Contacts of the helix formed by residues 525 - 538 (chain A) in PDB entry 1AD6
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 ALA 525 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518A LEU* 3.6 20.4 - - + +
523A LEU 3.4 3.0 + - - -
524A LYS* 1.3 72.4 - - - +
526A PHE* 1.3 59.0 + - - +
528A PHE* 3.5 0.7 - - - +
529A TYR* 3.0 26.2 + - - +
557A ILE* 3.4 32.4 - - + +
560A SER* 4.8 8.1 - - - +
561A LEU* 5.8 1.3 - - + -
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Residues in contact with PHE 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A LYS* 3.1 8.7 - - + +
525A ALA* 1.3 77.3 - - - +
527A ASP* 1.3 65.4 + - - +
529A TYR* 3.3 35.5 - + + +
530A LYS* 3.1 40.0 + - + +
557A ILE* 4.3 2.4 - - + +
561A LEU* 3.5 44.0 - - + -
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Residues in contact with ASP 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A ILE* 3.8 23.3 - - + +
485A SER* 3.4 16.7 + - - +
523A LEU* 3.8 17.8 - - + +
524A LYS* 3.0 47.5 + - - +
526A PHE* 1.3 75.4 - - - +
528A PHE* 1.3 68.0 + - - +
530A LYS* 2.7 51.7 + - - +
531A VAL 3.6 2.4 + - - -
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Residues in contact with PHE 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A SER* 4.4 5.8 - - - +
488A ALA* 3.5 31.2 - - + -
489A CYS* 3.6 20.4 - - + -
492A GLU* 3.9 21.3 - - + -
514A PHE* 3.2 32.5 - + - -
517A ILE* 3.8 2.9 - - + -
518A LEU* 3.2 29.4 - - + -
523A LEU* 3.6 12.0 - - + +
524A LYS 2.9 11.3 + - - +
525A ALA 3.5 9.2 - - - +
527A ASP* 1.3 77.4 - - - +
529A TYR* 1.3 65.4 + - - +
531A VAL* 3.2 21.1 + - - +
532A ILE* 3.6 21.4 - - + +
550A LEU* 5.3 1.6 - - + -
553A CYS* 4.5 5.4 - - + -
557A ILE* 4.0 4.7 - - + -
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Residues in contact with TYR 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A ALA 3.0 15.4 + - - +
526A PHE* 3.3 39.3 - + - +
528A PHE* 1.3 77.7 - - - +
530A LYS* 1.3 68.3 + - + +
531A VAL 3.1 1.4 + - - -
532A ILE* 3.2 25.7 + - - +
533A GLU 4.6 1.4 + - - -
554A GLU* 3.0 61.0 + - + +
557A ILE* 4.2 14.1 - - + -
558A MET* 5.2 7.6 - - + -
561A LEU* 6.4 0.4 - - + -
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Residues in contact with LYS 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A ILE* 4.6 13.1 - - - +
526A PHE* 3.1 34.8 + - + +
527A ASP* 2.7 40.8 + - - +
529A TYR* 1.3 85.6 - - + +
531A VAL* 1.3 57.8 + - - +
532A ILE 3.5 0.2 - - - -
533A GLU* 5.1 2.3 + - - +
534A SER* 5.4 4.3 + - - -
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Residues in contact with VAL 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A MET* 4.9 6.3 - - - -
482A PHE* 4.9 13.0 - - + -
485A SER* 3.5 32.3 - - - +
486A LEU* 4.3 30.7 - - + +
489A CYS* 3.8 20.0 - - + -
527A ASP 3.6 0.8 + - - -
528A PHE* 3.2 13.8 + - - +
529A TYR 3.1 1.0 + - - -
530A LYS* 1.3 77.8 - - - +
532A ILE* 1.3 73.2 + - - +
533A GLU 3.6 0.4 - - - -
534A SER* 3.6 6.7 + - - -
535A PHE* 2.9 21.4 + - + +
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Residues in contact with ILE 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A CYS* 4.6 6.7 - - - -
528A PHE* 3.6 30.5 - - + +
529A TYR* 3.2 21.8 + - - +
531A VAL* 1.3 78.0 - - - +
533A GLU* 1.3 68.2 + - - +
535A PHE* 2.9 17.0 + - - +
536A ILE* 2.9 21.6 + - + +
550A LEU* 3.5 47.1 - - + +
553A CYS* 4.6 1.1 - - + -
554A GLU* 3.7 37.9 - - + +
557A ILE* 4.9 0.4 - - + -
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Residues in contact with GLU 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A TYR 4.6 1.6 + - - -
530A LYS 5.1 2.6 + - - +
531A VAL 3.6 0.6 - - - -
532A ILE* 1.3 79.2 - - - +
534A SER* 1.3 64.8 + - - +
536A ILE* 3.4 3.8 + - - -
537A LYS* 2.8 63.3 + - + +
554A GLU* 4.3 11.6 + - - +
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Residues in contact with SER 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A MET* 4.7 13.7 - - - +
530A LYS 5.4 2.8 + - - -
531A VAL* 3.6 9.7 + - - -
532A ILE 3.3 0.6 - - - -
533A GLU* 1.3 81.4 + - - +
535A PHE* 1.3 56.5 + - - +
536A ILE 3.2 1.6 - - - -
537A LYS* 3.6 10.2 - - - +
538A ALA* 2.6 36.8 + - - +
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Residues in contact with PHE 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A LEU* 4.0 11.7 - - + -
456A VAL* 3.9 35.8 - - + +
460A MET* 5.1 2.2 - - - -
486A LEU* 4.1 12.1 - - + -
489A CYS* 3.7 23.3 - - + -
490A ALA* 3.8 29.6 - - + -
493A VAL* 3.7 31.4 - - + -
531A VAL* 2.9 21.6 + - + +
532A ILE 2.9 6.0 + - - +
534A SER* 1.3 77.1 - - - +
536A ILE* 1.3 59.2 + - - +
538A ALA* 3.2 2.1 + - - +
539A GLU* 2.8 30.1 + - + +
542A LEU* 4.1 18.6 - - + -
550A LEU* 4.1 8.7 - - + -
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Residues in contact with ILE 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532A ILE* 2.9 30.1 + - + +
533A GLU* 3.5 9.4 - - - +
535A PHE* 1.3 75.1 - - - +
537A LYS* 1.3 78.3 + - - +
538A ALA 3.3 0.5 + - - -
539A GLU 3.3 16.8 + - - +
540A GLY* 5.1 0.9 - - - -
542A LEU* 3.9 8.3 - - + -
547A ILE* 4.0 53.2 - - + +
550A LEU* 4.0 23.8 - - + -
551A GLU* 4.5 8.3 - - + +
554A GLU* 5.7 0.7 - - - +
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Residues in contact with LYS 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A GLU* 2.8 62.7 + - + +
534A SER* 3.3 9.8 + - - +
536A ILE* 1.3 93.0 - - - +
538A ALA* 1.3 61.7 + - - +
539A GLU 3.6 0.2 + - - -
540A GLY* 4.8 3.3 + - - -
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Residues in contact with ALA 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A VAL* 3.7 11.8 - - + +
459A SER* 2.9 34.8 + - - +
460A MET* 3.7 24.9 - - + +
463A SER* 5.9 1.1 - - - +
534A SER 2.6 22.2 + - - +
535A PHE 3.7 3.1 - - - +
537A LYS* 1.3 75.8 - - - +
539A GLU* 1.3 59.5 + - - +
540A GLY 3.8 3.2 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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