Contacts of the helix formed by residues 561 - 576 (chain C) in PDB entry 1DQ8
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 CYS 561 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C COA 3.7 31.0 - - + -
560C GLY* 1.3 73.9 - - - +
562C LEU* 1.3 58.9 + - - +
564C ALA* 3.8 4.4 - - - +
565C SER* 2.8 31.5 + - - -
865C SER* 3.4 36.6 - - - -
528D GLU* 2.7 27.3 + - - -
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Residues in contact with LEU 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C COA 3.4 15.2 - - + -
555C MET* 3.9 11.2 - - + -
557C THR* 3.4 36.6 - - + +
559C GLU* 3.3 20.8 + - + +
560C GLY 3.2 5.3 + - - -
561C CYS* 1.3 76.9 - - - +
563C VAL* 1.3 58.1 + - + +
565C SER* 3.3 1.3 + - - -
566C THR* 2.9 34.1 + - - +
752C HIS* 4.1 13.2 - - - +
755C ASN* 3.7 43.1 - - + +
756C ILE* 3.9 17.3 - - + -
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Residues in contact with VAL 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C COA 5.5 0.4 - - + -
539C GLY* 4.2 2.5 - - - -
540C VAL 3.4 32.1 - - - +
541C ALA* 4.2 4.0 - - + +
555C MET* 4.1 26.2 - - + +
557C THR* 4.9 7.4 - - - +
559C GLU 4.8 1.0 + - - +
562C LEU* 1.3 76.6 - - + +
564C ALA* 1.3 53.3 + - - +
566C THR* 3.2 5.7 + - - -
567C ASN* 2.7 34.9 + - + +
527D CYS* 3.9 21.3 - - - -
528D GLU* 3.4 37.4 + - + +
529D ASN* 4.2 2.0 - - + -
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Residues in contact with ALA 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C COA 3.6 61.2 + - + +
561C CYS* 3.8 7.9 - - - +
562C LEU 3.3 0.2 - - - -
563C VAL* 1.3 76.8 - - - +
565C SER* 1.3 57.1 + - - +
567C ASN* 3.3 2.3 + - - +
568C ARG* 3.0 28.9 + - - +
528D GLU* 3.0 22.8 + - + +
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Residues in contact with SER 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C COA 2.9 48.8 + - - +
561C CYS 2.8 21.9 + - - -
562C LEU* 3.7 4.5 - - - -
564C ALA* 1.3 71.5 - - - +
566C THR* 1.3 66.0 + - - +
568C ARG 3.2 1.6 + - - -
569C GLY 3.0 8.8 + - - -
752C HIS* 4.6 3.2 + - - -
849C GLY* 4.4 3.5 + - - -
852C SER* 2.8 42.4 + - - -
853C LEU 3.9 1.7 + - - -
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Residues in contact with THR 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C ALA* 3.8 8.1 - - + -
555C MET* 3.4 18.4 - - - +
562C LEU* 2.9 19.8 + - - +
563C VAL 3.7 3.4 - - - -
565C SER* 1.3 74.9 + - - +
567C ASN* 1.3 63.5 + - - +
569C GLY* 3.1 3.6 + - - -
570C CYS* 3.0 22.8 + - - -
752C HIS* 5.4 0.2 + - - -
756C ILE* 3.0 26.2 - - + +
845C THR* 3.4 37.9 - - + +
848C ALA* 3.8 3.9 - - + +
849C GLY* 4.4 9.5 - - - +
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Residues in contact with ASN 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C COA 2.9 47.3 + - + +
540C VAL 4.3 4.6 - - - +
541C ALA* 3.6 13.2 - - + +
542C GLY 2.9 39.2 + - - +
563C VAL 2.7 21.5 + - - +
564C ALA 3.5 5.2 - - - +
565C SER 3.2 0.2 - - - -
566C THR* 1.3 74.9 - - - +
568C ARG* 1.3 61.2 + - - +
570C CYS* 3.2 6.6 + - - +
571C ARG* 3.1 17.5 + - - +
479D TYR* 4.0 9.1 - - - -
529D ASN* 4.8 6.7 + - - +
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Residues in contact with ARG 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C COA 3.1 96.7 + - + +
564C ALA 3.0 9.4 + - - +
565C SER 3.4 6.5 - - - +
567C ASN* 1.3 77.6 - - - +
569C GLY* 1.3 61.6 + - - +
571C ARG* 3.1 4.9 + - - +
572C ALA* 3.0 18.9 + - - +
720C VAL* 3.4 18.4 + - + +
721C LEU* 3.6 25.4 + - + -
722C LYS* 3.7 10.3 - - - +
852C SER* 2.9 42.7 + - - -
855C ALA* 3.9 9.5 - - - +
856C ALA* 4.0 5.7 - - - +
861C HIS* 4.7 7.5 + - - -
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Residues in contact with GLY 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565C SER 3.0 11.3 + - - -
566C THR 3.1 1.5 + - - -
568C ARG* 1.3 75.8 - - - +
570C CYS* 1.3 61.6 + - - +
572C ALA* 3.4 5.5 + - - +
573C ILE* 3.1 27.7 + - - +
721C LEU* 5.1 0.9 - - - -
848C ALA* 3.3 31.6 - - - -
851C LEU* 4.1 8.3 - - - +
852C SER* 4.0 6.2 - - - -
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Residues in contact with CYS 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C ALA* 4.4 7.2 - - - -
542C GLY* 4.2 22.4 - - - -
543C PRO 3.7 20.6 - - - +
544C LEU* 4.1 25.6 - - - -
545C CYS 5.4 0.5 + - - -
553C VAL* 5.7 0.7 - - - -
566C THR* 3.0 21.7 + - - -
567C ASN 3.4 9.4 - - - +
568C ARG 3.2 0.2 - - - -
569C GLY* 1.3 75.8 - - - +
571C ARG* 1.3 57.1 + - - +
573C ILE* 3.2 7.2 + - - +
574C GLY* 2.8 27.7 + - - -
845C THR* 5.4 3.4 - - - -
848C ALA* 3.7 15.9 - - - +
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Residues in contact with ARG 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C COA 3.5 47.5 + - + +
543C PRO* 6.5 0.7 - - - -
567C ASN 3.1 12.2 + - - +
568C ARG* 3.1 10.5 + - - +
570C CYS* 1.3 77.4 - - - +
572C ALA* 1.3 63.1 + - - +
574C GLY* 3.3 3.1 + - - -
575C LEU* 3.0 67.1 + - + +
720C VAL* 4.4 9.8 - - + +
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Residues in contact with ALA 572 (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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568C ARG 3.0 12.2 + - - +
569C GLY 3.8 6.5 - - - +
570C CYS 3.4 0.2 - - - -
571C ARG* 1.3 74.7 - - - +
573C ILE* 1.3 63.1 + - - +
575C LEU* 3.3 2.8 + - - -
576C GLY* 3.1 17.2 + - - -
712C ILE* 3.8 22.1 - - + +
716C VAL* 3.6 28.2 - - + +
720C VAL* 4.0 10.9 - - + +
721C LEU* 4.1 18.6 - - + -
851C LEU* 4.5 2.5 - - + -
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Residues in contact with ILE 573 (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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544C LEU* 4.5 10.5 - - + -
545C CYS 4.0 8.3 - - - +
569C GLY 3.1 18.5 + - - +
570C CYS* 3.5 7.9 - - - +
572C ALA* 1.3 77.4 - - - +
574C GLY* 1.3 59.7 + - - +
576C GLY 3.1 7.8 + - - -
577C GLY 3.5 0.2 + - - -
578C GLY* 2.9 28.0 + - - +
579C ALA* 3.7 30.1 - - + +
710C ALA* 4.3 7.1 - - + +
712C ILE* 3.8 10.8 - - + -
844C GLY 4.3 4.3 - - - +
847C MET* 3.9 17.7 - - + -
848C ALA* 3.7 32.1 - - + +
851C LEU* 3.6 17.5 - - + -
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Residues in contact with GLY 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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543C PRO 5.4 0.2 - - - -
545C CYS* 3.9 30.2 - - - +
570C CYS 2.8 19.1 + - - -
571C ARG* 3.8 2.9 - - - -
573C ILE* 1.3 73.1 - - - +
575C LEU* 1.3 63.3 + - - +
577C GLY* 3.3 12.8 + - - -
578C GLY 4.1 0.4 + - - -
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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
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571C ARG* 3.0 57.4 + - - +
572C ALA 3.9 2.2 - - - +
574C GLY* 1.3 77.3 - - - +
576C GLY* 1.3 55.5 + - - +
577C GLY 3.3 2.7 + - - -
713C PRO* 4.1 8.5 - - - +
716C VAL* 3.8 23.6 - - + +
720C VAL* 3.8 27.6 - - + -
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Residues in contact with GLY 576 (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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572C ALA 3.1 10.3 + - - -
573C ILE 3.1 5.3 + - - -
575C LEU* 1.3 78.6 - - - +
577C GLY* 1.3 58.6 + - - +
578C GLY 3.5 6.7 + - - +
711C VAL* 3.4 19.6 + - - +
713C PRO* 3.5 27.4 - - - -
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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