Contacts of the helix formed by residues 526 - 544 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525H LEU* 1.3 76.0 - - - +
527H LEU* 1.3 65.6 + - - +
528H ASN* 3.5 8.7 + - - +
529H GLU* 3.0 41.7 + - - +
530H ILE* 3.0 20.8 + - - +
569I LYS* 6.1 4.7 - - + -
571I ALA 3.2 26.9 - - - +
572I VAL* 4.0 12.3 - - + +
573I TRP* 4.4 0.9 - - - +
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Residues in contact with LEU 527 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526H THR* 1.3 74.3 - - - +
528H ASN* 1.3 57.3 + - - +
530H ILE* 3.3 5.5 + - + +
531H TYR* 3.0 67.4 + - + +
552I VAL* 4.4 5.8 - - + -
553I ARG* 4.5 14.6 - - + -
556I LEU* 3.8 26.0 - - + -
571I ALA 4.6 1.0 + - - -
573I TRP* 4.0 19.3 - - + +
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Residues in contact with ASN 528 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526H THR* 3.1 8.5 + - - +
527H LEU* 1.3 82.0 - - - +
529H GLU* 1.3 59.6 + - - +
531H TYR* 3.2 17.7 + - - +
532H SER* 2.9 38.2 + - - -
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Residues in contact with GLU 529 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524H GLN 4.0 1.2 - - - +
525H LEU* 3.1 41.5 - - + +
526H THR* 3.0 36.5 + - - +
528H ASN* 1.3 77.6 - - + +
530H ILE* 1.3 64.3 + - - +
532H SER* 3.3 9.2 + - - -
533H TRP* 3.1 22.2 + - - +
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Residues in contact with ILE 530 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513H ILE* 4.5 9.9 - - + -
516H ALA* 5.3 3.6 - - + -
517H ILE* 4.4 13.7 - - + -
525H LEU* 3.8 22.2 - - + +
526H THR 3.0 17.0 + - - +
527H LEU* 3.6 8.5 - - + +
529H GLU* 1.3 75.4 - - - +
531H TYR* 1.3 65.5 + - - +
533H TRP* 3.1 7.4 + - - +
534H PHE* 2.9 46.1 + - + -
552I VAL* 4.0 19.5 - - + -
556I LEU* 4.2 17.3 - - + -
573I TRP* 4.2 27.4 - - + -
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Residues in contact with TYR 531 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527H LEU* 3.0 45.4 + - + +
528H ASN* 3.3 22.9 - - - +
530H ILE* 1.3 77.5 - - + +
532H SER* 1.3 56.9 + - - +
534H PHE 3.3 0.9 + - - -
535H THR* 2.8 34.0 + - - +
548I TRP* 3.4 21.6 - + + -
549I LYS* 3.7 46.8 - - + +
552I VAL* 4.3 10.8 - - + -
553I ARG* 3.2 39.0 + - - +
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Residues in contact with SER 532 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528H ASN* 2.9 26.1 + - - -
529H GLU* 3.5 12.0 - - - -
530H ILE 3.2 0.2 - - - -
531H TYR* 1.3 75.8 - - - +
533H TRP* 1.3 63.5 + - - +
535H THR* 3.2 8.5 + - - -
536H ARG* 3.0 28.8 + - - +
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Residues in contact with TRP 533 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512H LEU* 3.7 43.3 - - + -
515H GLN* 3.8 20.4 - - + -
516H ALA* 3.4 37.8 + - + +
519H GLU* 4.9 11.3 + - - +
525H LEU* 5.3 3.6 - - + -
529H GLU 3.1 13.1 + - - +
530H ILE* 3.1 7.6 + - - +
532H SER* 1.3 76.8 - - - +
534H PHE* 1.3 80.3 + + - +
536H ARG* 3.3 10.0 + - - +
537H THR* 2.9 54.0 + - + -
506I PRO* 3.8 29.2 - - + +
507I PHE* 4.0 5.8 - + - -
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Residues in contact with PHE 534 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509H TYR* 3.7 26.9 - + - -
512H LEU* 3.7 27.4 - - + -
513H ILE* 3.8 22.0 - - + -
516H ALA* 5.1 0.7 - - + -
530H ILE* 2.9 41.3 + - + +
531H TYR 3.3 1.3 + - - +
533H TRP* 1.3 91.6 - + - +
535H THR* 1.3 61.2 + - - +
537H THR* 4.2 2.0 - - - -
538H PHE* 2.8 59.3 + + - +
548I TRP* 3.5 30.5 - + + -
552I VAL* 3.7 17.5 - - + -
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Residues in contact with THR 535 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531H TYR* 2.8 21.2 + - - +
532H SER* 3.2 12.1 + - - -
534H PHE* 1.3 76.9 - - - +
536H ARG* 1.3 64.0 + - + +
538H PHE* 3.5 2.2 + - - +
539H ALA* 3.0 29.5 + - + +
548I TRP* 3.5 20.4 - - + -
549I LYS* 4.7 3.6 + - - -
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Residues in contact with ARG 536 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532H SER* 3.0 15.8 + - - +
533H TRP* 3.6 12.6 - - - +
535H THR* 1.3 77.1 - - + +
537H THR* 1.3 62.5 + - - +
539H ALA* 3.3 6.6 + - - +
540H TYR* 3.0 22.9 + - - +
543H ARG* 5.0 2.1 + - - -
503I VAL* 3.7 47.8 + - - +
504I ARG 4.4 4.8 + - - -
505I PRO* 5.4 1.0 - - - +
506I PRO* 4.5 24.0 - - + +
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Residues in contact with THR 537 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512H LEU* 5.0 0.7 - - + -
533H TRP* 2.9 41.2 + - + -
534H PHE* 3.6 4.9 - - - -
536H ARG* 1.3 76.7 - - - +
538H PHE* 1.3 67.1 + - + +
540H TYR* 3.2 14.3 + - - +
541H PHE* 3.2 23.0 - - + -
506I PRO* 3.5 19.5 - - - +
507I PHE* 3.6 25.4 - - + -
541I PHE* 3.8 24.0 - - + -
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Residues in contact with PHE 538 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509H TYR* 4.1 11.7 - + - -
512H LEU* 4.9 2.7 - - + -
534H PHE* 2.8 50.8 + + - +
535H THR* 4.3 2.0 - - - +
537H THR* 1.3 77.8 - - + +
539H ALA* 1.3 63.7 + - - +
541H PHE* 3.4 7.7 + - - +
542H ARG* 3.1 23.1 + - - +
540I TYR* 5.2 2.0 - + - -
541I PHE* 3.1 53.9 - + - +
543I ARG* 3.7 38.1 - - + +
548I TRP* 3.7 33.9 - + + +
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Residues in contact with ALA 539 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535H THR* 3.0 23.6 + - + +
536H ARG* 3.5 7.4 - - - +
538H PHE* 1.3 77.6 - - - +
540H TYR* 1.3 62.5 + - - +
542H ARG* 3.1 9.9 + - - +
543H ARG* 2.9 45.3 + - + +
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Residues in contact with TYR 540 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536H ARG 3.0 11.6 + - - +
537H THR* 3.2 11.6 + - - +
539H ALA* 1.3 77.6 - - - +
541H PHE* 1.3 85.9 + + + +
543H ARG* 3.4 22.6 + - - +
544H ASN* 2.8 47.9 + - - +
505I PRO* 5.9 3.4 - - + -
506I PRO* 6.2 4.7 - - + -
507I PHE* 3.7 27.1 - - + -
508I THR* 3.6 3.2 - - - -
509I TYR* 3.4 47.1 + + - -
512I LEU* 4.1 19.9 - - + +
538I PHE* 4.7 7.0 - + - -
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Residues in contact with PHE 541 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537H THR* 3.2 30.3 - - + -
538H PHE 3.4 4.2 + - - +
539H ALA 3.3 0.6 - - - -
540H TYR* 1.3 89.2 - + - +
542H ARG* 1.3 63.9 + - - +
545H ALA* 3.1 21.5 + - - +
507I PHE* 4.1 13.5 - + - -
512I LEU* 4.0 26.5 - - + -
537I THR* 3.9 15.3 - - + -
538I PHE* 3.3 42.6 - + + +
541I PHE* 3.4 68.4 - + + +
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Residues in contact with ARG 542 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538H PHE 3.1 14.6 + - - +
539H ALA* 3.1 11.6 + - - +
541H PHE* 1.3 76.7 - - - +
543H ARG* 1.3 67.1 + - - +
544H ASN 3.3 0.9 + - - -
545H ALA* 3.4 16.5 + - - +
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Residues in contact with ARG 543 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536H ARG 5.0 2.0 + - - -
539H ALA* 2.9 36.7 + - + +
540H TYR* 3.6 33.7 - - - +
542H ARG* 1.3 80.3 - - + +
544H ASN* 1.3 71.4 + - - +
545H ALA 3.8 0.5 + - - -
546H ALA 5.0 1.2 + - - -
547H THR* 4.6 4.5 + - - +
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Residues in contact with ASN 544 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540H TYR* 2.8 43.9 + - + +
543H ARG* 1.3 93.5 + - - +
545H ALA* 1.3 63.8 + - - +
546H ALA 3.1 5.0 + - - -
547H THR* 3.2 21.1 + - - +
548H TRP* 3.3 9.5 + - - -
509I TYR* 3.1 29.0 + - + +
538I PHE* 3.5 17.5 - - + -
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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