Contacts of the helix formed by residues 525 - 537 (chain A) in PDB entry 1OY6
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 HIS 525 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521A GLU* 2.6 43.7 + - + +
522A LYS 2.9 2.5 - - - +
524A THR* 1.3 84.0 - - + +
526A HIS* 1.3 70.7 + - + +
527A TYR 2.4 21.7 + - - -
528A THR 2.8 14.7 + - - -
529A ASP* 3.2 21.5 + - - +
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Residues in contact with HIS 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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521A GLU* 3.3 23.9 + - + +
522A LYS* 3.8 37.2 - - + +
525A HIS* 1.3 84.8 + - + +
527A TYR* 1.3 52.0 + - - +
529A ASP* 4.0 7.5 + - - +
530A SER* 2.4 38.7 + - - -
1020A PHE* 4.3 2.6 - - - -
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Residues in contact with TYR 527 (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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522A LYS* 2.9 21.7 + - + +
523A SER* 3.7 4.5 - - - +
525A HIS 2.4 11.1 + - - -
526A HIS* 1.3 68.0 - - - +
528A THR* 1.3 71.4 + - - +
530A SER* 2.6 21.2 + - - -
531A VAL* 2.7 38.4 + - + +
968A VAL* 3.1 40.3 - - + +
972A LEU* 3.9 24.0 - - + -
1019A ILE* 2.3 38.3 + - + +
1020A PHE* 3.3 46.2 - + + -
1025A PHE* 4.2 0.3 - - - -
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Residues in contact with THR 528 (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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523A SER* 2.2 27.8 + - - -
524A THR* 3.6 13.7 - - + +
525A HIS 2.8 5.7 + - - -
527A TYR* 1.3 82.8 - - - +
529A ASP* 1.3 62.0 + - - +
531A VAL* 3.5 7.1 + - - -
532A GLY 3.3 14.4 + - - -
965A LEU* 3.5 44.0 - - + +
968A VAL* 4.6 4.4 + - + -
969A ARG* 4.0 26.3 - - + -
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Residues in contact with ASP 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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524A THR 2.9 20.5 - - - +
525A HIS* 3.2 30.5 + - - +
526A HIS* 4.0 4.1 + - - +
527A TYR 3.2 0.4 - - - -
528A THR* 1.3 77.5 - - - +
530A SER* 1.3 61.7 + - - +
532A GLY* 3.2 11.8 + - - -
533A GLY* 3.3 7.8 + - - -
536A ARG* 5.6 2.8 + - - -
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Residues in contact with SER 530 (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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526A HIS 2.4 26.7 + - - -
527A TYR 2.6 11.1 + - - -
529A ASP* 1.3 75.2 - - - +
531A VAL* 1.3 58.4 + - - +
532A GLY 3.1 1.8 - - - -
533A GLY* 3.0 4.9 + - - +
534A ILE* 2.8 37.5 + - - +
1020A PHE* 3.1 22.2 - - - -
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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
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527A TYR* 2.7 62.6 + - + +
528A THR* 3.5 10.8 - - - +
529A ASP 3.3 0.2 - - - -
530A SER* 1.3 72.5 - - - +
532A GLY* 1.3 61.5 + - - +
534A ILE* 3.2 18.6 - - + +
535A LEU* 3.1 33.7 - - + +
965A LEU* 4.1 14.1 - - + -
968A VAL* 4.3 2.9 - - + -
1019A ILE 5.1 0.7 - - - +
1020A PHE* 4.3 6.5 - - + -
1025A PHE* 4.0 23.8 - - + -
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Residues in contact with GLY 532 (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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528A THR 3.3 4.9 + - - -
529A ASP 3.2 9.4 + - - -
530A SER 3.1 0.8 - - - -
531A VAL* 1.3 79.0 - - - +
533A GLY* 1.3 57.3 + - - +
535A LEU* 3.3 8.0 + - - +
536A ARG* 3.0 35.2 + - - +
961A ILE* 6.0 0.5 - - - +
965A LEU* 3.6 18.8 - - - +
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Residues in contact with GLY 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 ASP 3.3 8.5 + - - -
530A SER* 3.0 10.1 + - - -
532A GLY* 1.3 74.3 - - - +
534A ILE* 1.3 63.3 + - - +
536A ARG* 3.5 28.5 - - - +
537A SER* 3.4 10.9 + - - -
540A ARG* 5.3 2.6 + - - -
541A TYR* 5.1 1.5 + - - -
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Residues in contact with ILE 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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530A SER* 2.8 23.7 + - - +
531A VAL* 3.2 32.3 - - + +
533A GLY* 1.3 72.8 - - - -
535A LEU* 1.3 58.9 + - + +
537A SER* 2.8 35.9 + - - +
541A TYR* 3.5 28.5 - - + +
1020A PHE* 4.4 8.1 - - + +
1021A PHE* 3.7 39.3 - - + +
1025A PHE* 5.3 7.2 - - + -
1026A PHE* 3.0 30.7 - - + -
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Residues in contact with LEU 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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531A VAL* 3.1 37.4 + - + +
532A GLY* 3.5 6.7 - - - +
533A GLY 3.2 0.6 - - - -
534A ILE* 1.3 84.8 - - + +
536A ARG* 1.3 64.5 + - - +
537A SER 3.1 6.3 - - - +
538A THR* 4.1 4.9 + - - -
961A ILE* 4.1 42.9 - - + +
964A THR* 4.2 12.6 - - - +
965A LEU* 4.1 13.9 - - + +
1025A PHE* 4.2 17.9 - - + +
1026A PHE* 4.9 5.8 - - + +
1029A VAL* 3.5 35.3 - - + +
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Residues in contact with ARG 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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529A ASP 5.6 2.0 + - - -
532A GLY* 3.0 21.4 + - - +
533A GLY* 3.5 19.9 - - - +
534A ILE 3.3 0.2 - - - -
535A LEU* 1.3 78.1 - - - +
537A SER* 1.3 60.6 + - - +
538A THR* 4.5 2.6 + - - -
961A ILE* 5.6 5.8 - - + +
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Residues in contact with SER 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A GLY 3.4 9.5 + - - -
534A ILE 2.8 28.8 + - - +
535A LEU* 3.1 4.0 - - - +
536A ARG* 1.3 79.8 - - - +
538A THR* 1.3 70.7 + - - +
540A ARG* 4.0 20.6 + - - -
541A TYR* 3.1 27.3 - - - -
1026A PHE* 3.7 1.8 - - - -
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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
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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