Contacts of the strand formed by residues 539 - 546 (chain A) in PDB entry 4GT5
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 MET 539 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528A GLU* 3.4 3.8 - - - -
529A CYS 2.9 40.6 + - - +
532A LEU* 4.0 29.4 - - + -
533A LEU* 4.0 24.7 - - + -
534A PRO* 5.7 2.2 - - - -
537A ASP 5.2 4.7 - - - +
538A LYS* 1.3 77.4 - - - +
540A LEU* 1.3 74.9 + - - +
541A VAL* 4.4 8.1 - - + -
576A PHE* 4.0 24.9 - - + -
590A GLU* 5.8 2.9 - - + -
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Residues in contact with LEU 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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513A LYS* 4.2 9.0 - - + -
526A LEU* 3.8 34.5 - - + -
527A ALA 3.4 2.5 - - - +
528A GLU* 4.1 23.6 - - + -
538A LYS 5.2 3.1 - - - +
539A MET* 1.3 86.2 - - - +
541A VAL* 1.3 64.8 + - - +
591A TYR* 3.6 32.3 + - + +
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Residues in contact with VAL 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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510A ILE* 5.6 0.4 - - + -
526A LEU* 3.6 5.8 - - - +
527A ALA* 2.9 44.9 + - + +
529A CYS* 3.8 29.8 - - + -
532A LEU* 4.2 11.9 - - + -
539A MET* 4.4 6.5 - - + -
540A LEU* 1.3 81.6 - - - +
542A ALA* 1.3 59.3 + - - +
543A VAL* 3.9 14.1 - - + -
576A PHE* 4.3 9.9 - - + -
588A VAL* 3.8 22.9 - - + -
589A PHE 3.3 14.1 - - - +
590A GLU* 5.0 0.4 - - - -
591A TYR* 4.0 9.0 - - - +
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Residues in contact with ALA 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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516A LEU* 5.1 4.0 - - + -
524A VAL* 4.3 7.6 - - + -
525A PHE 3.4 7.0 - - - +
526A LEU* 4.9 0.9 - - - +
541A VAL* 1.3 73.2 - - - +
543A VAL* 1.3 60.5 + - - +
544A LYS 4.1 0.2 - - - -
587A MET 3.7 1.4 - - - +
589A PHE* 2.9 40.0 + - - +
590A GLU 3.9 16.2 - - - +
591A TYR* 4.1 13.2 - - + +
592A MET 5.5 0.4 - - - +
669A PHE* 4.0 23.8 - - + -
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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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510A ILE* 4.2 8.7 - - + -
512A LEU* 4.3 16.4 - - + -
524A VAL* 3.5 4.1 - - - -
525A PHE* 2.9 41.8 + - + +
527A ALA* 3.8 22.0 - - + -
541A VAL* 3.9 12.8 - - + -
542A ALA* 1.3 75.5 - - - +
544A LYS* 1.3 62.4 + - - +
545A ALA 3.7 1.4 + - - +
586A LEU* 3.7 41.5 - - + -
587A MET 3.3 5.6 - - - +
588A VAL* 4.0 16.4 - - + -
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Residues in contact with LYS 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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521A PHE* 4.5 5.6 - - - +
522A GLY* 4.1 24.9 - - - +
523A LYS 3.5 8.3 - - - +
524A VAL* 4.5 10.9 - - + +
542A ALA 4.1 1.0 + - - -
543A VAL* 1.3 72.3 - - - +
545A ALA* 1.3 63.9 + - - +
546A LEU* 4.0 20.8 + - + -
557A PHE* 5.3 1.0 - - - -
585A LEU 3.5 1.6 - - - +
586A LEU* 3.3 3.8 - - - -
587A MET* 2.9 65.3 + - + +
589A PHE* 4.4 8.7 - - + -
669A PHE* 3.1 35.6 + - + +
670A GLY* 4.7 5.8 + - - -
671A MET* 4.2 12.7 - - - +
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Residues in contact with ALA 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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522A GLY* 3.1 4.7 - - - -
523A LYS* 2.9 35.7 + - + +
525A PHE* 3.7 26.5 - - + -
543A VAL 3.7 1.2 + - - -
544A LYS* 1.3 76.5 - - - +
546A LEU* 1.3 61.8 + - - +
547A LYS* 4.9 0.2 - - - +
584A PRO* 3.9 13.9 - - + -
585A LEU 3.4 4.7 - - - -
586A LEU* 3.6 21.1 - - + -
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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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521A PHE* 3.3 22.0 - - + +
544A LYS* 4.0 21.9 + - + -
545A ALA* 1.3 76.7 - - - +
547A LYS* 1.3 68.8 + - - +
548A GLU* 3.5 8.5 - - - +
554A ARG* 3.7 38.4 - - + +
557A PHE* 4.2 23.3 - - + -
584A PRO* 3.1 23.4 - - - +
585A LEU* 3.0 34.2 + - + +
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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