Contacts of the helix formed by residues 542 - 553 (chain C) in PDB entry 3IW4
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 ASP 542 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540C GLY 3.9 3.5 - - - -
541C GLU* 1.3 78.2 - - - +
543C GLU* 1.3 59.8 + - - +
544C ASP* 3.0 11.5 + - - +
545C GLU* 2.9 27.7 + - - +
546C LEU* 3.0 28.2 + - - +
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Residues in contact with GLU 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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498C PHE* 4.6 8.6 - - - -
502C PRO* 3.3 29.8 - - + +
542C ASP* 1.3 77.9 - - - +
544C ASP* 1.3 61.0 + - - +
546C LEU* 3.4 8.1 + - - +
547C PHE* 3.0 59.1 + - + -
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Residues in contact with ASP 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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542C ASP* 3.0 10.3 + - - +
543C GLU* 1.3 81.1 - - - +
545C GLU* 1.3 58.4 + - - +
547C PHE* 3.5 12.5 + - - +
548C GLN* 3.1 33.1 + - - +
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Residues in contact with GLU 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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539C ASP 3.7 2.1 - - - +
540C GLY* 4.0 5.7 - - - -
541C GLU* 3.1 45.5 + - - +
542C ASP* 2.9 20.1 + - - +
544C ASP* 1.3 76.5 - - - +
546C LEU* 1.3 65.1 + - - +
548C GLN* 3.4 7.6 + - + +
549C SER* 3.1 22.0 + - - -
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Residues in contact with LEU 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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502C PRO* 3.5 19.1 - - + -
503C ASP* 3.4 52.0 - - - +
538C PHE* 3.9 9.2 - - + -
539C ASP* 3.8 35.2 - - - +
540C GLY* 3.8 4.4 - - - +
542C ASP 3.0 17.4 + - - +
543C GLU* 3.6 6.7 - - - +
544C ASP 3.3 0.2 - - - -
545C GLU* 1.3 75.3 - - - +
547C PHE* 1.3 61.3 + - + +
549C SER* 3.1 4.2 + - - -
550C ILE* 2.8 37.9 + - + +
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Residues in contact with PHE 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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498C PHE* 3.9 29.8 - + - -
502C PRO* 4.3 16.4 - - + -
505C ILE* 4.3 9.2 - - + -
510C ILE* 3.6 46.7 - - + -
543C GLU* 3.0 53.8 + - + +
544C ASP* 3.7 12.3 - - - +
546C LEU* 1.3 78.7 - - + +
548C GLN* 1.3 59.5 + - + +
550C ILE* 3.1 6.2 + - + +
551C MET* 2.8 36.3 + - + +
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Residues in contact with GLN 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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544C ASP* 3.1 18.9 + - - +
545C GLU* 3.7 8.5 - - + +
546C LEU 3.2 0.2 - - - -
547C PHE* 1.3 81.2 - - + +
549C SER* 1.3 61.4 + - - +
551C MET* 4.5 5.2 - - + +
552C GLU* 3.0 41.5 + - + +
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Residues in contact with SER 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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538C PHE* 3.5 8.2 - - - +
539C ASP* 3.2 43.4 + - - -
545C GLU 3.1 7.7 + - - -
546C LEU 3.1 6.3 + - - -
548C GLN* 1.3 77.6 - - - +
550C ILE* 1.3 57.3 + - - +
552C GLU* 4.9 0.4 - - - -
553C HIS* 2.7 58.5 + - - +
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Residues in contact with ILE 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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502C PRO 3.4 25.6 - - - +
503C ASP 4.4 7.9 - - - +
505C ILE 3.7 19.5 - - - +
507C PRO* 4.2 8.8 - - + +
510C ILE* 3.5 23.6 - - + -
522C TRP* 3.7 16.2 - - + -
538C PHE* 3.6 29.4 - - + -
546C LEU* 2.8 28.4 + - + +
547C PHE* 3.5 7.9 - - + +
549C SER* 1.3 73.6 - - - +
551C MET* 1.3 63.5 + - - +
575C LYS* 2.9 28.2 + - - +
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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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507C PRO* 3.5 40.8 - - + +
510C ILE* 3.8 24.5 - - + -
511C ALA* 4.5 11.9 - - + -
547C PHE* 2.8 25.0 + - + +
548C GLN* 3.9 6.5 - - + +
550C ILE* 1.3 73.6 - - - +
552C GLU* 1.3 75.3 + - + +
575C LYS* 3.2 17.4 - - + +
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Residues in contact with GLU 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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548C GLN* 3.0 32.2 + - + +
549C SER* 4.9 0.7 - - - -
551C MET* 1.3 96.2 - - + +
553C HIS* 1.3 64.5 + - - +
554C ASN* 4.0 4.2 + - - +
575C LYS* 4.0 3.8 - - - +
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Residues in contact with HIS 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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537C PRO 5.3 5.3 + - - -
538C PHE* 4.1 8.6 - - + -
539C ASP* 5.7 4.9 + - - -
549C SER* 2.7 44.1 + - - +
552C GLU* 1.3 74.9 - - + +
554C ASN* 1.3 87.3 + - + +
555C VAL 4.0 1.2 + - - -
556C SER* 5.4 5.8 - - - -
575C LYS* 3.0 27.2 + - - -
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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