Contacts of the helix formed by residues 576 - 593 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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571H ALA* 3.0 17.1 + - - +
572H GLU 4.5 0.2 + - - -
574H ARG* 2.8 40.1 + - + +
575H LYS* 1.3 75.2 - - - +
577H PHE* 1.3 56.0 + - - +
578H LEU* 3.3 2.8 + - - +
579H THR* 2.7 53.2 + - - +
580H ALA* 3.3 9.2 + - - +
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Residues in contact with PHE 577 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C THR* 4.3 4.6 + - - +
75C ALA* 5.7 6.7 - - + -
80C LEU* 3.5 35.0 - - + -
81C GLU* 5.9 8.5 - - + -
85C GLY* 5.8 2.2 - - - -
86C VAL* 3.9 14.4 - - + +
572H GLU* 4.1 35.0 - - + -
575H LYS* 3.1 53.9 + - + -
576H ASP* 1.3 74.8 - - - +
578H LEU* 1.3 61.8 + - + +
580H ALA* 3.6 5.0 + - - +
581H ALA* 3.1 24.8 + - - +
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Residues in contact with LEU 578 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C VAL* 4.2 23.7 - - + +
71C THR* 3.8 19.1 - - - +
72C ALA* 4.2 20.6 - - + -
576H ASP* 3.3 2.8 + - - +
577H PHE* 1.3 77.9 - - + +
579H THR* 1.3 63.9 + - - +
581H ALA* 3.5 3.8 - - - +
582H ARG* 3.2 25.5 + - - +
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Residues in contact with THR 579 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571H ALA* 4.6 3.8 - - + -
574H ARG* 4.5 11.0 - - - +
576H ASP* 2.7 41.9 + - - +
578H LEU* 1.3 76.4 - - - +
580H ALA* 1.3 65.1 + - - +
582H ARG* 3.1 10.8 + - + +
583H ILE* 3.0 31.8 + - + +
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Residues in contact with ALA 580 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C VAL* 3.9 23.8 - - + -
568H LYS* 3.5 30.4 - - + +
571H ALA* 4.0 5.5 - - + +
572H GLU* 4.0 12.3 - - + +
576H ASP 3.3 5.4 + - - +
577H PHE* 4.1 4.5 - - - +
579H THR* 1.3 78.4 - - - +
581H ALA* 1.3 57.1 + - - +
583H ILE* 3.1 9.9 + - - +
584H ALA* 2.8 30.5 + - - +
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Residues in contact with ALA 581 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C LEU* 3.7 6.3 - - - +
68C VAL* 3.8 30.7 - - + +
71C THR* 3.9 17.5 - - + +
86C VAL* 4.7 6.2 - - + +
577H PHE 3.1 17.7 + - - +
578H LEU* 3.5 8.7 - - - +
580H ALA* 1.3 76.4 - - - +
582H ARG* 1.3 51.9 + - - +
584H ALA* 2.9 9.8 + - - +
585H LYS* 2.7 33.6 + - - +
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Residues in contact with ARG 582 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C VAL* 3.9 17.5 - - + +
578H LEU 3.2 11.8 + - - +
579H THR* 3.1 12.5 + - + +
581H ALA* 1.3 77.6 - - - +
583H ILE* 1.3 58.1 + - + +
585H LYS* 2.9 8.5 + - + +
586H GLU* 2.8 54.4 + - - +
593I MSE 3.2 27.4 - - - +
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Residues in contact with ILE 583 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564H LYS* 3.5 35.2 - - + +
567H GLU* 3.7 25.1 - - + +
568H LYS* 3.7 29.6 - - + +
571H ALA* 5.1 1.6 - - + -
574H ARG* 6.3 0.4 - - - +
579H THR* 3.0 30.0 + - + +
580H ALA* 3.1 9.2 + - - +
582H ARG* 1.3 73.7 - - + +
584H ALA* 1.3 61.1 + - - +
586H GLU* 3.1 14.8 + - - +
587H MSE 2.8 32.4 + - + +
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Residues in contact with ALA 584 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 3.2 20.4 - - + -
86C VAL* 6.0 0.2 - - + -
90C SER* 3.0 33.0 - - - +
94C ASP* 4.2 1.1 - - - +
568H LYS* 4.4 2.0 - - + +
580H ALA 2.8 13.8 + - - +
581H ALA* 3.3 4.5 - - - +
583H ILE* 1.3 77.6 - - - +
585H LYS* 1.3 60.5 + - - +
587H MSE 3.1 25.1 + - + +
588H ILE* 3.1 18.2 + - + +
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Residues in contact with LYS 585 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ASP* 2.9 39.3 + - + +
67C LEU* 3.9 13.6 - - + +
68C VAL* 4.5 13.6 - - + +
581H ALA 2.7 15.8 + - - +
582H ARG* 3.5 11.0 - - + +
584H ALA* 1.3 73.3 - - - +
586H GLU* 1.3 60.6 + - - +
588H ILE* 3.7 16.5 + - + +
589H GLU* 3.5 21.5 + - + +
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Residues in contact with GLU 586 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564H LYS* 4.1 27.1 + - + +
582H ARG* 2.8 39.1 + - - +
583H ILE* 3.1 19.6 + - - +
585H LYS* 1.3 77.1 - - - +
587H MSE 1.3 61.1 + - + +
589H GLU* 3.1 17.5 + - + +
590H MSE 3.2 10.4 + - - +
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Residues in contact with MSE 587 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ASP* 3.3 32.3 - - - +
561H LEU* 4.1 18.2 - - + +
564H LYS* 4.1 22.9 - - + +
565H GLU* 3.4 48.5 - - - +
568H LYS* 3.6 21.5 - - + +
583H ILE* 2.8 29.6 - - - +
584H ALA* 3.1 12.7 + - + +
586H GLU* 1.3 74.4 - - - +
588H ILE* 1.3 55.0 + - - +
589H GLU 3.0 1.8 - - - -
590H MSE 3.1 2.9 + - - +
591H LYS* 2.6 44.5 + - + +
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Residues in contact with ILE 588 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C PHE* 4.6 14.4 - - + +
26C LEU* 3.7 26.9 - - + -
67C LEU* 4.5 11.9 - - + -
93C ALA* 3.2 32.5 - - + +
94C ASP* 3.4 20.0 - - - +
584H ALA* 3.1 14.1 + - + +
585H LYS* 3.7 17.7 - - + +
587H MSE 1.3 75.9 - - - +
589H GLU* 1.3 67.8 + - - +
591H LYS* 3.8 7.1 - - - +
592H LYS* 3.1 26.5 + - + +
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Residues in contact with GLU 589 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585H LYS* 3.5 11.7 + - + +
586H GLU* 3.1 13.6 + - + +
587H MSE 3.0 0.6 - - - -
588H ILE* 1.3 80.4 - - - +
590H MSE 1.3 67.4 + - + +
592H LYS* 3.1 41.3 + - - +
593H MSE 3.6 12.8 + - - +
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Residues in contact with MSE 590 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557H LYS* 4.1 41.7 - - + +
558H TRP* 5.6 0.9 - - - -
560H MSE 6.1 2.9 - - + -
561H LEU* 4.2 16.4 - - + -
564H LYS* 3.4 30.3 - - - +
586H GLU 3.2 2.6 + - - +
587H MSE 3.1 6.0 + - - +
589H GLU* 1.3 77.3 - - + +
591H LYS* 1.3 62.2 + - - +
593H MSE 3.1 40.6 + - + +
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Residues in contact with LYS 591 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ASP* 2.6 65.4 + - + +
558H TRP* 3.9 34.8 - - + -
561H LEU* 3.5 29.6 - - + -
565H GLU* 5.8 1.2 + - - -
587H MSE 2.6 27.1 + - - +
588H ILE* 3.8 6.5 - - - +
590H MSE 1.3 71.5 - - - +
592H LYS* 1.3 63.5 + - - +
593H MSE 3.3 6.2 + - - +
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Residues in contact with LYS 592 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU* 3.5 50.5 + - + +
97C PRO 6.1 0.9 - - - +
588H ILE* 3.1 14.8 + - + +
589H GLU* 3.1 34.5 + - - +
591H LYS* 1.3 76.3 - - - +
593H MSE 1.3 63.4 + - - +
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Residues in contact with MSE 593 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554H ASN* 5.7 5.5 + - - +
557H LYS* 6.5 0.2 - - + -
558H TRP* 4.6 13.9 + - - -
582H ARG* 3.2 5.9 - - - +
589H GLU* 3.6 12.2 + - - +
590H MSE 3.1 38.2 + - + +
591H LYS 3.9 5.1 - - - +
592H LYS* 1.3 84.5 - - - +
593I MSE 0.0 89.9 - - - +
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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