Contacts of the helix formed by residues 566 - 581 (chain C) in PDB entry 5DO7
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 THR 566 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541C GLY* 4.5 14.1 - - - +
544C VAL* 4.8 2.0 - - + -
545C GLY* 3.8 5.0 - - - -
562C ILE* 4.1 17.5 - - + +
563C SER* 2.4 27.3 + - - +
565C PHE* 1.3 81.5 - - + +
567C PHE* 1.3 63.6 + - - +
568C GLN* 3.2 25.4 - - - +
569C LYS* 3.6 13.3 + - - +
570C TYR* 3.0 20.1 - - - -
630C PHE* 3.6 2.5 - - - -
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Residues in contact with PHE 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427C VAL* 4.6 2.5 - - + -
431C PRO* 4.1 27.4 - - + -
509C PRO* 4.6 13.2 - - + -
512C ILE* 3.6 49.6 - - + -
516C LEU* 6.1 4.3 - - + -
538C SER* 4.9 4.7 - - - -
566C THR* 1.3 70.3 - - - +
568C GLN* 1.3 119.8 + - + +
570C TYR* 2.8 15.3 + - - +
571C CYS* 2.8 12.7 + - + +
627C LEU* 3.9 9.2 - - + +
630C PHE* 3.3 36.4 - + + -
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Residues in contact with GLN 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C VAL* 4.3 10.1 - - + +
431C PRO* 5.1 0.6 - - - +
537C LEU 4.2 0.6 + - - -
538C SER* 3.4 24.5 + - - +
541C GLY* 3.2 36.5 - - - +
542C VAL* 3.5 28.0 - - + +
545C GLY 3.7 4.5 - - - -
546C SER* 4.7 0.9 - - - +
566C THR* 3.1 25.1 - - - +
567C PHE* 1.3 125.5 - - + +
569C LYS* 1.3 67.0 + - - +
571C CYS* 2.9 2.1 + - - +
572C SER* 2.8 25.8 + - - -
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Residues in contact with LYS 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A ILE* 4.7 7.3 - - - +
545C GLY 2.5 25.6 + - - +
546C SER* 4.7 0.7 - - - +
552C ILE* 3.5 29.3 - - + +
563C SER 3.8 16.2 - - - +
564C TYR* 3.6 42.7 - - - +
566C THR* 3.6 16.8 + - - +
567C PHE 3.4 0.2 - - - -
568C GLN* 1.3 73.5 - - - +
570C TYR* 1.3 70.3 + - + +
572C SER* 3.1 0.7 + - - -
573C GLU* 2.8 84.4 + - - +
619C ARG* 4.3 2.2 - - - +
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Residues in contact with TYR 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A LEU* 4.4 7.4 - - - +
640A VAL* 4.1 17.8 - - + +
644A ILE* 4.6 3.1 - - + -
564C TYR* 2.4 55.0 + - - +
565C PHE 4.9 0.7 - - - -
566C THR 3.0 27.6 - - - -
567C PHE* 2.8 11.4 + - - +
569C LYS* 1.3 83.9 - - + +
571C CYS* 1.3 57.1 + - - +
573C GLU* 4.5 1.1 - - - -
574C ILE* 3.1 27.6 - - - +
619C ARG* 4.2 8.1 - - - -
623C ASN* 3.7 22.6 - - - +
626C ILE* 3.3 54.8 - - + +
627C LEU* 3.9 9.4 - - - +
630C PHE* 4.6 2.2 - + - -
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Residues in contact with CYS 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427C VAL* 3.6 24.5 - - + -
505C ALA* 3.6 23.8 - - - -
506C LEU* 4.5 1.3 - - - -
509C PRO* 4.1 7.9 - - + -
567C PHE* 2.8 10.6 + - + +
568C GLN* 2.9 8.0 + - - +
570C TYR* 1.3 78.2 - - - +
572C SER* 1.3 66.8 + - - +
574C ILE* 2.8 15.3 + - - +
575C LEU* 3.0 28.7 + - - +
627C LEU* 3.6 22.4 - - + +
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Residues in contact with SER 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C LEU* 6.0 0.2 - - - +
427C VAL* 3.7 16.1 - - - +
546C SER* 3.7 24.3 + - - -
548C PHE* 3.1 34.5 - - - -
568C GLN 2.8 17.7 + - - -
569C LYS 3.8 1.1 - - - -
571C CYS* 1.3 72.5 - - - +
573C GLU* 1.3 58.8 + - - +
575C LEU* 2.8 27.3 + - - +
576C VAL* 2.8 20.0 + - - +
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Residues in contact with GLU 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545C GLY 4.5 0.2 - - - +
546C SER 4.5 9.9 - - - +
552C ILE* 4.2 7.8 - - - +
569C LYS* 2.8 63.3 + - - +
572C SER* 1.3 69.4 - - - +
574C ILE* 1.3 56.3 + - - +
576C VAL* 4.7 0.9 - - - -
577C VAL* 3.4 23.7 - - - +
613C CYS* 3.4 39.0 - - + +
616C ALA* 3.5 6.3 - - + +
619C ARG* 1.9 45.2 + - - +
620C PHE* 4.7 1.4 - - - -
623C ASN* 3.4 16.3 + - - +
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Residues in contact with ILE 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501C TYR* 5.4 1.1 - - + +
505C ALA* 4.0 12.1 - - + -
570C TYR 3.1 23.1 + - - +
571C CYS 2.8 7.5 + - - +
572C SER 2.8 0.4 + - - -
573C GLU* 1.3 76.1 - - - +
575C LEU* 1.3 71.2 + - + +
577C VAL* 2.8 6.9 + - - +
578C ASN* 2.8 25.7 + - + -
620C PHE* 3.5 17.3 - - + -
623C ASN* 3.5 14.3 - - + +
624C PHE* 3.3 63.7 - - + +
627C LEU* 3.8 18.4 - - + -
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Residues in contact with LEU 575 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C LEU* 3.5 32.3 - - + +
426C PHE* 5.1 0.7 - - + -
427C VAL* 4.9 7.9 - - + -
502C PHE* 3.7 37.9 - - + +
505C ALA* 3.7 26.7 - - + -
506C LEU* 3.7 27.6 - - + -
571C CYS* 3.0 17.8 + - - +
572C SER* 2.8 13.7 + - - +
574C ILE* 1.3 79.4 - - + +
576C VAL* 1.3 56.4 + - + +
578C ASN* 3.7 5.2 - - - +
579C GLU* 2.8 35.3 + - - +
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Residues in contact with VAL 576 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C LEU* 4.9 4.5 - - + +
548C PHE* 3.3 36.6 - - + -
572C SER 2.8 25.4 + - - +
573C GLU* 4.9 0.4 - - - -
575C LEU* 1.3 71.6 - - - +
577C VAL* 1.3 59.4 + - + +
580C PHE* 2.8 45.1 + - + +
608C PHE* 3.9 28.9 - - + -
609C ILE* 4.2 15.5 - - + -
613C CYS* 4.3 24.9 - - - -
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Residues in contact with VAL 577 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573C GLU 3.4 8.1 - - - +
574C ILE 2.8 11.2 + - - +
576C VAL* 1.3 71.1 - - + +
578C ASN* 1.3 67.3 + - - +
579C GLU 3.1 0.2 + - - -
581C TYR* 2.8 46.0 + - + +
609C ILE* 4.1 22.2 - - + -
616C ALA* 3.3 35.9 - - + +
617C THR* 3.7 26.9 - - - +
620C PHE* 3.8 17.5 - - + -
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Residues in contact with ASN 578 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487C TYR* 4.5 3.3 + - - -
493C HIS* 3.9 11.1 + - - -
498C ARG* 2.5 59.6 + - - +
501C TYR* 3.4 16.8 - - - +
502C PHE* 3.7 16.9 - - - +
574C ILE* 2.8 22.8 + - + +
575C LEU* 3.7 8.7 - - - +
577C VAL* 1.3 75.7 - - - +
579C GLU* 1.3 85.2 + - - +
581C TYR* 3.7 7.1 + - - +
620C PHE* 3.8 19.6 - - + -
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Residues in contact with GLU 579 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419C ARG* 3.5 29.3 + - - -
423C LEU* 5.0 7.9 - - + -
487C TYR* 4.6 2.2 - - + +
492C LEU* 3.3 35.2 - - + -
493C HIS* 2.8 43.2 + - + +
502C PHE* 5.7 0.7 - - + -
575C LEU 2.8 21.0 + - - +
578C ASN* 1.3 84.8 + - - +
580C PHE* 1.3 83.4 + - + +
581C TYR 3.6 0.2 - - - -
583C LEU* 4.0 5.5 - - - +
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Residues in contact with PHE 580 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416C ILE* 3.8 25.8 - - + -
419C ARG* 4.5 19.3 - - + -
420C VAL* 5.5 1.6 - - - -
423C LEU* 4.4 19.3 - - + -
576C VAL* 2.8 30.3 + - + +
577C VAL 3.7 0.2 - - - -
579C GLU* 1.3 93.9 - - + +
581C TYR* 1.4 52.8 + - - +
582C GLY* 2.4 34.5 + - - -
583C LEU* 4.8 4.0 - - + -
585C PHE* 4.2 15.7 - + - -
605C GLY* 3.5 31.8 - - - +
608C PHE* 3.2 36.1 - + + -
609C ILE* 3.7 9.6 - - + +
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Residues in contact with TYR 581 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493C HIS* 4.0 18.1 + - + +
498C ARG* 3.3 46.4 + - - +
577C VAL* 2.8 36.2 + - + +
578C ASN* 3.7 2.9 + - - +
579C GLU 3.6 2.0 - - - -
580C PHE* 1.4 72.5 - - - +
582C GLY* 1.3 56.6 + - - +
606C ILE* 3.7 18.9 - - - +
609C ILE* 4.5 5.4 - - - +
617C THR 5.3 6.5 + - - -
620C PHE* 5.5 7.0 - + + -
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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