Contacts of the helix formed by residues 539 - 553 (chain C) in PDB entry 3J8B
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 TRP 539 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534C MET* 5.8 0.7 - - - +
537C GLY 3.5 6.3 + - - +
538C ASP* 1.3 72.8 - - - +
540C LYS* 1.3 62.2 + - - +
542C CYS* 3.2 7.7 + - - +
543C HIS* 2.9 29.7 + - - +
573C ILE* 5.0 7.2 - - + +
574C GLN* 5.1 8.5 - - + -
577C SER* 4.1 25.4 - - - -
601C PHE* 6.0 4.5 - - - +
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Residues in contact with LYS 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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538C ASP* 5.8 1.1 - - + -
539C TRP* 1.3 79.1 - - - +
541C THR* 1.3 60.9 + - - +
543C HIS* 3.3 7.3 + - - +
544C SER* 2.9 23.8 + - - -
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Residues in contact with THR 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533C ALA* 4.0 12.1 - - - -
538C ASP* 3.8 24.1 + - - +
539C TRP 3.3 0.4 - - - -
540C LYS* 1.3 78.1 - - - +
542C CYS* 1.3 58.3 + - - +
544C SER* 3.1 9.4 + - - -
545C PHE* 2.9 30.8 + - - +
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Residues in contact with CYS 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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530C ALA* 3.4 45.6 - - + +
533C ALA* 3.7 2.2 - - + +
534C MET* 4.5 5.8 - - + +
538C ASP 3.5 12.0 + - - +
539C TRP* 3.2 12.6 + - - +
541C THR* 1.3 78.7 - - - +
543C HIS* 1.3 62.3 + - - +
545C PHE 3.2 1.4 + - - -
546C ILE* 3.2 20.4 + - - +
573C ILE* 6.2 4.5 - - + -
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Residues in contact with HIS 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539C TRP 2.9 15.4 + - - +
540C LYS* 3.7 7.2 - - - +
542C CYS* 1.3 77.5 - - - +
544C SER* 1.3 63.2 + - - +
546C ILE* 3.5 12.2 + - - +
547C ILE* 3.7 9.5 + - - +
570C VAL* 5.7 12.6 - - + -
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Residues in contact with SER 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540C LYS 2.9 14.5 + - - -
541C THR* 3.1 12.8 + - - -
543C HIS* 1.3 76.7 - - - +
545C PHE* 1.3 62.3 + - - +
547C ILE* 3.2 11.9 + - - +
548C ASN* 3.1 17.7 + - - +
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Residues in contact with PHE 545 (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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526C HIS* 3.3 24.9 - - - +
529C ALA* 4.2 11.0 - - + -
530C ALA* 4.0 11.7 - - + +
541C THR 2.9 15.9 + - - +
542C CYS 3.2 5.6 + - - +
544C SER* 1.3 74.1 - - - +
546C ILE* 1.3 57.3 + - - +
548C ASN* 2.9 9.5 + - - +
549C GLU 2.7 32.1 + - - -
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Residues in contact with ILE 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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526C HIS* 4.6 4.2 + - - -
527C VAL* 5.4 2.5 - - - +
530C ALA* 4.7 5.4 - - + +
542C CYS 3.2 9.6 + - - +
543C HIS* 3.9 11.0 - - - +
544C SER 3.3 0.4 - - - -
545C PHE* 1.3 78.2 - - - +
547C ILE* 1.3 50.0 - - - +
549C GLU* 3.9 5.1 - - - +
550C LYS* 2.6 39.4 + - - +
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Residues in contact with ILE 547 (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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543C HIS 3.7 6.5 + - - +
544C SER* 3.2 11.9 + - - +
546C ILE* 1.3 79.8 - - - +
548C ASN* 1.3 53.5 + - - +
550C LYS* 3.8 7.0 - - - -
551C MET* 2.5 39.7 + - + +
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Residues in contact with ASN 548 (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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520C PRO* 6.2 3.4 - - + -
521C GLU 5.4 0.5 - - - +
526C HIS* 5.1 0.9 - - + -
544C SER 3.1 9.4 + - - +
545C PHE* 2.9 12.9 + - - +
547C ILE* 1.3 80.4 - - - +
549C GLU* 1.3 61.9 + - - +
551C MET* 3.6 9.6 + - - +
552C ASN* 3.7 12.3 + - - +
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Residues in contact with GLU 549 (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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520C PRO* 6.0 0.4 - - - -
521C GLU 5.2 4.0 - - - -
522C SER 4.9 1.3 - - - -
523C MET* 3.3 31.8 + - + +
526C HIS* 1.6 48.2 - - + +
527C VAL 3.9 0.7 - - - +
545C PHE 2.7 11.3 + - - +
546C ILE* 3.9 4.3 - - - +
548C ASN* 1.3 73.1 - - - +
550C LYS* 1.3 60.9 + - - +
552C ASN* 3.7 3.3 + - - +
553C GLY* 3.2 17.7 + - - -
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Residues in contact with LYS 550 (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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523C MET* 5.8 0.4 - - - -
546C ILE 2.6 24.5 + - - +
547C ILE* 3.4 9.2 - - - +
549C GLU* 1.3 74.1 - - - +
551C MET* 1.3 54.1 + - - +
553C GLY* 3.0 1.1 + - - +
554C LYS* 2.2 40.9 + - - +
555C VAL* 3.3 9.8 + - + +
556C TRP* 4.5 25.6 - - + +
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Residues in contact with MET 551 (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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547C ILE* 2.5 21.6 + - + +
548C ASN* 4.0 7.0 - - - +
549C GLU 3.4 0.4 - - - -
550C LYS* 1.3 72.8 - - - +
552C ASN* 1.3 64.0 + - - +
554C LYS* 3.5 10.3 + - - +
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Residues in contact with ASN 552 (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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521C GLU 4.2 17.5 - - - +
523C MET 6.2 0.4 - - - +
548C ASN 3.7 7.4 + - - +
549C GLU 3.7 7.5 + - - +
550C LYS 3.3 0.2 - - - -
551C MET* 1.3 79.3 - - - +
553C GLY* 1.3 62.9 + - - +
554C LYS* 4.6 1.6 - - - +
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Residues in contact with GLY 553 (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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470C GLU* 5.1 12.2 - - - +
523C MET* 5.1 9.6 - - - +
549C GLU 3.2 10.7 + - - -
550C LYS* 3.0 6.2 + - - -
552C ASN* 1.3 78.7 - - - +
554C LYS* 1.3 68.4 + - - +
555C VAL* 3.0 12.4 + - - -
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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