Contacts of the helix formed by residues 524 - 539 (chain O) in PDB entry 5G04
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 524 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519O ALA 3.3 7.7 + - - +
522O ASP* 3.3 46.7 + - - +
523O GLY* 1.3 76.2 + - - +
525O TYR* 1.3 63.6 + - - +
526O HIS* 3.6 24.9 - - + +
527O LEU* 3.4 25.2 + - + +
528O ALA* 3.2 19.9 + - - +
708O GLU* 4.6 8.9 + - - -
743O GLU* 6.3 0.2 - - - +
744O LEU* 5.8 4.9 - - - +
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Residues in contact with TYR 525 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519O ALA 5.1 1.1 - - - -
520O MET* 4.0 29.7 + - + +
523O GLY* 3.1 33.9 + - - -
524O LYS* 1.3 70.1 - - - +
526O HIS* 1.3 71.2 + - - +
528O ALA* 3.0 7.3 + - + +
529O ASP* 2.9 21.5 + - - +
550O VAL* 3.8 9.5 - - + +
553O ALA* 3.6 46.7 - - + +
554O GLN* 3.9 26.7 - - + -
746O SER* 5.3 11.7 - - - -
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Residues in contact with HIS 526 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 3.1 60.2 + - + +
524O LYS* 4.1 33.6 - - + +
525O TYR* 1.3 74.8 + - - +
527O LEU* 1.3 73.1 + - + +
529O ASP* 3.2 13.0 + - - +
530O SER* 3.0 19.6 + - - -
554O GLN* 4.3 5.1 - - - +
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Residues in contact with LEU 527 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG 6.1 1.1 - - - -
16A ASP* 6.4 0.4 - - - -
519O ALA* 4.1 19.3 - - + -
522O ASP* 5.2 2.9 - - - +
524O LYS* 3.4 30.5 - - + +
525O TYR 3.2 0.4 - - - -
526O HIS* 1.3 91.7 - - + +
528O ALA* 1.3 62.0 + - - +
530O SER* 3.3 13.0 - - - -
531O LEU* 3.2 26.8 + - + +
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Residues in contact with ALA 528 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516O PHE* 4.2 15.3 - - + -
519O ALA* 4.1 20.0 - - + -
520O MET* 4.8 7.0 - - - -
524O LYS 3.2 8.8 + - - +
525O TYR* 3.0 11.7 + - + +
527O LEU* 1.3 77.8 - - - +
529O ASP* 1.3 60.7 + - - +
530O SER 3.1 0.4 - - - -
531O LEU* 3.0 10.1 + - - +
532O VAL* 2.8 28.6 + - - +
550O VAL* 3.8 16.4 - - + -
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Residues in contact with ASP 529 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 5.9 0.9 - - - +
88A ASP* 3.9 12.8 - - - +
611A GLU* 5.5 3.7 - - - +
525O TYR 2.9 12.0 + - - +
526O HIS* 3.2 9.6 + - - +
528O ALA* 1.3 76.9 - - - +
530O SER* 1.3 63.1 + - - +
532O VAL* 3.1 14.8 + - - +
533O THR* 3.1 17.2 + - - +
547O LYS* 4.0 15.0 + - - -
550O VAL* 4.0 15.6 - - + +
551O LEU* 4.7 1.9 - - - +
554O GLN* 3.5 27.8 + - - +
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Residues in contact with SER 530 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 4.9 6.2 - - - +
16A ASP* 3.3 37.2 + - - +
18A GLN* 4.5 7.6 + - - -
107A LYS* 3.5 16.8 - - - -
608A THR* 5.8 0.5 - - - +
526O HIS 3.0 14.9 + - - -
527O LEU* 3.3 13.6 + - - -
528O ALA 3.1 0.2 - - - -
529O ASP* 1.3 78.5 - - - +
531O LEU* 1.3 56.5 - - - +
533O THR* 3.0 25.2 + - - +
534O GLY 3.7 0.9 + - - -
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Residues in contact with LEU 531 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LYS* 3.5 25.8 - - - +
109A GLN* 5.9 0.4 - - + -
512O GLN* 3.6 44.6 - - + +
515O GLN* 3.6 34.3 - - + +
516O PHE* 3.7 20.6 - - + +
519O ALA* 5.6 3.1 - - + -
527O LEU* 3.2 18.2 + - + +
528O ALA* 3.0 16.2 + - - +
530O SER* 1.3 75.4 - - - +
532O VAL* 1.3 58.8 + - - +
534O GLY* 3.0 6.8 + - - -
535O ILE* 2.9 28.2 + - + +
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Residues in contact with VAL 532 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASP* 3.4 23.6 - - - +
516O PHE* 3.7 23.6 - - + -
528O ALA 2.8 9.9 + - - +
529O ASP* 3.1 17.4 + - - +
531O LEU* 1.3 73.2 - - - +
533O THR* 1.3 59.2 + - - +
535O ILE* 3.1 12.6 + - + -
536O THR* 2.8 38.3 + - + +
543O GLY 3.8 3.8 - - - +
546O ARG 3.7 1.6 - - - +
547O LYS* 3.5 47.1 - - + +
550O VAL* 4.3 4.3 - - + -
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Residues in contact with THR 533 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLN* 6.0 0.2 + - - -
88A ASP* 3.2 37.0 + - - +
89A TYR* 3.4 9.4 - - - +
90A ASP* 4.3 7.3 + - - -
107A LYS* 5.5 2.9 - - - +
594A ARG* 3.8 28.7 + - - +
529O ASP* 3.1 14.6 - - - +
530O SER* 3.0 23.5 + - - +
532O VAL* 1.3 71.5 - - - +
534O GLY* 1.3 67.8 + - - +
536O THR* 3.2 15.3 - - - +
537O ALA* 3.3 5.4 + - - +
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Residues in contact with GLY 534 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLY* 6.1 0.7 - - - -
106A SER 6.2 0.7 - - - -
107A LYS* 3.9 23.0 - - - +
110A ALA* 4.0 8.7 - - - -
512O GLN* 4.0 4.9 - - - -
530O SER 3.7 2.8 + - - -
531O LEU 3.0 11.1 + - - -
533O THR* 1.3 85.2 + - - +
535O ILE* 1.3 61.9 + - - -
537O ALA* 3.0 16.9 + - - +
538O LEU* 3.4 12.9 - - - +
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Residues in contact with ILE 535 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509O LEU* 3.9 24.0 - - + -
512O GLN* 3.6 24.7 - - + +
513O LYS* 4.4 6.1 - - + -
516O PHE* 3.5 36.3 - - + -
531O LEU* 2.9 12.7 + - + +
532O VAL* 3.1 21.9 + - + +
534O GLY* 1.3 71.4 - - - +
536O THR* 1.3 58.3 + - - +
538O LEU* 3.2 8.7 + - + +
539O ASN* 3.0 27.2 + - - -
540O SER 3.9 0.7 + - - -
542O GLU* 4.4 12.1 - - - +
543O GLY* 3.9 10.6 - - - +
546O ARG* 3.9 14.4 - - + -
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Residues in contact with THR 536 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A SER* 5.1 2.4 + - - -
87A VAL* 3.3 28.5 + - - +
88A ASP* 3.4 7.9 - - - +
89A TYR* 3.5 19.3 - - + -
532O VAL* 2.8 20.1 + - - +
533O THR 3.2 15.5 - - - +
535O ILE* 1.3 73.8 - - - +
537O ALA* 1.3 57.1 + - - +
540O SER* 2.8 45.7 + - - +
543O GLY* 3.6 18.8 - - - -
544O VAL* 3.8 10.3 - - - +
547O LYS* 6.0 0.2 - - - -
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Residues in contact with ALA 537 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A TYR* 3.5 32.4 - - + -
104A LYS* 3.6 34.0 - - + +
105A GLY* 3.9 13.9 - - - -
110A ALA* 5.3 0.2 - - + -
112A ALA* 5.9 2.3 - - + +
533O THR 3.8 5.2 - - - +
534O GLY* 3.0 12.3 + - - +
536O THR* 1.3 82.6 - - - +
538O LEU* 1.3 65.6 + - + +
539O ASN 4.7 0.5 - - - -
540O SER* 4.5 2.6 + - - -
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Residues in contact with LEU 538 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ALA* 3.2 39.5 - - + +
112A ALA* 4.4 15.0 - - + -
505O GLN* 3.8 26.9 - - + +
508O MET* 4.0 20.6 - - + +
509O LEU* 4.1 22.3 - - + +
512O GLN* 4.4 5.4 - - + -
534O GLY 3.4 26.0 - - - +
535O ILE* 3.2 9.1 + - - +
537O ALA* 1.3 80.1 - - + +
539O ASN* 1.3 62.9 + - - +
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Residues in contact with ASN 539 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D SER* 4.9 12.3 + - - -
509O LEU* 4.0 26.6 - - + +
513O LYS* 6.0 0.4 - - - +
535O ILE 3.0 8.4 + - - +
538O LEU* 1.3 77.5 - - - +
540O SER* 1.3 68.1 + - - +
541O ILE* 3.2 16.5 + - - +
542O GLU* 2.7 39.8 - - + +
543O GLY 3.9 11.2 - - - +
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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
------------------------------------------------------------
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