Contacts of the helix formed by residues 533 - 546 (chain C) in PDB entry 3T6A
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 GLU 533 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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526C PRO* 4.6 7.1 - - - +
528C GLU 4.2 1.0 - - - +
529C ASN* 2.8 11.7 - - - +
530C LYS* 2.7 54.3 + - + +
531C PRO 3.1 4.3 + - - -
532C LEU* 1.3 74.1 - - - +
534C THR* 1.3 68.0 + - + +
535C ALA* 3.3 3.3 - - + +
536C LEU* 3.0 48.4 + - + +
537C LEU* 3.0 11.1 + - - +
786C LEU* 4.6 1.6 + - - +
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Residues in contact with THR 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532C LEU 3.0 8.2 + - - -
533C GLU* 1.3 71.3 - - + +
535C ALA* 1.3 60.6 + - + +
537C LEU* 3.3 9.3 + - - +
538C LYS* 2.9 27.9 + - - +
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Residues in contact with ALA 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533C GLU* 3.3 3.9 - - + +
534C THR* 1.3 80.2 + - + +
536C LEU* 1.3 61.2 + - + +
538C LYS* 3.2 11.7 + - + +
539C ARG* 2.9 30.0 + - - +
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Residues in contact with LEU 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524C PHE 4.2 11.7 - - - +
525C LEU* 4.5 5.4 - - + -
526C PRO* 3.6 34.3 - - + -
529C ASN* 4.0 13.5 - - + +
533C GLU* 3.0 45.1 + - + +
535C ALA* 1.3 79.3 - - + +
537C LEU* 1.3 60.5 + - - +
539C ARG* 3.6 7.8 + - + +
540C ALA* 3.1 22.2 + - - +
782C PHE* 5.2 3.8 - - + -
786C LEU* 3.5 29.0 - - + +
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Residues in contact with LEU 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532C LEU* 3.5 45.5 - - + +
533C GLU 3.0 12.4 + - - +
534C THR* 3.3 8.3 + - - +
536C LEU* 1.3 73.2 - - - +
538C LYS* 1.3 67.6 + - - +
540C ALA* 3.2 6.3 + - + +
541C LYS* 3.0 24.6 + - - +
611C VAL* 4.5 17.7 - - + -
615C GLY* 6.2 3.6 - - - -
616C CYS* 4.1 25.8 - - - -
786C LEU* 4.2 24.5 - - + -
787C LEU* 5.9 2.2 - - + -
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Residues in contact with LYS 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534C THR* 2.9 15.1 + - - +
535C ALA* 3.2 13.9 + - + +
537C LEU* 1.3 77.9 - - - +
539C ARG* 1.3 56.6 + - - +
541C LYS* 3.5 4.8 + - - +
542C GLU* 2.7 61.0 + - + +
616C CYS* 5.8 0.2 - - - -
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Residues in contact with ARG 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535C ALA 2.9 16.7 + - - +
536C LEU* 3.8 9.0 - - + +
538C LYS* 1.3 74.0 - - - +
540C ALA* 1.3 67.2 + - - +
542C GLU* 3.0 46.4 + - - +
543C LEU* 3.0 40.1 + - + +
546C ASN* 5.1 3.8 - - - +
773C GLU* 2.7 43.1 + - - +
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Residues in contact with ALA 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536C LEU 3.1 14.9 + - - +
537C LEU* 3.2 6.7 + - + +
539C ARG* 1.3 79.4 - - - +
541C LYS* 1.3 62.9 + - - +
543C LEU* 3.1 18.9 + - - +
544C PHE* 3.2 21.8 + - + -
612C ASP* 5.9 1.1 - - - +
616C CYS* 6.0 1.3 - - - -
777C ILE* 3.7 25.1 - - + -
782C PHE* 5.9 1.3 - - + -
786C LEU* 4.3 16.8 - - + -
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Residues in contact with LYS 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537C LEU 3.0 16.1 + - - +
538C LYS* 3.8 4.9 - - - +
540C ALA* 1.3 73.1 - - - +
542C GLU* 1.3 56.3 + - - +
544C PHE* 2.9 10.7 + - + +
545C THR* 2.7 50.9 + - - +
612C ASP* 3.3 29.2 + - - +
616C CYS* 2.9 42.1 + - + +
617C THR* 3.6 6.3 - - - +
622C ASP* 5.6 1.4 - - - +
626C THR* 2.7 35.6 + - - +
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Residues in contact with GLU 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538C LYS* 2.7 60.6 + - + +
539C ARG* 3.1 40.9 + - - +
541C LYS* 1.3 75.6 - - - +
543C LEU* 1.3 53.7 + - - +
545C THR* 3.4 7.0 + - - -
546C ASN* 2.9 43.9 + - - +
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Residues in contact with LEU 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539C ARG* 3.0 39.6 + - + +
540C ALA* 3.2 10.8 - - - +
541C LYS 3.1 0.4 - - - -
542C GLU* 1.3 72.9 - - - +
544C PHE* 1.3 73.4 + - + +
546C ASN* 3.4 2.4 + - + +
547C ASN* 2.7 43.3 + - - +
771C ASP* 5.1 4.9 - - - +
773C GLU* 3.8 48.0 - - + +
774C MET* 4.3 11.6 - - + +
777C ILE* 4.7 14.4 - - + -
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Residues in contact with PHE 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540C ALA* 3.2 12.1 + - + -
541C LYS* 2.9 12.1 + - + +
543C LEU* 1.3 80.7 - - + +
545C THR* 1.3 59.3 + - - +
547C ASN 3.4 5.0 - - - +
552C ILE* 3.8 27.4 - - + +
609C ILE* 6.2 4.5 - - + -
612C ASP* 3.9 23.8 - - + +
629C LYS* 3.0 29.3 - - + -
774C MET* 4.3 21.3 - - - -
777C ILE* 3.4 39.3 - - + -
778C CYS* 5.8 4.5 - - - -
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Residues in contact with THR 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C LYS* 2.7 43.4 + - - +
542C GLU* 3.6 8.5 - - - -
544C PHE* 1.3 74.9 - - - +
546C ASN* 1.3 66.8 + - - +
547C ASN 3.2 7.4 + - - +
629C LYS* 4.0 10.9 + - - +
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Residues in contact with ASN 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539C ARG* 5.1 4.4 - - - +
542C GLU* 2.9 33.7 + - - +
543C LEU* 3.4 5.2 + - + +
545C THR* 1.3 84.9 - - - +
547C ASN* 1.3 68.1 + - - +
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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