Contacts of the helix formed by residues 556 - 574 (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 GLN 556 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611A GLU* 5.1 7.9 + - - +
614A THR* 3.6 17.0 + - - +
616A GLU* 3.1 33.8 - - + +
619A GLN* 2.8 35.0 + - - +
551O LEU* 3.2 36.8 + - + +
554O GLN* 3.7 1.7 - - + +
555O ASN* 1.3 76.7 - - - +
557O MET* 1.3 65.3 + - - +
559O GLU* 3.0 41.7 + - + +
560O ALA* 3.2 10.0 + - - +
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Residues in contact with MET 557 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A GLU* 3.0 5.3 + - + +
617A LEU* 5.2 6.3 - - + -
778A LEU* 3.4 33.4 - - + +
779A MET* 3.7 27.6 - - - -
780A GLY 5.2 5.8 - - - +
782A GLY* 5.9 1.6 - - - -
552O GLN* 4.3 4.7 - - - +
555O ASN* 3.2 36.9 + - - +
556O GLN* 1.3 74.4 - - - +
558O SER* 1.3 62.8 + - - +
560O ALA* 3.1 10.8 + - - +
561O HIS* 3.0 16.0 + - - +
590O LEU* 3.7 26.6 - - + +
593O ARG* 3.8 37.5 - - - +
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Residues in contact with SER 558 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A GLU* 2.7 22.1 + - - -
776A ASN* 3.1 34.9 + - - -
778A LEU* 3.6 11.3 - - - +
779A MET* 4.9 1.6 - - - -
869A ARG* 5.0 1.8 + - - -
557O MET* 1.3 69.3 - - - +
559O GLU* 1.3 67.1 + - - -
560O ALA 2.9 1.8 - - - -
561O HIS* 2.7 21.6 + - - +
562O LYS* 2.8 35.2 + - - +
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Residues in contact with GLU 559 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A GLU* 2.8 17.4 + - - +
619A GLN* 5.7 0.5 - - - +
551O LEU* 4.0 13.7 - - + -
556O GLN* 3.0 40.0 + - + +
558O SER* 1.3 76.0 - - - +
560O ALA* 1.3 63.7 + - - +
562O LYS* 3.2 18.1 + - + +
563O LEU* 3.0 24.2 + - + +
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Residues in contact with ALA 560 (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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548O ALA 4.0 7.2 - - - +
551O LEU* 3.8 31.3 - - + +
552O GLN* 4.0 20.9 - - + +
556O GLN 3.2 5.1 + - - +
557O MET 3.1 14.3 + - - +
559O GLU* 1.3 80.5 - - - +
561O HIS* 1.3 49.3 + - - +
563O LEU* 3.3 9.4 - - + +
564O LEU* 2.6 39.6 + - + +
590O LEU* 4.5 1.3 - - + -
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Residues in contact with HIS 561 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778A LEU* 3.5 16.8 - - + +
942A ARG 4.5 0.2 - - - -
943A ASP* 4.4 11.5 + - - -
946A THR* 3.5 32.7 + - + +
557O MET 3.0 11.4 + - - +
558O SER* 2.7 16.3 + - - +
560O ALA* 1.3 74.2 - - - +
562O LYS* 1.3 58.0 + - + +
564O LEU* 3.1 2.7 + - - +
565O GLN* 2.8 63.9 + - + +
587O VAL* 4.0 19.5 - - + +
590O LEU* 3.8 17.7 - - + +
591O TYR* 3.2 23.0 + + - -
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Residues in contact with LYS 562 (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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616A GLU* 5.4 1.2 + - - -
869A ARG* 5.5 6.3 - - - +
943A ASP* 4.3 18.4 - - - +
558O SER* 2.8 38.2 + - - +
559O GLU* 3.6 16.8 + - + +
561O HIS* 1.3 69.4 - - + +
563O LEU* 1.3 66.9 + - - +
565O GLN* 3.3 10.9 + - - +
566O LYS* 2.9 25.0 + - - +
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Residues in contact with LEU 563 (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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86A ASP* 3.0 37.1 - - + +
544O VAL* 3.8 24.0 - - + +
547O LYS* 3.6 25.4 - - + -
548O ALA* 3.8 16.8 - - + -
551O LEU* 3.6 24.2 - - + -
559O GLU* 3.0 10.9 + - + +
560O ALA* 3.3 9.0 - - - +
562O LYS* 1.3 75.7 - - - +
564O LEU* 1.3 51.2 + - - +
566O LYS* 3.0 10.3 + - - +
567O LEU* 2.8 47.9 + - + +
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Residues in contact with LEU 564 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545O TYR* 4.5 4.3 - - + -
548O ALA* 3.7 25.6 - - + -
552O GLN* 3.6 24.0 - - - +
560O ALA* 2.6 24.8 + - + +
561O HIS* 3.1 6.3 + - - +
563O LEU* 1.3 73.2 - - - +
565O GLN* 1.3 54.2 + - - +
567O LEU* 3.5 9.3 - - + +
568O LEU* 2.7 32.8 + - - +
583O VAL* 3.4 34.7 - - + +
586O SER* 3.6 24.0 - - - -
587O VAL* 4.0 11.1 - - + +
590O LEU* 3.7 17.7 - - + -
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Residues in contact with GLN 565 (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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940A THR* 3.8 8.3 + - - +
942A ARG* 3.2 31.2 - - + +
943A ASP* 3.1 41.9 - - - +
561O HIS* 2.8 52.7 + - + +
562O LYS* 3.7 10.1 - - - +
564O LEU* 1.3 73.4 - - - +
566O LYS* 1.3 67.1 + - - +
567O LEU 3.1 0.2 - - - -
568O LEU* 3.5 7.0 - - + +
569O VAL* 2.9 32.8 + - + +
587O VAL* 5.5 3.6 - - + -
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Residues in contact with LYS 566 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ILE 4.8 7.4 - - - +
84A GLY 3.3 21.1 + - - +
85A GLU* 3.4 30.7 + - - +
86A ASP* 4.0 15.3 + - - +
562O LYS 2.9 16.0 + - - +
563O LEU* 3.1 11.2 - - - +
565O GLN* 1.3 75.2 - - - +
567O LEU* 1.3 60.9 - - - +
569O VAL* 3.4 9.6 + - - +
570O HIS* 3.3 20.5 + - - +
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Residues in contact with LEU 567 (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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83A ILE 5.3 2.9 - - - -
86A ASP* 5.7 0.4 + - - +
541O ILE* 4.6 7.9 - - + +
544O VAL* 3.6 22.9 - - + +
545O TYR* 3.2 47.6 - - + +
563O LEU* 2.8 23.6 + - + +
564O LEU* 3.5 14.6 - - + +
566O LYS* 1.3 74.9 - - - +
568O LEU* 1.3 59.6 - - - +
570O HIS* 3.5 9.4 + - + +
571O CYS* 3.0 44.9 + - - -
579O MET* 4.6 3.6 - - - -
583O VAL* 4.1 11.2 - - + -
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Residues in contact with LEU 568 (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* 3.8 27.8 - - + +
564O LEU 2.7 20.6 + - - +
565O GLN* 3.0 8.2 + - - +
567O LEU* 1.3 71.7 - - - +
569O VAL* 1.3 65.3 + - + +
571O CYS* 3.4 2.3 + - - -
572O GLN* 3.2 45.7 + - - +
580O VAL* 3.7 11.9 - - + -
583O VAL* 3.6 27.1 - - + +
584O LEU* 3.7 26.9 - - + -
587O VAL* 4.7 11.7 - - + -
603O MET* 4.4 3.6 - - + -
606O GLN* 5.7 0.9 - - - +
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Residues in contact with VAL 569 (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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565O GLN* 2.9 21.1 + - + +
566O LYS* 3.4 11.0 - - - +
568O LEU* 1.3 76.3 - - + +
570O HIS* 1.3 58.1 - - - +
572O GLN* 3.2 15.6 + - - +
573O LYS* 3.2 39.6 + - + +
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Residues in contact with HIS 570 (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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82A GLU 4.7 5.6 + - - -
83A ILE* 3.3 45.9 - - + +
541O ILE* 3.4 32.9 - - + +
566O LYS 3.3 10.7 + - - +
567O LEU* 3.9 8.3 - - + +
568O LEU 3.3 0.2 - - - -
569O VAL* 1.3 78.1 - - + +
571O CYS* 1.3 76.2 + - - +
572O GLN 3.1 1.3 - - - -
573O LYS* 3.1 14.7 + - + +
574O LEU* 3.0 56.9 + - + +
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Residues in contact with CYS 571 (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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541O ILE* 4.0 6.7 - - - -
567O LEU* 3.0 37.7 + - - +
568O LEU* 3.4 5.6 + - - +
570O HIS* 1.3 87.4 - - - +
572O GLN* 1.3 56.7 + - - +
574O LEU* 4.6 0.2 - - - -
575O LYS* 2.9 22.8 + - - -
576O ASN* 3.2 20.3 + - - +
579O MET* 3.6 33.9 - - + -
580O VAL* 3.8 19.1 - - + +
583O VAL* 5.1 1.1 - - + -
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Residues in contact with GLN 572 (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* 3.2 42.1 + - - +
569O VAL* 3.2 12.9 + - - +
570O HIS 3.1 0.8 - - - -
571O CYS* 1.3 75.4 - - - +
573O LYS* 1.3 72.5 + - - +
575O LYS* 3.4 28.3 + - - +
580O VAL* 3.6 21.5 - - + +
606O GLN* 4.9 10.1 - - - +
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Residues in contact with LYS 573 (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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972A GLU* 5.3 6.4 + - - -
354O ARG* 2.6 46.2 + - - +
569O VAL* 3.2 29.2 + - + +
570O HIS* 3.3 18.8 - - + +
572O GLN* 1.3 85.8 + - - +
574O LEU* 1.3 54.4 + - - +
575O LYS* 3.3 13.7 + - - +
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Residues in contact with LEU 574 (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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353O LYS 5.1 2.1 - - - +
354O ARG* 3.3 33.2 - - + +
541O ILE* 3.5 30.7 - - + -
570O HIS* 3.0 37.3 + - + +
573O LYS* 1.3 73.9 - - + +
575O LYS* 1.3 61.7 + - - +
576O ASN* 3.0 35.6 + - + +
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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