Contacts of the helix formed by residues 526 - 544 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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570F GLY* 5.9 2.0 - - - -
571F ALA 3.9 17.5 - - - +
572F VAL* 3.8 22.7 - - + -
573F TRP* 4.8 0.4 - - - +
525G LEU* 1.3 77.4 - - - +
527G LEU* 1.3 65.4 + - - +
528G ASN* 3.6 7.7 + - - +
529G GLU* 2.7 46.0 + - - +
530G ILE* 3.0 20.9 + - - +
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Residues in contact with LEU 527 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552F VAL* 4.3 5.6 - - + -
553F ARG* 4.6 13.7 - - + -
556F LEU* 3.7 27.6 - - + -
571F ALA 4.8 2.2 + - - -
573F TRP* 4.3 14.2 - - - +
526G THR* 1.3 74.6 - - - +
528G ASN* 1.3 57.6 + - - +
530G ILE* 3.4 7.1 + - + +
531G TYR* 3.0 66.6 + - + +
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Residues in contact with ASN 528 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526G THR* 3.1 8.3 + - - +
527G LEU* 1.3 79.3 - - - +
529G GLU* 1.3 61.0 + - + +
531G TYR* 3.2 19.5 + - - +
532G SER* 2.9 37.0 + - - -
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Residues in contact with GLU 529 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572F VAL* 5.2 0.9 - - - +
524G GLN 4.7 1.0 - - - +
525G LEU* 3.7 29.5 - - + +
526G THR* 2.7 53.7 + - - +
528G ASN* 1.3 76.9 - - + +
530G ILE* 1.3 66.5 + - - +
532G SER* 3.4 8.7 + - - -
533G TRP* 3.1 21.7 + - - +
536G ARG* 5.1 1.4 + - - -
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Residues in contact with ILE 530 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552F VAL* 4.1 17.3 - - + -
556F LEU* 4.3 18.4 - - + -
573F TRP* 4.3 8.5 - - + -
513G ILE* 4.3 24.0 - - + -
516G ALA* 5.2 3.4 - - + -
517G ILE* 4.4 9.2 - - + -
525G LEU* 3.7 33.0 - - + +
526G THR 3.0 18.8 + - - +
527G LEU* 3.7 8.1 - - + +
529G GLU* 1.3 75.3 - - - +
531G TYR* 1.3 63.5 + - - +
533G TRP* 3.1 7.8 + - - +
534G PHE* 3.0 47.6 + - + -
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Residues in contact with TYR 531 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548F TRP* 3.4 22.1 - + + -
549F LYS* 3.7 43.6 - - + +
552F VAL* 4.3 15.7 - - + -
553F ARG* 3.2 39.4 + - + +
527G LEU* 3.0 44.9 + - + +
528G ASN* 3.2 23.8 + - - +
530G ILE* 1.3 78.3 - - - +
532G SER* 1.3 56.6 + - - +
534G PHE 3.4 0.7 + - - -
535G THR* 2.9 33.9 + - - -
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Residues in contact with SER 532 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528G ASN* 2.9 23.2 + - - -
529G GLU* 3.6 12.2 - - - -
530G ILE 3.2 0.2 - - - -
531G TYR* 1.3 76.0 - - - +
533G TRP* 1.3 62.4 + - - +
535G THR* 3.3 7.8 + - - -
536G ARG* 3.0 46.4 + - - +
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Residues in contact with TRP 533 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506F PRO* 3.6 31.4 - - + +
507F PHE* 3.9 13.9 - + - -
512G LEU* 3.7 40.2 - - + -
515G GLN* 3.7 20.0 - - + -
516G ALA* 3.4 40.7 - - + +
519G GLU* 4.0 11.6 + - + +
525G LEU* 5.3 2.9 - - + -
529G GLU 3.1 12.8 + - - +
530G ILE* 3.1 9.3 + - - +
532G SER* 1.3 77.2 - - - +
534G PHE* 1.3 73.1 + + - +
536G ARG* 3.4 25.4 + - - +
537G THR* 2.9 50.2 + - + -
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Residues in contact with PHE 534 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548F TRP* 3.5 30.3 - + + -
552F VAL* 3.7 19.1 - - + -
509G TYR* 3.7 25.6 - + - -
512G LEU* 3.7 32.3 - - + -
513G ILE* 3.8 20.6 - - + -
516G ALA* 5.1 0.2 - - + -
530G ILE* 3.0 44.5 + - + +
533G TRP* 1.3 93.0 - + - +
535G THR* 1.3 57.8 + - - +
537G THR* 4.2 2.2 - - - -
538G PHE* 2.7 61.1 + + - +
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Residues in contact with THR 535 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548F TRP* 3.5 19.9 - - + +
549F LYS* 4.6 3.8 + - - -
531G TYR* 2.9 23.7 + - - +
532G SER* 3.5 9.3 - - - -
534G PHE* 1.3 77.1 - - - +
536G ARG* 1.3 63.7 + - + +
538G PHE* 4.0 2.4 - - - +
539G ALA* 3.0 29.3 + - + +
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Residues in contact with ARG 536 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503F VAL* 4.8 20.4 - - - +
506F PRO* 4.7 20.9 - - + +
529G GLU 5.1 1.0 + - - -
532G SER* 3.0 38.6 + - - +
533G TRP* 3.6 34.5 - - - +
535G THR* 1.3 78.4 - - + +
537G THR* 1.3 64.1 - - - +
539G ALA* 3.4 6.7 + - - +
540G TYR* 3.1 22.3 + - - +
543G ARG* 4.9 2.6 + - - -
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Residues in contact with THR 537 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506F PRO* 3.6 15.8 - - - +
507F PHE* 3.6 28.3 - - + -
541F PHE* 3.7 24.0 - - + -
512G LEU* 5.0 0.2 - - + -
533G TRP* 2.9 46.9 + - + -
534G PHE* 3.2 5.4 + - - -
536G ARG* 1.3 74.9 - - - +
538G PHE* 1.3 68.2 + - + +
540G TYR* 3.2 14.2 + - - +
541G PHE* 3.2 20.5 - - + -
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Residues in contact with PHE 538 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540F TYR* 5.3 2.0 - + - -
541F PHE* 3.2 54.1 - + - +
543F ARG* 3.6 38.6 - - + +
548F TRP* 3.7 34.8 - + + +
509G TYR* 4.1 11.2 - + - -
512G LEU* 5.0 2.2 - - + -
534G PHE* 2.7 53.8 + + - +
535G THR* 4.3 2.7 - - - +
537G THR* 1.3 78.8 - - + +
539G ALA* 1.3 61.8 + - - +
541G PHE* 3.3 8.1 + - - +
542G ARG* 3.1 22.4 + - - +
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Residues in contact with ALA 539 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535G THR* 3.0 23.8 + - + +
536G ARG* 3.6 7.2 - - - +
538G PHE* 1.3 79.1 - - - +
540G TYR* 1.3 63.2 + - - +
542G ARG* 3.2 8.5 + - - +
543G ARG* 2.9 45.1 + - + +
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Residues in contact with TYR 540 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505F PRO* 5.8 3.8 - - + -
506F PRO* 6.1 4.5 - - + -
507F PHE* 3.7 30.7 - - + +
508F THR* 3.6 2.0 - - - -
509F TYR* 3.4 46.7 + + - -
512F LEU* 4.1 20.1 - - + +
538F PHE* 4.7 7.4 - + - -
536G ARG 3.1 14.0 + - - +
537G THR* 3.2 11.2 + - - +
539G ALA* 1.3 76.5 - - - +
541G PHE* 1.3 85.1 + + - +
543G ARG* 3.6 22.6 - - - +
544G ASN* 2.9 47.4 + - - +
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Residues in contact with PHE 541 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507F PHE* 4.1 14.4 - + - -
512F LEU* 3.9 28.9 - - + -
537F THR* 3.9 17.5 - - + -
538F PHE* 3.3 44.0 - + + +
541F PHE* 3.4 63.3 - + + +
537G THR* 3.2 31.9 - - + -
538G PHE 3.3 5.5 + - - +
540G TYR* 1.3 90.7 - + - +
542G ARG* 1.3 61.2 + - - +
545G ALA* 3.1 21.3 + - - +
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Residues in contact with ARG 542 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538G PHE 3.1 17.3 + - - +
539G ALA* 3.6 7.9 - - - +
541G PHE* 1.3 74.9 - - - +
543G ARG* 1.3 68.6 + - + +
544G ASN 3.3 0.5 + - - -
545G ALA* 3.5 16.1 + - - +
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Residues in contact with ARG 543 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536G ARG 4.9 2.2 + - - -
539G ALA* 2.9 35.9 + - + +
540G TYR* 3.6 36.0 - - - +
542G ARG* 1.3 79.3 - - + +
544G ASN* 1.3 73.9 + - - +
545G ALA 3.9 0.5 + - - -
546G ALA 5.1 0.9 + - - -
547G THR* 4.6 5.0 + - - +
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Residues in contact with ASN 544 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509F TYR* 3.2 25.6 + - + +
538F PHE* 3.6 17.8 - - + -
540G TYR* 2.9 44.3 + - + +
543G ARG* 1.3 94.2 + - - +
545G ALA* 1.3 62.8 + - - +
546G ALA 3.1 4.4 + - - -
547G THR* 3.2 24.0 + - - +
548G TRP* 3.3 8.8 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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