Contacts of the helix formed by residues 517 - 530 (chain A) in PDB entry 1TK0
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 517 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444A ARG* 6.2 4.5 - - - -
510A GLN* 3.5 14.6 - - - +
515A LEU* 4.4 0.5 - - - +
516A PRO* 1.3 88.9 - - + +
518A ARG* 1.3 64.3 + - - +
519A ASP* 3.9 10.1 + - - +
520A ASN* 3.1 32.9 + - - +
521A ALA 3.2 9.2 + - - -
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Residues in contact with ARG 518 (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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504A ASP* 3.0 36.9 + - - -
506A HIS* 3.8 16.8 - - + -
507A THR* 3.7 16.9 + - - +
510A GLN* 3.1 21.2 + - - +
517A THR* 1.3 73.1 - - - +
519A ASP* 1.3 64.1 + - - +
521A ALA* 3.3 12.2 + - - +
522A LYS* 3.4 32.4 + - - +
823A DCT 2.9 37.9 + - - -
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Residues in contact with ASP 519 (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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444A ARG* 3.4 36.8 + - - +
517A THR* 3.1 7.8 + - - +
518A ARG* 1.3 78.9 + - - +
520A ASN* 1.3 64.5 + - - +
522A LYS* 3.1 35.4 + - - +
523A THR* 3.1 15.0 + - - +
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Residues in contact with ASN 520 (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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515A LEU* 3.6 17.8 - - + +
516A PRO* 3.6 25.0 - - + +
517A THR* 3.1 29.2 + - - +
519A ASP* 1.3 81.3 - - - +
521A ALA* 1.3 55.7 + - - +
523A THR* 2.9 30.0 - - - +
524A PHE* 3.0 14.9 + - - +
540A ILE* 2.9 28.4 + - - +
541A VAL* 4.2 3.3 - - - -
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Residues in contact with ALA 521 (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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506A HIS* 3.4 28.0 + - - +
509A ASN* 4.5 4.9 - - + +
510A GLN* 3.6 26.7 - - + +
515A LEU* 3.5 13.0 - - + +
517A THR 3.2 5.9 + - - +
518A ARG 3.6 7.9 - - - +
519A ASP 3.1 0.6 - - - -
520A ASN* 1.3 76.6 - - - +
522A LYS* 1.3 59.3 + - - +
524A PHE* 3.5 3.4 - - + +
525A ILE* 2.8 31.9 + - - +
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Residues in contact with LYS 522 (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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506A HIS* 3.3 34.8 - - + +
518A ARG* 3.4 31.8 + - - +
519A ASP* 3.1 24.5 + - - +
521A ALA* 1.3 73.5 - - - +
523A THR* 1.3 66.6 + - - +
524A PHE 3.1 1.1 - - - -
525A ILE* 3.3 3.8 - - - +
526A TYR* 3.0 34.0 + - + +
823A DCT 2.8 67.1 + - + -
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Residues in contact with THR 523 (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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519A ASP 3.1 4.6 + - - +
520A ASN* 2.9 50.0 - - - +
522A LYS* 1.3 79.0 - - - +
524A PHE* 1.3 55.7 + - - +
527A GLY* 3.0 24.6 + - - -
540A ILE* 3.7 22.9 - - + +
823A DCT 4.1 18.7 + - - -
854T 8OG 3.9 12.5 + - - +
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Residues in contact with PHE 524 (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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509A ASN* 5.5 3.1 - - + -
513A ALA* 4.3 5.2 - - + -
515A LEU* 3.7 18.8 - - + -
520A ASN 3.0 18.8 + - - +
521A ALA* 3.5 6.7 - - - +
523A THR* 1.3 76.4 - - - +
525A ILE* 1.3 80.4 + - + +
527A GLY* 3.0 1.2 + - - -
528A PHE* 2.8 44.0 + - + +
537A ILE* 3.9 18.8 - - + +
540A ILE* 3.9 14.6 - - + -
541A VAL* 4.0 15.5 - - + -
551A LEU* 3.6 29.4 - - + -
552A LYS* 6.5 0.2 - - + -
555A PHE* 3.5 50.9 - + - -
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Residues in contact with ILE 525 (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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481A LEU* 4.1 20.2 - - + -
496A TYR* 6.0 0.4 - - - +
506A HIS* 3.8 25.6 - - + +
509A ASN* 4.0 20.9 - - - +
521A ALA 2.8 20.0 + - - +
522A LYS 3.3 10.5 - - - +
524A PHE* 1.3 82.5 - - + +
526A TYR* 1.3 71.8 + - + +
528A PHE* 3.6 14.4 - - + +
529A LEU* 2.8 31.0 + - + +
555A PHE* 3.9 33.4 - - + -
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Residues in contact with TYR 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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478A GLY 3.9 0.5 + - - -
480A GLU* 3.3 27.8 + - + -
481A LEU* 3.2 39.8 + - + +
506A HIS* 3.7 12.6 - + - -
522A LYS* 3.0 25.3 + - + +
523A THR 4.6 0.7 - - - +
525A ILE* 1.3 81.4 - - + +
527A GLY* 1.3 65.1 + - - +
529A LEU* 3.9 7.9 - - + -
530A TYR* 3.1 51.2 + + + +
823A DCT 2.8 79.1 + + + +
854T 8OG 3.6 5.5 + - - +
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Residues in contact with GLY 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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523A THR 3.0 16.8 + - - -
524A PHE 3.0 3.8 + - - -
526A TYR* 1.3 77.5 - - - +
528A PHE* 1.3 60.8 + - - +
530A TYR 3.5 5.4 + - - -
531A GLY 3.6 0.3 + - - -
532A ALA* 3.0 31.7 + - - +
537A ILE* 4.1 0.4 - - - -
540A ILE* 4.5 3.8 - - - -
854T 8OG 3.7 27.7 - - - +
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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
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524A PHE* 2.8 25.9 + + + +
525A ILE* 3.6 22.0 - - + +
527A GLY* 1.3 73.6 - - - +
529A LEU* 1.3 81.4 + - + +
530A TYR 3.1 1.2 + - - -
531A GLY* 3.3 12.1 + - - -
532A ALA* 4.2 2.3 + - - +
537A ILE* 3.7 18.4 - - + +
551A LEU 4.9 0.7 - - - -
552A LYS* 3.6 46.9 - - + -
555A PHE* 3.8 27.1 - + + -
556A LEU* 4.0 28.0 - - + -
562A ILE* 4.2 20.0 - - + -
566A ARG* 3.4 16.1 + - - -
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Residues in contact with LEU 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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480A GLU 4.7 0.9 - - - +
481A LEU* 4.1 17.3 - - + -
484A LEU* 3.7 34.5 - - + -
525A ILE* 2.8 22.1 + - + +
526A TYR* 4.1 10.8 - - + +
528A PHE* 1.3 82.3 - - + +
530A TYR* 1.3 75.7 + - + +
531A GLY 3.6 0.3 + - - -
562A ILE* 4.4 17.0 - - + -
566A ARG* 3.1 18.1 + - - +
610A LEU* 3.5 24.9 - - + +
614A LEU* 3.5 24.0 - - + -
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Residues in contact with TYR 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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480A GLU* 2.7 34.4 + - - +
526A TYR* 3.1 41.5 + + - +
527A GLY 3.7 1.6 - - - -
528A PHE 3.1 1.4 + - - -
529A LEU* 1.3 90.7 - - + +
531A GLY* 1.3 58.2 + - - +
532A ALA 3.7 2.0 - - - -
607A HIS* 4.6 12.2 - - - +
608A ALA* 5.9 0.2 - - - -
610A LEU* 4.0 4.5 - - + -
611A ASN* 3.2 58.8 - - + +
614A LEU* 3.1 38.2 - - + +
854T 8OG 3.3 39.6 + - + +
855T C 4.8 5.4 - - - +
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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