Contacts of the helix formed by residues 576 - 593 (chain I) in PDB entry 2R6C
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 576 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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571I ALA* 3.0 19.8 + - - +
572I GLU 4.7 0.2 + - - -
574I ARG* 2.6 41.1 + - + +
575I LYS* 1.3 73.0 - - - +
577I PHE* 1.3 64.5 + - - +
578I LEU* 3.3 2.6 + - - +
579I THR* 2.8 44.6 + - - +
580I ALA 3.3 7.3 + - - -
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Residues in contact with PHE 577 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E THR* 5.0 2.9 - - - +
75E ALA* 5.7 6.7 - - + -
80E LEU* 3.6 33.2 - - + -
81E GLU* 5.9 9.4 - - + -
85E GLY* 5.7 2.9 - - - -
86E VAL* 4.2 13.6 - - + +
572I GLU* 4.2 33.0 - - + +
575I LYS* 3.1 49.4 + - + -
576I ASP* 1.3 75.8 - - - +
578I LEU* 1.3 61.6 + - + +
580I ALA* 3.3 8.0 + - - +
581I ALA* 3.1 27.4 + - - +
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Residues in contact with LEU 578 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E VAL* 4.2 19.3 - - + +
71E THR* 3.8 20.6 - - - +
72E ALA* 4.1 24.0 - - + -
576I ASP* 3.0 2.9 + - - +
577I PHE* 1.3 77.9 - - + +
579I THR* 1.3 63.4 + - - +
581I ALA* 3.8 3.9 + - - +
582I ARG* 3.4 23.9 + - - +
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Residues in contact with THR 579 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571I ALA* 4.7 4.9 - - + -
574I ARG* 4.7 10.3 - - - +
576I ASP* 2.8 38.9 + - - +
578I LEU* 1.3 77.0 - - - +
580I ALA* 1.3 64.3 + - - +
582I ARG* 3.0 20.3 + - + +
583I ILE* 3.0 23.6 + - + +
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Residues in contact with ALA 580 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E VAL* 3.9 20.6 - - + -
568I LYS* 3.6 29.4 - - + +
571I ALA* 4.1 12.5 - - + +
572I GLU* 4.2 7.9 - - - +
576I ASP 3.3 4.6 + - - +
577I PHE* 3.3 10.0 + - - +
579I THR* 1.3 77.7 - - - +
581I ALA* 1.3 57.7 + - - +
583I ILE* 3.4 8.8 + - - +
584I ALA* 2.9 28.6 + - - +
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Residues in contact with ALA 581 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E LEU* 3.8 6.0 - - + +
68E VAL* 3.7 32.2 - - + +
71E THR* 3.8 22.2 - - + +
86E VAL* 4.6 5.3 - - + +
577I PHE 3.1 17.0 + - - +
578I LEU* 3.9 4.7 - - - +
579I THR 3.2 0.2 - - - -
580I ALA* 1.3 77.3 - - - +
582I ARG* 1.3 56.5 + - - +
584I ALA* 3.3 7.3 + - - +
585I LYS* 2.8 28.4 + - - +
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Residues in contact with ARG 582 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E VAL* 3.7 17.2 - - + +
578I LEU 3.4 12.6 + - - +
579I THR* 3.0 15.9 + - + +
581I ALA* 1.3 74.4 - - - +
583I ILE* 1.3 68.3 + - + +
585I LYS* 2.9 13.6 + - + +
586I GLU* 2.8 46.8 + - - +
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Residues in contact with ILE 583 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564I LYS* 3.4 32.3 - - + +
567I GLU* 3.7 26.0 - - + +
568I LYS* 3.7 32.3 - - + +
571I ALA* 5.3 1.6 - - + -
579I THR* 3.0 24.9 + - + +
580I ALA* 3.7 8.5 - - - +
582I ARG* 1.3 73.8 - - - +
584I ALA* 1.3 58.2 + - - +
586I GLU* 3.0 17.5 + - - +
587I MSE 2.9 37.9 + - + +
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Residues in contact with ALA 584 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E LEU* 3.3 18.2 - - + -
90E SER* 3.1 32.5 - - - +
94E ASP* 4.2 1.5 - - - +
568I LYS* 4.5 3.1 - - + -
580I ALA 2.9 17.1 + - - +
581I ALA* 3.6 1.8 - - - +
582I ARG 3.1 0.2 - - - -
583I ILE* 1.3 77.9 - - - +
585I LYS* 1.3 58.0 + - - +
587I MSE 3.3 17.7 + - + +
588I ILE* 3.2 28.1 + - - +
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Residues in contact with LYS 585 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E ASP* 3.4 32.6 + - + -
67E LEU* 3.8 15.9 - - + +
68E VAL* 4.4 16.5 - - + +
581I ALA 2.8 20.0 + - - +
582I ARG* 2.9 14.9 + - + +
584I ALA* 1.3 72.5 - - - +
586I GLU* 1.3 61.7 + - - +
588I ILE* 3.9 9.9 + - + +
589I GLU* 3.7 21.2 + - + +
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Residues in contact with GLU 586 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564I LYS* 4.2 21.7 + - + +
582I ARG* 2.8 33.4 + - - +
583I ILE* 3.1 23.1 + - - +
585I LYS* 1.3 77.7 - - - +
587I MSE 1.3 59.4 + - - +
589I GLU* 2.9 23.2 + - + +
590I MSE 3.1 13.0 + - - +
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Residues in contact with MSE 587 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E ASP* 3.3 30.1 - - - +
561I LEU* 4.0 16.8 - - + +
564I LYS* 3.8 26.0 - - + +
565I GLU* 3.3 50.5 - - - +
568I LYS* 3.8 17.7 - - + -
583I ILE* 2.9 20.4 + - - +
584I ALA* 3.3 13.9 + - + +
586I GLU* 1.3 75.7 - - - +
588I ILE* 1.3 51.6 + - - +
590I MSE 3.0 3.0 + - - +
591I LYS* 2.6 45.2 + - + +
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Residues in contact with ILE 588 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E PHE 4.5 13.2 - - - +
26E LEU* 3.5 31.2 - - + -
67E LEU* 4.0 15.7 - - + -
93E ALA* 3.2 34.8 - - + +
94E ASP* 3.3 17.5 - - - +
584I ALA 3.2 16.1 + - - +
585I LYS* 4.0 10.1 - - + +
587I MSE 1.3 76.6 - - - +
589I GLU* 1.3 58.9 + - - +
591I LYS* 3.9 7.8 - - + +
592I LYS* 3.1 30.8 + - + +
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Residues in contact with GLU 589 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585I LYS* 3.7 12.8 + - + +
586I GLU* 2.9 15.8 + - + +
588I ILE* 1.3 82.0 - - + +
590I MSE 1.3 64.7 + - + +
592I LYS* 3.1 41.3 + - - +
593I MSE 3.6 14.4 + - - +
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Residues in contact with MSE 590 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557I LYS* 4.3 39.0 - - + +
558I TRP* 5.5 2.3 - - - -
560I MSE 6.2 1.6 - - + -
561I LEU* 4.2 15.8 - - + +
564I LYS* 3.4 29.6 - - - +
586I GLU 3.1 4.9 + - - +
587I MSE 3.0 5.6 + - - +
589I GLU* 1.3 78.5 - - + +
591I LYS* 1.3 59.7 + - - +
592I LYS 3.3 0.2 - - - -
593I MSE 3.6 38.8 + - + +
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Residues in contact with LYS 591 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E ASP* 2.8 62.6 + - + +
558I TRP* 3.6 43.5 - - + -
561I LEU* 3.6 23.7 - - + +
562I LYS* 6.5 0.4 - - - +
565I GLU* 5.6 1.8 + - - -
587I MSE 2.6 23.4 + - + +
588I ILE* 4.0 6.3 - - - +
590I MSE 1.3 70.3 - - - +
592I LYS* 1.3 64.8 + - - +
593I MSE 3.3 6.3 + - - +
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Residues in contact with LYS 592 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E LEU* 3.3 48.2 + - + +
27E ASP* 5.6 1.2 + - - -
588I ILE* 3.1 19.0 + - + +
589I GLU* 3.1 32.9 + - - +
591I LYS* 1.3 78.2 - - - +
593I MSE 1.3 63.4 + - - +
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Residues in contact with MSE 593 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582H ARG* 3.2 5.9 - - - +
593H MSE 0.0 89.9 - - - +
554I ASN* 5.5 7.6 + - - -
557I LYS* 6.5 0.7 - - + -
558I TRP* 4.8 12.6 + - - -
589I GLU* 3.6 13.3 + - - +
590I MSE 3.6 36.1 + - + +
591I LYS 3.3 5.4 - - - +
592I LYS* 1.3 83.1 - - - +
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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