Contacts of the helix formed by residues 526 - 542 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525F LEU* 1.3 78.4 - - - +
527F LEU* 1.3 65.6 + - - +
528F ASN* 3.7 7.8 + - - +
529F GLU* 3.1 35.5 + - - +
530F ILE* 3.0 19.5 + - - +
569G LYS 6.1 0.7 - - - +
570G GLY* 5.9 1.6 - - - -
571G ALA 3.6 24.0 - - - +
572G VAL* 3.9 13.2 - - + +
573G TRP* 4.4 0.7 - - - -
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Residues in contact with LEU 527 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526F THR* 1.3 73.4 - - - +
528F ASN* 1.3 62.5 + - - +
530F ILE* 2.9 10.0 + - + +
531F TYR* 2.9 71.7 + - + +
552G VAL* 4.6 3.8 - - + -
553G ARG* 4.5 13.9 - - + -
556G LEU* 3.6 30.1 - - + -
571G ALA 4.7 1.4 + - - -
573G TRP* 4.1 16.9 - - + +
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Residues in contact with ASN 528 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526F THR* 3.3 8.1 + - - +
527F LEU* 1.3 85.6 - - - +
529F GLU* 1.3 57.7 + - + +
531F TYR* 3.2 20.2 + - - +
532F SER* 2.9 30.8 + - - +
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Residues in contact with GLU 529 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524F GLN 4.4 1.4 - - - +
525F LEU* 3.6 29.6 - - + +
526F THR* 3.1 44.0 + - - +
528F ASN* 1.3 74.6 - - + +
530F ILE* 1.3 64.9 + - - +
532F SER* 3.3 9.8 + - - +
533F TRP* 3.0 22.9 + - - +
536F ARG* 4.9 1.4 + - - -
572G VAL* 5.7 0.3 - - - +
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Residues in contact with ILE 530 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513F ILE* 4.6 7.0 - - + -
516F ALA* 5.3 5.4 - - + -
517F ILE* 4.5 10.5 - - + -
525F LEU* 3.8 21.8 - - + +
526F THR 3.0 14.0 + - - +
527F LEU* 2.9 9.9 + - + +
529F GLU* 1.3 76.5 - - - +
531F TYR* 1.3 59.4 + - + +
533F TRP* 3.2 6.8 + - - +
534F PHE* 2.9 51.3 + - + -
552G VAL* 4.0 18.2 - - + -
556G LEU* 4.4 17.0 - - + -
573G TRP* 4.1 33.0 - - + -
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Residues in contact with TYR 531 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527F LEU* 2.9 45.1 + - + +
528F ASN* 3.4 22.2 - - - +
530F ILE* 1.3 77.7 - - + +
532F SER* 1.3 60.6 + - - +
534F PHE 3.2 0.5 + - - -
535F THR* 2.8 35.1 + - - +
548G TRP* 3.5 25.4 - + + -
549G LYS* 4.0 38.8 - - + +
552G VAL* 4.3 11.4 - - + -
553G ARG* 2.7 44.2 + - - +
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Residues in contact with SER 532 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528F ASN* 2.9 15.6 + - - +
529F GLU* 3.5 12.0 - - - -
531F TYR* 1.3 75.8 - - - +
533F TRP* 1.3 63.2 + - - +
535F THR* 3.4 7.6 + - - -
536F ARG* 3.1 46.1 + - - +
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Residues in contact with TRP 533 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512F LEU* 3.6 49.8 - - + -
515F GLN* 3.9 26.9 - - + -
516F ALA* 3.4 37.3 + - + +
519F GLU* 4.1 13.6 + - + +
525F LEU* 5.2 3.1 - - + -
529F GLU 3.0 12.8 + - - +
530F ILE* 3.4 8.1 - - - +
532F SER* 1.3 78.2 - - - +
534F PHE* 1.3 75.2 + + - +
536F ARG* 3.3 27.7 + - - +
537F THR* 2.9 53.2 + - + -
506G PRO* 4.8 8.0 - - + +
507G PHE* 3.9 9.2 - + - -
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Residues in contact with PHE 534 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509F TYR* 4.1 18.2 - + - -
512F LEU* 3.6 32.1 - - + -
513F ILE* 3.9 20.4 - - + -
516F ALA* 5.2 0.2 - - + -
530F ILE* 2.9 41.4 + - + +
531F TYR 3.2 2.0 + - - +
533F TRP* 1.3 94.8 - + - +
535F THR* 1.3 61.0 + - - +
537F THR* 4.2 2.5 - - - -
538F PHE* 2.7 56.2 + + - -
548G TRP* 3.4 35.2 - + + -
552G VAL* 3.6 20.0 - - + -
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Residues in contact with THR 535 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531F TYR* 2.8 26.2 + - - +
532F SER* 3.6 8.2 - - - -
533F TRP 3.3 0.2 - - - -
534F PHE* 1.3 73.5 - - - +
536F ARG* 1.3 65.7 + - + +
538F PHE* 3.9 2.3 - - - +
539F ALA* 3.0 26.0 + - + +
548G TRP* 3.5 19.6 - - + -
549G LYS* 4.7 3.6 + - - -
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Residues in contact with ARG 536 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529F GLU 4.9 1.6 + - - -
532F SER* 3.1 33.7 + - - +
533F TRP* 3.6 37.3 - - - +
535F THR* 1.3 79.8 - - + +
537F THR* 1.3 63.3 + - - +
539F ALA* 3.3 7.3 + - - +
540F TYR* 3.1 22.2 + - - +
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Residues in contact with THR 537 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512F LEU* 4.7 1.6 - - + -
533F TRP* 2.9 52.6 + - + -
534F PHE* 3.1 5.1 + - - -
536F ARG* 1.3 74.1 - - - +
538F PHE* 1.3 70.0 + - + +
540F TYR* 3.1 15.2 + - - +
541F PHE* 3.3 22.2 - - + -
506G PRO* 5.8 0.7 - - - +
507G PHE* 3.8 28.0 - - + -
541G PHE* 3.9 24.9 - - + -
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Residues in contact with PHE 538 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509F TYR* 4.8 3.1 - + - -
512F LEU* 5.0 0.7 - - + -
534F PHE* 2.7 52.3 + + - +
535F THR* 4.1 2.7 - - - +
537F THR* 1.3 75.5 - - + +
539F ALA* 1.3 62.6 + - - +
541F PHE* 3.2 11.1 + - - +
542F ARG* 3.3 13.0 + - - +
540G TYR* 4.7 7.0 - + - -
541G PHE* 3.3 65.1 - + + +
544G ASN* 3.6 22.9 - - + -
545G ALA* 3.8 9.6 - - + -
548G TRP* 3.6 37.2 - + + +
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Residues in contact with ALA 539 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535F THR* 3.0 20.6 + - + +
536F ARG* 3.6 7.9 - - - +
537F THR 3.2 0.2 - - - -
538F PHE* 1.3 76.2 - - - +
540F TYR* 1.3 63.9 + - - +
542F ARG* 3.2 23.5 + - - +
543F ARG* 4.7 2.1 + - - -
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Residues in contact with TYR 540 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B G 2.7 31.7 + - - -
536F ARG 3.1 13.2 + - - +
537F THR* 3.1 12.1 + - - +
539F ALA* 1.3 77.1 - - - +
541F PHE* 1.3 78.4 + + + +
542F ARG 3.4 0.7 + - - -
543F ARG* 2.8 59.3 + - - +
507G PHE* 3.6 31.6 - - + -
508G THR* 3.4 11.3 - - - -
509G TYR* 3.4 22.3 + + - -
512G LEU* 4.1 14.8 - - + +
538G PHE* 5.3 2.0 - + - -
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Residues in contact with PHE 541 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507F PHE* 4.9 1.1 - + - -
537F THR* 3.3 30.2 + - + -
538F PHE 3.2 6.0 + - - +
540F TYR* 1.3 90.8 - + - +
542F ARG* 1.3 51.6 + - - +
543F ARG 2.7 19.4 + - - +
507G PHE* 4.1 17.9 - + - -
512G LEU* 4.0 33.2 - - + -
537G THR* 3.7 19.5 - - + -
538G PHE* 3.2 44.8 - + + +
541G PHE* 3.4 60.2 - + + +
542G ARG 5.9 0.2 + - - -
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Residues in contact with ARG 542 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538F PHE 3.3 10.0 + - - +
539F ALA* 3.2 19.8 + - - +
540F TYR 3.3 0.2 - - - -
541F PHE* 1.3 73.8 - - - +
543F ARG* 1.3 62.6 + - - +
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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