Contacts of the helix formed by residues 544 - 559 (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 GLY 544 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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535A GLU* 5.2 1.6 - - - -
538A GLY* 3.4 13.6 - - - -
543A ALA* 1.3 78.2 - - - +
545A LYS* 1.3 65.8 + - - -
546A GLU* 3.2 21.1 + - - -
547A ARG* 3.4 2.2 + - - +
548A GLY 3.1 14.7 + - - -
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Residues in contact with LYS 545 (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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534A ASP* 3.6 16.6 - - + +
535A GLU* 4.1 34.5 + - + +
544A GLY* 1.3 70.1 - - - -
546A GLU* 1.3 85.3 + - - +
548A GLY* 3.2 1.3 + - - -
549A LYS* 2.9 40.4 + - + +
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Residues in contact with GLU 546 (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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544A GLY* 3.4 18.6 + - - -
545A LYS* 1.3 111.2 + - - +
547A ARG* 1.3 66.8 + - - +
549A LYS* 3.3 12.6 + - - +
550A GLU* 3.1 30.3 + - - +
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Residues in contact with ARG 547 (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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512A ALA 5.2 0.2 + - - -
513A ALA* 3.3 24.9 + - - +
514A GLU* 3.6 25.5 + - - +
515A LEU* 5.7 0.6 - - - +
541A VAL* 4.1 7.0 - - + +
543A ALA* 3.5 35.7 - - + -
544A GLY 3.4 3.7 + - - +
545A LYS 3.3 0.2 - - - -
546A GLU* 1.3 78.9 + - - +
548A GLY* 1.3 64.7 + - - +
550A GLU* 3.4 32.8 + - - +
551A LEU* 3.1 62.3 + - + +
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Residues in contact with GLY 548 (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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534A ASP* 3.2 25.6 - - - -
537A ILE* 3.7 16.7 - - - +
538A GLY* 4.1 2.0 - - - -
544A GLY 3.1 10.2 + - - -
545A LYS 3.2 0.6 + - - -
546A GLU 3.1 0.6 - - - -
547A ARG* 1.3 80.5 - - - +
549A LYS* 1.3 59.8 + - - +
551A LEU* 3.4 2.9 + - - +
552A LYS* 2.9 31.5 + - - +
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Residues in contact with LYS 549 (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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534A ASP* 3.1 36.7 + - + +
545A LYS* 2.9 25.5 + - + +
546A GLU* 3.3 13.0 + - - +
548A GLY* 1.3 75.7 - - - +
550A GLU* 1.3 63.0 + - + +
552A LYS* 3.2 2.6 + - - +
553A LYS* 3.0 34.3 + - + +
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Residues in contact with GLU 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A GLU* 3.1 15.0 + - - +
547A ARG* 3.4 48.3 + - - +
548A GLY 3.3 0.4 - - - -
549A LYS* 1.3 77.9 - - + +
551A LEU* 1.3 59.2 + - + +
553A LYS* 3.2 11.6 - - + +
554A LYS* 2.9 32.6 + - - +
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Residues in contact with LEU 551 (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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513A ALA* 4.7 12.6 - - + +
515A LEU* 5.8 0.2 - - + -
524A PHE* 3.6 31.3 - - + -
528A PHE* 4.8 0.4 - - - -
537A ILE* 4.4 3.8 - - + -
541A VAL* 4.5 21.1 - - + -
547A ARG* 3.1 70.0 + - + +
548A GLY 3.9 4.3 - - - +
550A GLU* 1.3 76.8 - - - +
552A LYS* 1.3 66.2 + - - +
554A LYS* 4.0 9.2 - - + -
555A PHE* 3.0 41.7 + - + +
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Residues in contact with LYS 552 (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 PHE* 3.6 31.4 - - + -
531A GLY 6.0 0.2 - - - -
532A ALA 3.6 17.9 + - - +
533A GLY* 4.4 1.8 - - - +
534A ASP* 3.2 31.6 + - - +
537A ILE* 3.7 26.0 - - + +
548A GLY 2.9 22.7 + - - +
549A LYS* 3.2 6.9 + - - +
551A LEU* 1.3 76.7 - - - +
553A LYS* 1.3 56.9 + - - +
556A LEU* 3.0 29.8 + - - +
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Residues in contact with LYS 553 (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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549A LYS* 3.0 26.9 - - + +
550A GLU* 3.2 14.1 - - + +
552A LYS* 1.3 75.2 - - - +
554A LYS* 1.3 58.5 + - - +
556A LEU* 4.3 4.9 - - - -
557A GLU* 2.7 61.4 + - - +
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Residues in contact with LYS 554 (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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512A ALA* 3.8 32.2 - - - +
550A GLU 2.9 23.0 + - - +
551A LEU* 3.7 12.6 - - + +
552A LYS 3.3 0.2 - - - -
553A LYS* 1.3 79.8 - - + +
555A PHE* 1.3 79.8 + - + +
557A GLU* 4.3 3.7 - - - +
558A ASN* 3.7 21.9 + - - +
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Residues in contact with PHE 555 (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* 3.2 35.0 - - + -
512A ALA* 4.9 2.7 - - + -
513A ALA* 4.0 23.8 - - + -
524A PHE* 3.5 30.3 - + - -
525A ILE* 3.9 18.2 - - + -
528A PHE* 3.8 23.3 - + + -
551A LEU* 3.0 34.0 + - + +
554A LYS* 1.3 100.8 - - + +
556A LEU* 1.3 65.4 + - - +
557A GLU 3.3 0.4 - - - -
558A ASN* 3.6 17.0 + - + +
559A THR* 3.4 22.7 + - - -
562A ILE* 4.5 1.0 - - - +
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Residues in contact with LEU 556 (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 PHE* 4.0 16.7 - - + -
552A LYS 3.0 17.3 + - - +
553A LYS* 4.0 3.4 - - - +
555A PHE* 1.3 74.6 - - - +
557A GLU* 1.3 77.3 + - - +
559A THR 3.0 24.4 - - - +
560A PRO* 3.1 9.0 - - + +
562A ILE* 4.5 16.2 - - + -
563A ALA* 4.9 17.3 - - + +
566A ARG* 3.8 26.0 - - - +
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Residues in contact with GLU 557 (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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553A LYS* 2.7 58.2 + - - +
554A LYS* 4.3 4.7 - - - +
556A LEU* 1.3 84.2 - - - +
558A ASN* 1.3 66.5 + - - +
560A PRO* 3.1 18.3 - - - +
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Residues in contact with ASN 558 (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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495A GLU* 4.7 8.0 - - - +
496A TYR* 5.5 1.8 - - - -
499A GLU* 4.3 20.6 + - - +
509A ASN* 5.9 0.6 + - - -
554A LYS* 3.7 18.8 + - + +
555A PHE* 3.6 21.8 + - + +
557A GLU* 1.3 80.7 - - - +
559A THR* 1.3 77.7 + - - +
560A PRO* 3.7 3.1 - - - +
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Residues in contact with THR 559 (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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484A LEU* 5.6 0.2 - - - +
488A MET* 4.0 16.7 - - + +
495A GLU* 5.7 3.8 - - - +
496A TYR* 3.9 29.3 - - + -
499A GLU* 4.8 4.0 - - - +
555A PHE 3.4 4.9 + - - -
556A LEU* 3.0 8.6 + - - +
557A GLU 3.1 0.4 - - - -
558A ASN* 1.3 101.0 - - - +
560A PRO* 1.3 59.2 - - - +
561A ALA* 3.1 9.9 + - - +
562A ILE* 2.9 39.7 + - - +
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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