Contacts of the helix formed by residues 569 - 588 (chain C) in PDB entry 1S0V
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 ASP 569 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472C LYS* 2.6 44.0 + - + +
567C VAL 3.3 5.3 + - - +
568C GLN* 1.3 73.9 - - - +
570C ILE* 1.3 53.8 + - - +
571C TYR* 3.1 3.6 - - - -
572C GLY* 2.4 41.6 + - - +
573C ILE* 2.6 21.7 + - - +
576C LYS* 6.1 1.6 - - - +
627C ARG* 2.7 33.6 + - - -
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Residues in contact with ILE 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C LYS* 6.2 0.7 - - - +
539C SER* 6.0 1.3 - - - -
540C CYS* 3.5 28.7 - - - -
543C ILE* 3.6 19.5 - - + -
558C ALA* 3.4 25.8 + - + +
559C VAL* 4.1 13.9 - - + -
568C GLN 4.0 0.6 + - - -
569C ASP* 1.3 72.3 - - - +
571C TYR* 1.4 72.3 + - + +
573C ILE* 2.9 23.7 - - + +
574C VAL* 2.9 34.7 + - + +
634C VAL* 4.5 8.7 - - + -
688C THR* 4.9 1.1 - - + -
689C VAL* 3.6 30.5 - - + -
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Residues in contact with TYR 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C LYS* 4.5 5.8 - - - -
539C SER 5.1 0.9 + - - -
540C CYS* 4.0 18.5 - - - -
569C ASP* 3.1 2.4 - - - -
570C ILE* 1.4 88.1 - - + +
572C GLY* 1.3 62.8 + - - +
574C VAL* 4.4 4.9 - - - -
575C ALA* 3.6 5.5 + - - +
627C ARG* 3.1 48.8 - - + +
630C THR* 2.9 24.7 + - - -
631C LYS* 3.4 26.5 - - + -
634C VAL* 3.1 30.5 - - + -
635C MET* 3.5 23.6 - - + +
2002C APC 2.7 41.7 + - - -
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Residues in contact with GLY 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569C ASP* 2.4 33.5 + - - -
571C TYR* 1.3 74.0 - - - +
573C ILE* 1.3 56.9 + - - -
575C ALA* 2.8 26.4 - - - +
576C LYS* 3.2 20.2 + - - +
627C ARG* 4.2 8.5 - - - -
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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
----------------------------------------------------------
558C ALA* 4.3 13.2 - - + -
568C GLN* 6.0 0.9 - - + -
569C ASP 2.6 14.7 + - - +
570C ILE* 2.9 41.5 - - + +
572C GLY* 1.3 67.5 - - - +
574C VAL* 1.3 64.9 + - - +
575C ALA 2.9 2.9 + - - -
576C LYS* 2.9 35.2 + - + +
577C LYS* 3.3 25.1 + - + +
688C THR* 4.2 22.7 - - + +
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Residues in contact with VAL 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570C ILE* 2.9 31.0 + - + +
571C TYR* 4.4 4.9 - - - +
573C ILE* 1.3 76.6 - - + +
575C ALA* 1.3 52.2 + - - +
577C LYS* 3.4 3.4 + - - +
578C VAL* 2.7 39.0 + - + +
630C THR* 4.5 15.3 - - + -
634C VAL* 4.4 9.0 - - + -
681C ILE* 4.1 6.7 - - + +
684C SER* 3.4 27.6 + - - -
685C VAL* 3.8 31.9 - - + +
688C THR* 5.0 8.5 - - + -
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Residues in contact with ALA 575 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571C TYR 3.6 12.1 + - - +
572C GLY* 2.8 18.1 - - - +
573C ILE 2.9 0.2 - - - -
574C VAL* 1.3 77.5 - - - +
576C LYS* 1.3 55.7 + - - +
578C VAL* 2.7 35.7 + - - +
579C ASN* 2.9 19.4 + - - +
625C VAL* 4.9 1.8 - - + +
626C THR* 4.0 18.4 - - - +
627C ARG* 4.5 0.4 - - - -
630C THR* 3.8 11.8 + - + +
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Residues in contact with LYS 576 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569C ASP* 5.5 1.6 + - - +
572C GLY* 3.9 21.1 - - - +
573C ILE* 2.9 28.5 + - + +
575C ALA* 1.3 79.1 - - + +
577C LYS* 1.3 61.7 + - + +
579C ASN* 3.5 8.7 + - - +
580C GLU* 3.0 33.9 + - + +
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Residues in contact with LYS 577 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573C ILE* 3.3 22.3 + - + +
574C VAL* 3.6 5.8 - - - +
575C ALA 3.1 0.4 - - - -
576C LYS* 1.3 77.0 - - + +
578C VAL* 1.3 64.6 + - - +
580C GLU* 3.4 34.8 + - - +
581C ILE* 3.1 29.8 - - - +
684C SER* 3.5 18.4 - - - +
687C VAL* 4.4 22.6 - - + +
688C THR* 4.7 7.0 - - - +
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Residues in contact with VAL 578 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574C VAL* 2.7 29.1 + - + +
575C ALA* 2.7 16.7 + - - +
577C LYS* 1.3 75.4 - - - +
579C ASN* 1.3 55.1 + - - +
581C ILE* 2.7 31.2 + - - +
582C LEU* 3.0 19.9 + - + +
625C VAL* 3.9 21.3 - - + -
630C THR* 4.1 13.5 - - + -
677C MET* 4.1 18.8 - - - -
680C LEU* 4.1 9.9 - - + +
681C ILE* 4.7 7.6 - - - +
684C SER* 3.4 16.8 - - - +
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Residues in contact with ASN 579 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575C ALA* 2.9 27.1 + - - +
576C LYS* 3.9 8.3 - - - +
578C VAL* 1.3 79.3 - - - +
580C GLU* 1.3 55.6 + - - +
582C LEU* 2.8 30.9 + - + +
583C GLN* 2.7 37.5 + - - +
621C LEU* 4.9 4.8 - - + +
625C VAL* 3.5 32.1 + - - +
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Residues in contact with GLU 580 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576C LYS* 3.0 30.2 + - - +
577C LYS* 3.4 37.8 + - - +
578C VAL 3.0 1.0 + - - -
579C ASN* 1.3 77.4 - - - +
581C ILE* 1.3 59.6 + - + +
583C GLN* 4.3 4.3 - - - +
584C ALA* 3.3 23.2 + - - +
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Residues in contact with ILE 581 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577C LYS* 3.1 26.0 - - + +
578C VAL 2.7 9.8 + - - +
580C GLU* 1.3 74.1 - - + +
582C LEU* 1.3 58.3 + - - +
583C GLN 3.6 0.2 - - - -
584C ALA* 3.9 8.2 - - + +
585C ASP* 2.5 49.1 + - - +
676C TYR* 3.7 2.1 + - - -
680C LEU* 4.1 22.4 - - + -
683C GLU* 4.2 31.9 - - + +
684C SER* 4.0 13.9 - - - +
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Residues in contact with LEU 582 (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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578C VAL* 3.0 10.6 + - + +
579C ASN* 2.8 49.6 - - + +
581C ILE* 1.3 77.4 - - - +
583C GLN* 1.3 58.6 + - - +
585C ASP 3.4 0.5 + - - -
586C ALA 3.0 21.8 + - - -
617C ALA* 3.4 17.0 - - - +
620C TRP* 3.8 24.9 - - + -
621C LEU* 3.3 24.3 - - + +
625C VAL* 3.4 22.7 - - + -
676C TYR* 4.3 11.9 - - + -
677C MET* 5.2 0.2 - - + -
680C LEU* 3.6 21.3 - - + -
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Residues in contact with GLN 583 (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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579C ASN* 2.7 17.4 + - + +
580C GLU* 4.8 4.3 - - - +
582C LEU* 1.3 72.5 - - + +
584C ALA* 1.3 59.7 + - - +
586C ALA* 3.7 9.0 + - + +
587C ILE* 2.9 35.2 + - + +
621C LEU* 4.5 7.9 - - + -
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Residues in contact with ALA 584 (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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580C GLU 3.3 20.7 + - - +
581C ILE* 4.1 9.6 - - + +
582C LEU 3.2 0.4 - - - -
583C GLN* 1.3 78.8 - - - +
585C ASP* 1.3 60.2 + - - +
587C ILE* 3.6 7.9 + - - +
588C ASN* 3.2 27.4 + - - +
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Residues in contact with ASP 585 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581C ILE* 2.5 38.7 + - - +
583C GLN 3.4 0.2 - - - -
584C ALA* 1.3 76.3 - - - +
586C ALA* 1.3 58.0 + - - +
587C ILE 3.2 0.4 - - - -
588C ASN 2.6 28.2 - - - +
589C GLY* 3.8 5.9 + - - -
613C THR* 3.0 28.3 + - - +
614C LYS* 3.7 10.6 - - - -
617C ALA* 3.7 10.5 - - + -
676C TYR* 3.0 24.8 + - - +
680C LEU* 4.6 0.5 - - - +
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Residues in contact with ALA 586 (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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582C LEU 3.0 7.7 + - - +
583C GLN* 3.8 10.5 - - + +
584C ALA 3.3 0.2 - - - -
585C ASP* 1.3 77.0 - - - +
587C ILE* 1.3 63.2 + - + +
588C ASN 4.2 0.2 - - - -
614C LYS* 3.5 23.3 + - - -
617C ALA* 3.9 6.5 - - + +
618C GLY* 5.2 2.0 - - - +
621C LEU* 3.4 30.5 - - + -
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Residues in contact with ILE 587 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583C GLN* 2.9 27.8 - - + +
584C ALA* 3.6 7.6 - - - +
585C ASP 3.2 0.2 - - - -
586C ALA* 1.3 78.6 - - + +
588C ASN* 1.3 78.7 + - - +
614C LYS* 3.3 19.6 + - - -
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Residues in contact with ASN 588 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584C ALA 3.2 10.9 + - - +
585C ASP 2.6 20.9 - - - +
587C ILE* 1.3 101.2 + - - +
589C GLY* 1.3 68.0 + - - +
614C LYS* 3.6 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
------------------------------------------------------------
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