Contacts of the helix formed by residues 526 - 542 (chain I) in PDB entry 2A07
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 THR 526 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570H GLY* 6.0 1.6 - - - -
571H ALA 3.7 22.9 - - - +
572H VAL* 3.9 12.3 - - + +
573H TRP* 4.5 0.2 - - - -
525I LEU* 1.3 77.4 - - - +
527I LEU* 1.3 65.4 + - - +
528I ASN* 3.6 12.3 + - - +
529I GLU* 2.9 43.5 + - - +
530I ILE* 3.0 20.4 + - - +
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Residues in contact with LEU 527 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552H VAL* 4.5 3.8 - - + -
553H ARG* 4.5 14.1 - - + -
556H LEU* 3.6 30.7 - - + -
571H ALA 4.7 1.8 + - - -
573H TRP* 4.1 17.3 - - - +
525I LEU 4.0 0.2 + - - -
526I THR* 1.3 72.1 - - - +
528I ASN* 1.3 62.5 + - - +
530I ILE* 2.9 9.7 + - + +
531I TYR* 2.8 74.7 + - + +
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Residues in contact with ASN 528 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526I THR* 3.2 9.3 + - - +
527I LEU* 1.3 79.8 - - - +
529I GLU* 1.3 57.9 + - + +
531I TYR* 3.3 19.9 + - - +
532I SER* 2.9 31.0 + - - -
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Residues in contact with GLU 529 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572H VAL* 5.2 0.9 - - - +
524I GLN 4.9 0.9 - - - +
525I LEU* 3.5 30.3 - - + +
526I THR* 2.9 51.8 + - - +
528I ASN* 1.3 74.5 - - + +
530I ILE* 1.3 66.3 + - - +
532I SER* 3.3 9.1 + - - -
533I TRP* 3.0 22.2 + - - +
536I ARG* 4.8 1.9 + - - -
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Residues in contact with ILE 530 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552H VAL* 4.1 17.5 - - + -
556H LEU* 4.4 18.2 - - + -
573H TRP* 4.0 33.4 - - + -
513I ILE* 4.6 7.9 - - + -
516I ALA* 5.2 4.3 - - + -
517I ILE* 4.5 11.0 - - + -
525I LEU* 3.8 24.7 - - + +
526I THR 3.0 16.5 + - - +
527I LEU* 2.9 10.6 + - + +
529I GLU* 1.3 76.5 - - - +
531I TYR* 1.3 58.0 + - + +
533I TRP* 3.3 4.0 + - - +
534I PHE* 2.9 50.9 + - + -
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Residues in contact with TYR 531 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548H TRP* 3.5 24.0 - + + -
549H LYS* 3.9 47.9 + - + +
552H VAL* 4.3 10.8 - - + -
553H ARG* 3.1 32.8 - - + +
527I LEU* 2.8 44.5 + - + +
528I ASN* 3.5 22.0 - - - +
529I GLU 3.2 0.2 - - - -
530I ILE* 1.3 76.1 - - + +
532I SER* 1.3 59.5 - - - +
534I PHE 3.2 0.7 + - - -
535I THR* 2.8 35.0 + - - +
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Residues in contact with SER 532 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528I ASN 2.9 16.4 + - - -
529I GLU* 3.6 10.7 - - - -
530I ILE 3.3 0.2 - - - -
531I TYR* 1.3 75.6 - - - +
533I TRP* 1.3 62.6 + - - +
535I THR* 3.3 7.5 + - - -
536I ARG* 3.1 47.9 + - - +
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Residues in contact with TRP 533 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506H PRO* 4.7 9.1 - - + +
507H PHE* 4.0 10.1 - + - -
512I LEU* 3.6 50.3 - - + -
515I GLN* 3.8 26.0 - - + -
516I ALA* 3.4 37.9 - - + +
519I GLU* 3.9 12.5 + - - +
525I LEU* 5.1 2.9 - - + -
529I GLU 3.0 13.2 + - - +
530I ILE* 3.5 7.9 - - - +
531I TYR 3.2 0.2 - - - -
532I SER* 1.3 77.0 - - - +
534I PHE* 1.3 76.2 + + - +
536I ARG* 3.3 25.5 + - + +
537I THR* 2.9 54.9 + - + -
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Residues in contact with PHE 534 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548H TRP* 3.4 36.3 - + + -
552H VAL* 3.6 20.9 - - + -
509I TYR* 4.0 17.9 - + - -
512I LEU* 3.6 32.3 - - + -
513I ILE* 3.9 20.9 - - + -
516I ALA* 5.2 0.2 - - + -
530I ILE* 2.9 43.9 + - + +
533I TRP* 1.3 94.3 - + - +
535I THR* 1.3 67.7 + - - +
537I THR* 4.2 2.7 - - + -
538I PHE* 2.8 49.9 + + - +
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Residues in contact with THR 535 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548H TRP* 3.5 20.2 - - + -
549H LYS* 4.6 3.6 + - - -
531I TYR* 2.8 28.5 + - - +
532I SER* 3.5 9.5 - - - -
533I TRP 3.2 0.2 - - - -
534I PHE* 1.3 74.1 - - - +
536I ARG* 1.3 64.1 + - + +
538I PHE* 4.0 2.1 - - - +
539I ALA* 3.1 24.3 + - + +
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Residues in contact with ARG 536 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506H PRO* 6.4 2.2 - - + -
529I GLU 4.8 1.6 + - - -
532I SER* 3.1 37.2 + - - +
533I TRP* 3.6 36.1 - - - +
534I PHE 3.2 0.2 - - - -
535I THR* 1.3 80.0 - - + +
537I THR* 1.3 62.1 + - - +
539I ALA* 3.4 7.1 + - - +
540I TYR* 3.1 22.0 + - - +
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Residues in contact with THR 537 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506H PRO* 5.1 4.0 - - - +
507H PHE* 3.7 27.5 - - + -
541H PHE* 3.9 16.2 - - + -
512I LEU* 4.7 1.8 - - + -
533I TRP* 2.9 53.1 + - + -
534I PHE* 3.3 4.5 + - + -
536I ARG* 1.3 73.6 - - - +
538I PHE* 1.3 69.8 + - + +
540I TYR* 3.1 15.0 + - - +
541I PHE* 3.2 30.7 + - + -
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Residues in contact with PHE 538 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540H TYR* 4.7 7.0 - + - -
541H PHE* 3.3 66.6 - + + +
544H ASN* 3.5 23.3 - - + -
545H ALA* 3.8 14.1 - - + -
548H TRP* 3.6 33.0 - + + +
509I TYR* 4.7 2.7 - + - -
512I LEU* 5.0 0.4 - - + -
534I PHE* 2.8 51.7 + + - +
535I THR* 4.2 2.5 - - - +
537I THR* 1.3 75.3 - - + +
539I ALA* 1.3 62.0 + - - +
541I PHE* 3.3 3.8 + - - +
542I ARG* 3.2 20.8 + - - +
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Residues in contact with ALA 539 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535I THR* 3.1 20.6 + - + +
536I ARG* 3.5 8.5 - - - +
537I THR 3.2 0.2 - - - -
538I PHE* 1.3 78.1 - - - +
540I TYR* 1.3 63.3 + - - +
542I ARG* 3.2 23.3 + - - +
543I ARG* 4.7 1.6 + - - -
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Residues in contact with TYR 540 (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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13D G 2.8 31.4 + - - -
506H PRO* 6.3 2.9 - - + -
507H PHE* 3.7 26.7 - + + -
508H THR* 3.4 15.8 - - - -
509H TYR* 3.4 14.8 + + - -
512H LEU* 4.0 21.4 - - + +
538H PHE* 5.2 2.2 - + - -
536I ARG 3.1 13.5 + - - +
537I THR* 3.1 11.6 + - - +
539I ALA* 1.3 77.7 - - - +
541I PHE* 1.3 78.0 + + + +
542I ARG 3.4 0.7 + - - -
543I ARG* 2.8 63.1 + - - +
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Residues in contact with PHE 541 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507H PHE* 4.2 15.7 - + - -
512H LEU* 3.8 38.8 - - + -
537H THR* 3.8 16.6 - - + -
538H PHE* 3.1 44.7 - + + +
541H PHE* 3.4 62.7 - + + +
507I PHE* 4.8 0.9 - + - -
537I THR* 3.2 32.7 + - + -
538I PHE 3.3 5.4 + - - +
539I ALA 3.2 0.6 - - - -
540I TYR* 1.3 87.8 - + - +
542I ARG* 1.3 51.1 + - - +
543I ARG 2.7 19.2 + - - +
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Residues in contact with ARG 542 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538I PHE 3.2 10.0 + - - +
539I ALA* 3.2 20.2 + - - +
540I TYR 3.3 0.2 - - - -
541I PHE* 1.3 73.6 - - - +
543I ARG* 1.3 60.2 + - - +
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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