Contacts of the helix formed by residues 542 - 554 (chain C) in PDB entry 3IAD
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 ILE 542 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C HIS* 3.6 34.1 + - + +
443C MET* 5.9 1.3 - - - -
485C LEU* 4.3 6.5 - - + -
538C PHE* 3.3 28.0 + - + +
540C ASP 3.6 1.2 - - - -
541C TYR* 1.3 83.0 - - - +
543C VAL* 1.3 69.4 + - - +
544C HIS 3.5 0.7 - - - -
545C PRO* 3.6 3.7 - - - +
546C LEU* 3.3 23.4 + - - +
600C ILE* 3.3 36.6 - - + -
604C PHE* 3.1 50.9 - - + -
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Residues in contact with VAL 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485C LEU* 4.0 16.4 - - + +
488C PRO* 4.2 9.9 - - + -
489C THR* 4.4 1.3 - - + -
538C PHE* 3.2 52.9 + - + +
539C ILE* 4.1 7.0 - - - -
542C ILE* 1.3 75.5 - - + +
544C HIS* 1.3 62.4 + - - +
546C LEU* 3.4 6.0 + - - +
547C TRP* 2.9 49.2 + - + -
565C LEU* 3.8 23.8 - - + -
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Residues in contact with HIS 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539C ILE* 2.9 27.1 + - + +
540C ASP* 4.7 3.6 - - - +
543C VAL* 1.3 74.9 - - - +
545C PRO* 1.4 63.8 - - + +
547C TRP* 4.2 0.2 - - - +
548C GLU* 2.8 65.9 + - + +
562C LEU* 4.0 8.8 - - + +
565C LEU* 3.7 27.3 - - + +
566C GLU* 3.2 37.6 + - + +
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Residues in contact with PRO 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C LEU* 4.1 17.0 - - + -
450C LYS* 5.3 7.8 - - - +
540C ASP 3.6 20.9 - - - +
541C TYR* 4.0 14.6 - - - +
542C ILE 3.6 13.0 - - - +
544C HIS* 1.4 95.5 - - + +
546C LEU* 1.3 56.0 + - - +
548C GLU* 3.9 8.8 - - + +
549C THR* 2.7 34.6 + - - -
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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
----------------------------------------------------------
442C HIS* 4.0 10.1 - - + -
446C LEU* 3.8 17.2 - - + +
449C LEU* 4.2 15.4 - - + +
478C ASN* 4.5 6.3 - - - +
481C HIS* 3.7 31.6 - - + +
482C CYS* 3.6 34.1 - - - -
485C LEU* 3.8 24.9 - - + -
542C ILE 3.3 16.5 + - - +
543C VAL* 3.6 3.4 - - - +
544C HIS 3.3 0.4 - - - -
545C PRO* 1.3 79.7 - - - +
547C TRP* 1.3 63.8 + - + +
549C THR* 3.5 2.8 + - - -
550C TRP* 3.1 23.2 + - - +
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Residues in contact with TRP 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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268C TRP* 3.7 30.7 - + - -
341C LEU* 3.8 16.6 - - + -
482C CYS* 3.3 41.0 + - + +
485C LEU 3.0 19.7 + - - -
486C SER* 4.2 4.9 - - - -
489C THR* 3.8 15.8 - - + +
543C VAL* 2.9 41.0 + - + +
544C HIS 4.2 1.6 - - - +
546C LEU* 1.3 82.0 - - + +
548C GLU* 1.3 55.1 + - - +
550C TRP* 3.4 33.4 + + + +
551C ALA* 2.7 34.3 + - - +
558C ALA* 5.0 4.0 - - + -
561C ILE* 4.0 22.4 - - + -
562C LEU* 4.1 14.4 - - + +
565C LEU* 4.3 5.2 - - + -
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Residues in contact with GLU 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 HIS* 2.8 44.6 + - + +
545C PRO* 3.9 7.4 - - - +
547C TRP* 1.3 75.9 - - - +
549C THR* 1.3 57.6 + - - +
551C ALA* 3.3 7.1 - - + +
552C ASP* 2.8 44.9 + - - +
562C LEU* 3.9 14.3 - - + +
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Residues in contact with THR 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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446C LEU* 3.8 13.0 - - + +
449C LEU* 4.0 9.9 - - + -
450C LYS* 3.7 41.3 - - + +
453C VAL* 3.4 28.1 - - + +
545C PRO 2.7 22.3 + - - -
546C LEU 3.8 3.8 - - - -
548C GLU* 1.3 76.5 + - - +
550C TRP* 1.3 59.2 + - - +
552C ASP* 3.3 7.0 + - - +
553C LEU* 3.0 23.4 + - - +
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Residues in contact with TRP 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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341C LEU* 4.1 23.7 - - + +
344C THR* 5.5 2.2 + - + +
347C LEU* 4.1 13.7 - - + -
449C LEU* 4.1 18.2 - - + +
475C VAL* 3.7 30.7 - - + -
478C ASN* 4.4 4.0 - - + -
479C MET* 3.7 45.8 - - + -
482C CYS* 4.0 22.0 - - - -
546C LEU 3.1 15.1 + - - +
547C TRP* 3.7 28.5 - + + +
549C THR* 1.3 72.8 - - - +
551C ALA* 1.3 66.3 + - - +
553C LEU* 3.2 17.9 + - + +
554C VAL* 3.1 52.0 + - + +
558C ALA* 4.4 6.6 - - + +
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Residues in contact with ALA 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 TRP 2.7 23.0 + - - +
548C GLU* 3.3 11.0 - - + +
549C THR 3.3 0.2 - - - -
550C TRP* 1.3 74.5 - - - +
552C ASP* 1.3 58.6 + - - +
554C VAL 3.5 1.0 - - - -
555C HIS* 2.9 35.2 + - + +
556C PRO* 5.0 0.7 - - - +
557C ASP 5.3 0.3 + - - -
558C ALA* 4.4 27.4 + - + +
559C GLN* 5.3 5.6 - - - +
562C LEU* 4.3 17.5 - - + -
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Residues in contact with ASP 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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453C VAL* 3.8 24.7 - - + +
456C LYS* 3.4 13.7 + - - +
548C GLU* 2.8 29.7 + - - +
549C THR* 3.6 11.5 - - - +
550C TRP 3.2 0.2 - - - -
551C ALA* 1.3 79.6 - - - +
553C LEU* 1.3 63.0 + - - +
555C HIS* 3.3 19.4 + - - +
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Residues in contact with LEU 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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346C ALA* 5.1 0.3 - - - +
449C LEU* 3.6 27.4 - - + -
452C MET* 4.6 22.0 - - + +
453C VAL* 4.0 17.9 - - + +
456C LYS* 3.3 23.5 + - + +
464C LEU* 3.4 50.1 - - + +
475C VAL* 4.4 10.8 - - + -
549C THR 3.0 14.2 + - - +
550C TRP* 3.2 28.0 + - + +
552C ASP* 1.3 76.4 - - - +
554C VAL* 1.3 60.9 + - + +
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Residues in contact with VAL 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C THR* 4.3 6.3 - - + +
346C ALA* 3.8 25.0 - - + +
347C LEU* 4.3 18.6 - - + -
456C LYS* 4.9 0.9 - - - +
464C LEU* 5.1 0.4 - - + -
550C TRP* 3.1 53.3 + - + +
551C ALA 4.2 2.7 - - - +
553C LEU* 1.3 86.9 - - + +
555C HIS* 1.3 67.2 + - - +
557C ASP* 3.0 32.1 + - + +
558C ALA* 4.2 14.4 - - + -
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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