Contacts of the helix formed by residues 576 - 592 (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 ASN 576 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D SER* 4.0 9.5 + - - -
541O ILE* 5.2 2.8 - - - +
571O CYS* 3.2 23.7 + - - +
574O LEU* 3.0 29.6 + - + +
575O LYS* 1.3 72.0 - - - +
577O THR* 1.3 66.8 + - - +
578O GLU* 3.3 11.6 + - + +
579O MET* 3.0 40.4 + - - +
580O VAL* 3.4 10.8 + - - +
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Residues in contact with THR 577 (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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390O PHE* 5.7 2.4 - - - -
575O LYS 3.1 11.8 + - - -
576O ASN* 1.3 69.1 - - - +
578O GLU* 1.3 70.1 + - - +
580O VAL* 2.9 21.1 + - - +
581O ILE* 3.0 30.4 + - + +
610O LEU* 4.8 3.7 - - + +
614O TYR* 3.7 55.8 + - + -
616O LEU* 4.4 7.6 - - + -
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Residues in contact with GLU 578 (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* 3.4 18.6 + - - +
3D THR* 2.9 38.1 + - - +
5D PHE* 4.7 0.2 - - - -
390O PHE* 3.6 27.6 - - + -
431O LEU* 3.4 31.0 - - + +
576O ASN* 3.3 9.7 + - + +
577O THR* 1.3 77.9 - - - +
579O MET* 1.3 59.6 + - - +
581O ILE* 3.6 0.5 + - - -
582O SER* 2.8 31.4 + - - +
616O LEU* 3.3 22.0 - - + +
619O LEU* 4.0 6.4 - - + +
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Residues in contact with MET 579 (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* 3.8 24.7 - - - +
541O ILE* 4.4 7.0 - - + -
542O GLU* 3.7 37.2 - - + +
545O TYR* 3.8 37.9 - - + -
567O LEU* 4.6 3.1 - - - -
571O CYS* 3.6 24.5 - - - -
576O ASN* 3.0 30.5 + - - +
577O THR 3.2 0.4 - - - -
578O GLU* 1.3 77.8 - - - +
580O VAL* 1.3 54.6 + - - +
582O SER* 2.9 9.9 + - - +
583O VAL* 2.6 39.8 + - - +
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Residues in contact with VAL 580 (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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568O LEU* 3.7 9.2 - - + -
571O CYS* 3.8 31.6 - - + +
572O GLN* 3.6 33.0 - - + +
575O LYS* 5.4 1.6 - - - -
576O ASN 3.4 8.7 + - - +
577O THR* 2.9 17.7 + - - +
579O MET* 1.3 72.2 - - - +
581O ILE* 1.3 59.8 + - + +
583O VAL* 2.9 10.8 - - - +
584O LEU* 2.8 42.9 + - + +
606O GLN* 5.5 0.7 - - - +
610O LEU* 4.5 11.0 - - + -
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Residues in contact with ILE 581 (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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577O THR* 3.0 25.6 + - + +
578O GLU 4.4 2.2 - - - +
580O VAL* 1.3 72.8 - - + +
582O SER* 1.3 69.0 + - - +
584O LEU* 4.0 6.6 - - - +
585O LEU* 3.3 19.3 + - + +
607O ALA* 4.0 17.0 - - + +
610O LEU* 3.4 36.8 - - + -
611O SER* 3.5 26.0 - - - +
616O LEU* 4.6 5.6 - - + -
619O LEU* 3.4 33.9 - - + -
623O THR* 4.1 13.9 - - + -
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Residues in contact with SER 582 (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 5.6 1.9 + - - -
545O TYR* 4.0 28.8 + - - -
578O GLU* 2.8 23.3 + - - +
579O MET* 2.9 18.3 + - - +
581O ILE* 1.3 75.4 - - - +
583O VAL* 1.3 54.1 + - - +
585O LEU* 2.6 27.7 + - - +
586O SER 2.9 10.0 + - - -
619O LEU* 3.4 28.2 - - - +
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Residues in contact with VAL 583 (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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545O TYR* 4.0 13.9 - - + -
564O LEU* 3.4 42.2 - - + +
567O LEU* 4.1 19.5 - - + -
568O LEU* 3.6 26.7 - - + -
571O CYS* 5.1 4.0 - - + -
579O MET* 2.6 19.7 + - - +
580O VAL* 2.9 28.9 - - - +
582O SER* 1.3 67.2 - - - +
584O LEU* 1.3 65.6 + - - +
585O LEU 3.0 0.9 - - - -
586O SER* 3.0 3.3 + - - -
587O VAL* 2.9 28.0 + - + +
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Residues in contact with LEU 584 (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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942A ARG* 5.5 0.2 - - - -
568O LEU* 3.7 24.5 - - + -
580O VAL* 2.8 35.9 + - + +
581O ILE* 4.0 2.9 - - - +
583O VAL* 1.3 73.4 - - - +
585O LEU* 1.3 53.2 + - - +
587O VAL* 3.2 8.2 + - - +
588O ALA* 2.7 34.7 + - - +
603O MET* 3.8 23.2 - - + +
606O GLN* 3.4 44.6 - - + +
607O ALA* 3.5 35.0 - - + -
610O LEU* 4.5 4.0 - - + -
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Residues in contact with LEU 585 (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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581O ILE 3.3 14.7 + - - +
582O SER* 2.6 21.4 + - - +
584O LEU* 1.3 74.0 - - + +
586O SER* 1.3 57.4 + - - -
588O ALA* 4.2 2.7 - - + -
589O GLU* 3.1 29.7 + - - +
604O LEU* 4.1 13.9 - - + +
607O ALA* 3.8 18.6 - - + -
619O LEU* 5.0 7.9 - - + -
622O GLU* 4.5 17.4 - - - +
623O THR* 3.6 44.4 - - + +
626O ASN* 3.5 28.0 - - - +
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Residues in contact with SER 586 (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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545O TYR* 3.5 29.9 + - - -
548O ALA* 5.2 0.7 - - - +
549O VAL* 4.7 9.7 - - - +
552O GLN* 3.3 24.9 + - - +
564O LEU* 3.6 22.3 - - - +
582O SER 2.9 6.3 + - - -
583O VAL 3.0 7.3 + - - -
585O LEU* 1.3 76.0 - - - +
587O VAL* 1.3 55.8 + - - +
589O GLU* 3.3 9.6 + - - +
590O LEU* 3.0 23.2 + - - +
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Residues in contact with VAL 587 (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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942A ARG* 5.3 2.2 - - + -
561O HIS* 4.0 14.8 - - + +
564O LEU* 4.0 28.7 - - + +
565O GLN* 5.2 1.8 - - + +
568O LEU* 4.7 13.2 - - + -
583O VAL 2.9 21.1 + - - +
584O LEU* 3.4 8.5 - - - +
586O SER* 1.3 75.3 - - - +
588O ALA* 1.3 55.3 + - - +
590O LEU* 3.2 11.8 + - - +
591O TYR* 3.1 45.4 + - + +
603O MET* 3.6 26.2 - - + -
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Residues in contact with ALA 588 (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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584O LEU 2.7 19.5 + - - +
585O LEU* 3.9 12.6 - - + +
587O VAL* 1.3 69.6 - - - +
589O GLU* 1.3 61.4 + - - +
591O TYR* 3.1 26.0 + - - +
592O TRP* 3.3 21.6 + - - -
600O ALA* 4.4 3.4 - - - +
603O MET* 5.2 2.0 - - + +
604O LEU* 3.8 40.4 - - + +
626O ASN* 4.8 1.8 - - - +
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Residues in contact with GLU 589 (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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549O VAL* 4.7 11.5 - - - +
552O GLN* 3.5 21.3 + - - +
585O LEU 3.1 20.8 + - - +
586O SER* 3.4 11.4 + - - +
588O ALA* 1.3 73.9 - - - +
590O LEU* 1.3 61.4 + - - +
592O TRP* 3.6 20.3 + - + +
593O ARG* 3.9 10.9 - - - +
622O GLU* 4.2 14.6 - - - +
626O ASN* 4.9 7.8 + - - +
662O ARG* 4.5 11.4 + - - -
753O ASN 5.1 1.0 - - - +
754O HIS 5.4 5.2 - - - +
755O LEU* 5.2 11.4 - - + +
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Residues in contact with LEU 590 (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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778A LEU* 3.4 26.0 - - + +
552O GLN* 3.7 26.4 - - + +
557O MET* 3.7 29.8 - - + +
561O HIS* 3.8 34.5 - - + +
564O LEU* 3.7 29.4 - - + -
586O SER 3.0 6.9 + - - +
587O VAL* 3.2 11.6 + - - +
589O GLU* 1.3 76.6 - - - +
591O TYR* 1.3 58.8 + - + +
592O TRP 3.2 0.4 - - - -
593O ARG* 3.2 30.3 + - + +
594O SER* 3.3 9.3 + - - -
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Residues in contact with TYR 591 (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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778A LEU* 5.2 0.9 - - + -
942A ARG 3.6 4.7 + - - -
945A GLU* 3.5 24.2 - - + +
946A THR* 3.6 24.0 - - + -
561O HIS* 3.2 23.1 + + - -
565O GLN* 4.5 0.5 + - - -
587O VAL* 3.1 32.0 + - + +
588O ALA* 3.1 11.1 + - - +
590O LEU* 1.3 76.0 - - + +
592O TRP* 1.3 60.2 - - - +
593O ARG 3.2 0.9 - - - -
594O SER* 3.0 32.8 + - - -
595O SER 4.4 0.9 + - - -
596O SER 4.6 0.5 - - - +
597O PRO* 4.6 12.3 - - - +
599O ILE* 3.5 21.5 - - + -
600O ALA* 3.7 33.7 - - + +
603O MET* 3.6 30.6 - - + +
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Residues in contact with TRP 592 (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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588O ALA 3.3 24.7 + - - -
589O GLU* 3.8 12.3 - - + +
590O LEU 3.2 1.0 - - - -
591O TYR* 1.3 75.8 - - - +
593O ARG* 1.3 62.3 + - - +
594O SER 3.3 0.4 - - - -
595O SER 4.7 2.5 + - - -
597O PRO* 3.6 35.2 - - + -
600O ALA* 4.3 8.0 - - + +
601O LEU* 5.7 0.7 - - + -
604O LEU* 4.1 15.0 - - - +
626O ASN* 3.9 23.3 + - - -
629O PHE* 3.4 33.4 - + + -
630O ALA* 3.4 33.0 - - + -
633O ILE* 3.4 37.0 - - + -
634O LEU* 5.7 0.2 - - + -
752O ILE 5.2 1.1 - - - -
753O ASN* 3.7 37.2 - - - +
754O HIS 5.8 0.9 - - - +
755O LEU* 6.1 2.5 - - + -
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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