Contacts of the helix formed by residues 569 - 581 (chain C) in PDB entry 1RR8
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 569 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492C GLU* 3.5 24.5 - - - +
505C CYS* 4.1 10.9 - - - -
568C LEU* 1.3 84.1 + - - +
570C THR* 1.3 62.3 + - - +
571C GLY* 3.1 9.9 - - - +
572C ILE* 3.0 51.3 - - - +
573C LEU* 3.4 18.4 + - - +
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Residues in contact with THR 570 (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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117B C 5.0 0.7 - - - -
489C ALA* 3.5 38.4 - - + +
490C GLY 3.7 17.7 - - - +
491C ASN* 3.1 32.1 + - - +
492C GLU* 3.6 10.9 + - - -
505C CYS* 4.2 6.0 - - + +
569C ASN* 1.3 73.8 - - - +
571C GLY* 1.3 59.4 + - - +
573C LEU* 3.6 6.3 + - - +
574C ASN* 3.1 41.6 + - - -
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Residues in contact with GLY 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B T 6.3 3.4 - - - -
492C GLU* 5.6 0.2 + - - -
569C ASN* 3.1 9.3 - - - +
570C THR* 1.3 78.2 + - - +
572C ILE* 1.3 61.0 + - - +
574C ASN* 4.0 4.1 - - - +
575C LYS* 3.1 30.5 + - - +
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Residues in contact with ILE 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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471C LYS* 5.7 3.4 - - + +
475C ARG* 4.7 10.7 - - - +
567C ARG 3.6 25.6 - - - +
568C LEU* 4.1 14.1 - - + -
569C ASN* 3.0 40.8 - - - +
570C THR 3.4 0.2 - - - -
571C GLY* 1.3 73.9 - - - +
573C LEU* 1.3 65.0 + - - +
575C LYS* 3.4 7.2 + - - +
576C HIS* 3.3 21.8 + - - +
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Residues in contact with LEU 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C ARG* 4.1 31.6 - - + +
478C ALA* 5.2 2.2 - - + -
479C LEU* 4.2 26.0 - - + +
482C ILE* 3.6 22.9 - - + -
489C ALA* 4.8 2.7 - - + -
505C CYS* 3.5 26.5 - - - -
568C LEU* 4.1 10.7 - - + +
569C ASN 3.4 13.6 + - - +
570C THR* 3.9 4.9 - - - +
571C GLY 3.4 0.2 - - - -
572C ILE* 1.3 78.0 - - - +
574C ASN* 1.3 58.3 + - - +
576C HIS* 3.4 6.3 + - - +
577C LEU* 3.1 39.3 + - + +
586C ALA* 4.1 12.3 - - + -
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Residues in contact with ASN 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B C 3.3 38.2 + - - +
118B T 5.3 5.3 - - - +
489C ALA* 5.4 0.2 - - - +
570C THR* 3.1 26.1 + - - +
571C GLY* 4.3 4.7 - - - +
573C LEU* 1.3 75.0 - - - +
575C LYS* 1.3 62.5 + - - +
576C HIS 3.3 0.9 - - - -
577C LEU* 3.8 7.3 - - - +
578C GLN* 3.2 23.4 + - - +
584C LEU 4.1 3.1 - - - +
585C THR* 3.5 15.3 - - + +
586C ALA* 2.9 33.8 + - - +
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Residues in contact with LYS 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 GLY 3.1 21.5 + - - +
572C ILE* 3.7 8.1 - - - +
573C LEU 3.3 0.2 - - - -
574C ASN* 1.3 75.9 - - - +
576C HIS* 1.3 61.1 + - - +
578C GLN* 3.7 9.6 + - + +
579C ASP* 3.2 36.6 + - - +
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Residues in contact with HIS 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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460C GLN* 3.8 19.8 + - - -
461C TYR* 6.3 2.0 - - + -
464C ASP* 4.8 4.9 - - - -
475C ARG* 3.5 57.5 + - + +
479C LEU* 5.1 13.1 - - + +
572C ILE 3.3 9.8 + - - +
573C LEU* 3.6 8.8 + - - +
574C ASN 3.3 0.2 - - - -
575C LYS* 1.3 76.9 - - - +
577C LEU* 1.3 61.0 + - - +
578C GLN 3.1 2.0 - - - -
579C ASP* 3.0 28.5 + - + +
580C LEU* 3.3 34.0 + - + +
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Residues in contact with LEU 577 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C ILE* 5.2 0.2 - - + -
479C LEU* 3.9 28.9 - - + -
573C LEU* 3.1 33.2 + - + +
574C ASN* 3.8 20.6 - - - +
575C LYS 3.5 0.4 - - - -
576C HIS* 1.3 77.0 - - - +
578C GLN* 1.3 57.3 + - - +
579C ASP 3.3 0.2 - - - -
580C LEU* 3.9 13.9 - - + +
581C MET 3.0 26.3 + - - +
584C LEU* 3.4 42.5 - - + +
585C THR 3.9 3.8 - - - +
586C ALA* 3.8 19.7 - - - +
589C PHE* 3.9 15.0 - - + -
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Residues in contact with GLN 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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118B T 5.4 3.8 + - - -
574C ASN 3.2 17.1 + - - +
575C LYS* 3.8 12.8 - - + +
576C HIS 3.1 0.4 - - - -
577C LEU* 1.3 76.0 - - - +
579C ASP* 1.3 65.8 + - - +
580C LEU 3.3 0.9 - - - -
581C MET 3.4 13.1 - - - +
582C GLU* 3.5 18.2 + - - +
583C GLY* 3.1 37.5 + - - +
584C LEU 3.8 6.4 + - - +
585C THR* 5.6 1.7 - - - +
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Residues in contact with ASP 579 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575C LYS* 3.2 28.3 + - - +
576C HIS* 3.0 18.6 + - + +
578C GLN* 1.3 81.9 - - - +
580C LEU* 1.3 63.4 + - + +
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Residues in contact with LEU 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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453C CYS* 5.5 3.9 - - - -
456C LYS* 5.1 14.7 - - - +
457C ILE* 3.9 42.2 - - + -
460C GLN* 3.3 38.6 - - + +
479C LEU* 5.1 1.3 - - + -
576C HIS* 3.3 35.4 + - + +
577C LEU* 3.6 21.3 + - + +
578C GLN 3.3 0.2 - - - -
579C ASP* 1.3 82.6 - - + +
581C MET* 1.3 60.4 + - - +
582C GLU* 4.8 3.0 - - - +
584C LEU* 4.9 0.4 - - + -
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Residues in contact with MET 581 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C THR* 3.5 33.7 - - + +
449C ARG* 3.5 44.2 - - + +
450C LEU* 3.7 11.4 - - - +
453C CYS* 4.3 18.8 - - - -
457C ILE* 5.0 2.7 - - + -
577C LEU 3.0 16.3 + - - +
578C GLN* 3.4 9.7 - - - +
580C LEU* 1.3 80.2 - - + +
582C GLU* 1.3 86.5 + - - +
583C GLY 3.4 0.7 + - - -
584C LEU* 3.4 40.4 + - + -
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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
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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