + - + +
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Residues in contact with GLU 549 (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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548A ARG* 1.3 69.6 - - - +
550A GLY* 1.3 66.9 + - - +
551A ASP 3.5 0.5 + - - -
552A HIS 3.8 0.9 + - - -
553A GLY* 3.1 29.6 + - - -
554A ARG 4.3 2.2 + - - +
572A LYS* 3.0 44.8 + - - +
575A THR* 4.3 12.1 + - - +
576A GLU 4.3 4.3 - - - +
577A TYR* 3.8 28.4 + - + -
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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