Contacts of the helix formed by residues 533 - 548 (chain i) in PDB entry 5JPQ
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 SER 533 (chain i).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525i THR* 3.1 19.8 - - - +
528i SER 2.7 21.3 - - - -
529i PHE* 3.2 5.8 - - - -
530i HIS 3.2 31.4 + - - -
532i VAL* 1.3 68.7 - - - +
534i GLU* 1.3 69.6 + - - +
535i LYS* 3.0 11.0 + - - +
536i PHE* 3.4 13.2 + - - +
537i LEU* 3.8 6.4 + - - +
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Residues in contact with GLU 534 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526i LEU* 3.9 19.5 - - - +
528i SER 3.3 5.4 + - - +
529i PHE* 5.7 4.5 - - + -
533i SER* 1.3 80.6 - - - +
535i LYS* 1.3 55.5 + - - +
536i PHE 3.4 0.3 + - - -
537i LEU* 3.5 4.0 + - - +
538i GLN* 2.8 31.1 + - + +
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Residues in contact with LYS 535 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530i HIS 5.9 0.2 - - - +
533i SER* 3.9 8.0 - - - +
534i GLU* 1.3 76.4 - - - +
536i PHE* 1.4 58.6 + - - +
538i GLN* 3.4 7.1 - - - +
539i GLN* 2.8 32.1 + - - +
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Residues in contact with PHE 536 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525i THR* 5.4 5.2 - - - -
532i VAL* 4.5 11.2 - - + -
533i SER 3.4 18.5 + - - +
535i LYS* 1.4 76.7 - - - +
537i LEU* 1.3 63.6 + - - +
539i GLN* 3.2 8.2 + - - +
540i MET* 3.0 21.1 + - - +
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Residues in contact with LEU 537 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525i THR* 5.2 7.8 - - - -
526i LEU* 5.2 12.6 - - + +
533i SER 3.8 6.5 + - - +
534i GLU* 3.5 8.2 + - - +
535i LYS 3.3 0.2 - - - -
536i PHE* 1.3 76.0 - - - +
538i GLN* 1.3 67.6 + - - +
540i MET* 3.1 8.7 + - - +
541i VAL* 2.8 23.7 + - - +
559i MET* 6.6 0.2 - - + -
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Residues in contact with GLN 538 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534i GLU* 2.8 20.4 + - + +
535i LYS* 3.4 9.4 - - - +
537i LEU* 1.3 76.7 - - - +
539i GLN* 1.4 55.7 - - - +
541i VAL* 3.1 9.5 + - - +
542i ALA* 2.9 28.5 + - - +
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Residues in contact with GLN 539 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500i LEU* 5.7 1.7 - - - +
535i LYS 2.8 13.1 + - - +
536i PHE* 3.2 10.7 + - - +
538i GLN* 1.4 73.1 - - - +
540i MET* 1.3 66.3 + - - +
542i ALA* 3.2 7.5 + - - +
543i LEU* 3.1 22.0 + - - +
582i PRO* 5.6 11.5 - - + +
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Residues in contact with MET 540 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536i PHE 3.0 13.5 + - - +
537i LEU* 3.4 12.3 - - - +
539i GLN* 1.3 75.0 - - - +
541i VAL* 1.3 63.8 + - - +
543i LEU* 3.2 7.6 + - - +
544i TYR* 2.9 23.0 + - - +
569i VAL* 5.9 7.0 - - + -
582i PRO* 5.9 4.9 - - - +
585i VAL* 4.5 18.5 - - + +
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Residues in contact with VAL 541 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495i CYS* 6.0 6.7 - - + -
537i LEU 2.8 12.7 + - - +
538i GLN* 3.3 12.6 - - - +
540i MET* 1.3 74.2 - - - +
542i ALA* 1.3 66.3 + - - +
544i TYR* 3.3 2.4 + - - +
545i VAL* 2.8 30.9 + - + +
556i LEU* 6.2 5.4 - - + -
559i MET* 5.9 7.4 - - + -
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Residues in contact with ALA 542 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497i ASP 4.5 15.7 - - - +
498i ALA* 5.8 3.4 - - - -
500i LEU* 4.9 17.3 - - + +
538i GLN 2.9 12.6 + - - +
539i GLN* 3.2 11.6 + - - +
541i VAL* 1.3 75.1 - - - +
543i LEU* 1.3 58.6 + - - +
545i VAL* 3.8 3.9 - - - +
546i ALA* 2.8 33.3 + - - +
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Residues in contact with LEU 543 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423i SER* 5.4 0.2 - - - -
500i LEU* 5.5 7.8 - - + +
539i GLN 3.1 13.5 + - - +
540i MET* 3.2 8.9 + - - +
542i ALA* 1.3 75.1 - - - +
544i TYR* 1.4 68.6 + - - +
546i ALA* 3.2 6.1 + - - +
547i SER* 3.2 20.3 + - - -
582i PRO* 5.6 10.5 - - + +
583i LEU 6.5 0.4 - - - -
584i CYS* 5.8 4.7 - - - -
585i VAL* 5.1 9.4 - - + -
639i ALA* 4.4 6.6 - - + +
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Residues in contact with TYR 544 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540i MET 2.9 15.3 + - - +
541i VAL* 4.4 2.5 - - - +
543i LEU* 1.4 77.7 - - - +
545i VAL* 1.3 66.1 + - - +
547i SER* 3.1 13.9 + - - -
548i HIS* 3.3 11.4 + - - +
585i VAL* 5.2 8.7 - - + +
587i GLN* 5.9 3.8 - - + -
637i ARG* 4.2 25.6 - - + -
639i ALA* 4.3 15.5 - - + +
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Residues in contact with VAL 545 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421i GLY* 3.9 5.4 - - - -
541i VAL* 2.8 21.0 + - + +
542i ALA* 3.8 4.9 - - - +
544i TYR* 1.3 75.6 - - - +
546i ALA* 1.3 64.0 + - - +
548i HIS* 3.1 21.6 + - - +
550i LYS 4.8 2.6 - - - +
551i ASN* 4.8 15.6 - - + +
552i SER 6.3 0.2 - - - +
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Residues in contact with ALA 546 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421i GLY* 3.1 20.0 - - - -
422i ARG* 4.5 4.0 - - + +
423i SER* 2.9 36.5 + - - +
424i LEU 3.3 0.3 + - - -
498i ALA* 5.2 14.4 - - + +
500i LEU* 6.5 0.9 - - + -
501i PRO* 5.3 7.2 - - + -
542i ALA 2.8 20.6 + - - +
543i LEU* 3.6 6.1 - - - +
545i VAL* 1.3 79.6 - - - +
547i SER* 1.3 57.6 + - - +
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Residues in contact with SER 547 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423i SER* 3.4 15.0 - - - -
424i LEU* 3.9 11.0 - - - +
543i LEU 3.2 5.5 + - - -
544i TYR 3.1 9.4 + - - -
546i ALA* 1.3 76.4 - - - +
548i HIS* 1.3 62.9 + - - +
549i TYR 3.9 0.2 + - - -
639i ALA* 3.8 26.9 - - - -
640i THR 5.9 1.6 - - - -
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Residues in contact with HIS 548 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421i GLY* 3.1 22.9 + - - -
424i LEU* 3.9 3.7 - - - +
544i TYR 3.3 8.7 + - - +
545i VAL* 3.1 13.0 + - - +
547i SER* 1.3 80.0 - - - +
549i TYR* 1.4 65.3 + - - +
550i LYS 3.2 19.3 - - - +
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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