Contacts of the helix formed by residues 558 - 574 (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 ALA 558 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341C LEU* 6.1 0.4 - - + -
344C THR* 5.8 0.2 - - - +
547C TRP* 5.0 4.2 - - + -
550C TRP* 4.4 11.4 - - + +
551C ALA* 4.4 20.6 + - + +
554C VAL* 4.2 19.1 - - + +
556C PRO 3.3 0.8 - - - -
557C ASP* 1.3 76.1 - - + +
559C GLN* 1.3 57.7 + - - +
560C ASP 3.4 2.2 - - - +
561C ILE* 3.5 27.3 + - + +
562C LEU* 3.1 25.1 + - - +
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Residues in contact with GLN 559 (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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551C ALA* 5.3 5.0 - - - +
555C HIS* 4.6 15.6 + - - -
556C PRO* 3.5 18.2 + - + +
557C ASP 3.3 3.2 + - - -
558C ALA* 1.3 75.9 - - - +
560C ASP* 1.3 63.7 + - - +
562C LEU* 3.3 25.6 + - - +
563C ASP* 2.8 56.0 + - - +
566C GLU* 5.7 0.6 + - - -
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Residues in contact with ASP 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557C ASP 4.6 5.2 + - - +
558C ALA* 3.4 0.6 - - - +
559C GLN* 1.3 76.7 - - - +
561C ILE* 1.3 61.3 + - + +
563C ASP* 3.4 12.0 + - - +
564C THR* 2.8 35.0 + - - -
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Residues in contact with ILE 561 (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* 3.8 45.3 - - + +
340C VAL* 5.9 1.6 - - + -
341C LEU* 4.4 6.5 - - + -
489C THR* 3.5 33.9 - - + +
547C TRP* 4.0 28.7 - - + -
558C ALA* 3.5 23.0 + - + +
559C GLN 3.3 0.2 - - - -
560C ASP* 1.3 79.3 - - + +
562C LEU* 1.3 62.5 + - - +
564C THR* 3.4 7.5 + - - -
565C LEU* 3.1 20.6 + - - +
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Residues in contact with LEU 562 (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* 4.0 20.4 - - + +
547C TRP* 4.1 16.4 - - + +
548C GLU* 3.9 36.8 - - + +
551C ALA* 4.3 16.6 - - + -
558C ALA 3.1 13.7 + - - +
559C GLN* 3.6 29.6 - - - +
561C ILE* 1.3 77.2 - - - +
563C ASP* 1.3 58.4 + - - +
565C LEU* 3.4 7.0 + - + +
566C GLU* 3.1 47.2 + - - +
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Residues in contact with ASP 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559C GLN* 2.8 46.5 + - - +
560C ASP* 3.7 13.8 - - - +
561C ILE 3.3 0.2 - - - -
562C LEU* 1.3 78.4 - - - +
564C THR* 1.3 57.0 + - - +
566C GLU* 3.6 15.6 + - - +
567C ASP* 3.0 34.3 + - - +
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Residues in contact with THR 564 (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* 6.1 0.5 - - - -
488C PRO 4.4 0.2 - - - -
489C THR 3.5 22.9 - - - +
490C LYS 3.9 10.1 - - - +
491C PRO* 4.2 10.1 - - + -
560C ASP* 2.8 22.4 + - - +
561C ILE* 3.7 2.3 - - - -
562C LEU 3.3 0.4 - - - -
563C ASP* 1.3 74.3 - - - +
565C LEU* 1.3 60.4 + - - +
567C ASP* 3.4 9.3 - - + +
568C ASN* 2.9 44.5 + - - +
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Residues in contact with LEU 565 (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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488C PRO* 3.5 42.3 + - + +
489C THR* 3.8 11.6 - - + +
539C ILE* 4.0 16.2 - - + -
543C VAL* 3.8 21.1 - - + +
544C HIS* 3.7 40.2 - - + -
547C TRP* 4.3 9.4 - - + -
561C ILE 3.1 13.8 + - - +
562C LEU* 3.5 11.2 - - + +
563C ASP 3.3 0.2 - - - -
564C THR* 1.3 73.7 - - - +
566C GLU* 1.3 60.5 + - - +
568C ASN* 3.4 2.3 + - - +
569C ARG* 2.9 27.8 + - - +
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Residues in contact with GLU 566 (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* 3.2 32.7 + - + +
559C GLN* 5.7 0.7 + - - -
562C LEU* 3.1 28.4 + - - +
563C ASP* 3.9 15.1 - - - +
564C THR 3.4 0.2 - - - -
565C LEU* 1.3 73.2 - - - +
567C ASP* 1.3 65.5 + - - +
569C ARG* 3.4 8.9 + - - +
570C GLU* 3.2 27.4 + - + +
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Residues in contact with ASP 567 (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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563C ASP* 3.0 21.6 + - - +
564C THR* 3.4 14.4 - - + +
566C GLU* 1.3 76.3 - - - +
568C ASN* 1.3 61.9 + - - +
570C GLU* 3.1 8.9 + - - +
571C TRP* 3.0 26.0 + - - +
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Residues in contact with ASN 568 (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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488C PRO 2.6 29.4 + - - +
490C LYS 2.8 24.2 + - - -
492C LEU* 3.7 25.9 + - + +
495C TYR* 3.6 24.0 - - + -
539C ILE* 4.5 2.9 - - + -
564C THR* 2.9 24.7 + - - +
565C LEU 3.8 2.2 - - - +
567C ASP* 1.3 76.7 - - - +
569C ARG* 1.3 65.2 + - - +
571C TRP* 3.7 7.4 - - - +
572C TYR* 3.1 28.2 + - - +
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Residues in contact with ARG 569 (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 VAL* 3.7 20.3 - - + +
539C ILE* 3.8 29.5 - - + +
540C ASP* 3.3 38.9 + - - +
565C LEU 2.9 14.5 + - - +
566C GLU* 3.4 13.5 - - - +
568C ASN* 1.3 77.3 - - - +
570C GLU* 1.3 87.9 + - - +
572C TYR* 3.3 3.2 + - - +
573C GLN* 3.0 50.2 + - - +
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Residues in contact with GLU 570 (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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566C GLU* 3.2 12.5 + - + +
567C ASP* 3.1 9.4 + - - +
569C ARG* 1.3 110.3 + - - +
571C TRP* 1.3 65.4 + - - +
573C GLN* 3.8 8.8 - - - +
574C SER* 3.1 25.3 + - - -
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Residues in contact with TRP 571 (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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492C LEU* 3.4 46.2 - - + +
496C ARG* 4.2 24.5 - - + -
567C ASP 3.0 12.9 + - - +
568C ASN* 3.7 11.4 - - - +
570C GLU* 1.3 77.0 - - - +
572C TYR* 1.3 84.9 + + - +
574C SER* 2.7 20.5 + - - -
575C THR* 2.6 45.0 + - + -
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Residues in contact with TYR 572 (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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492C LEU* 4.7 2.0 - - + -
495C TYR* 3.5 47.6 - + - +
496C ARG* 4.2 17.6 - - + +
499C THR* 3.3 28.6 + - - +
500C ASP* 5.1 0.9 + - - -
531C VAL* 4.6 6.9 - - + +
532C GLU* 3.9 39.9 - - + +
535C GLN* 4.1 17.3 - - + -
536C VAL* 4.1 14.6 - - + -
539C ILE* 5.8 0.7 - - + -
568C ASN 3.1 15.9 + - - +
569C ARG* 3.9 3.8 - - - +
571C TRP* 1.3 100.4 - + - +
573C GLN* 1.3 65.1 + - - +
575C THR* 3.2 16.1 + - - -
576C ILE* 3.8 10.7 + - - +
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Residues in contact with GLN 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C VAL* 3.7 19.2 - - + +
569C ARG* 3.0 49.6 + - - +
570C GLU* 3.8 11.4 - - - +
572C TYR* 1.3 77.2 - - - +
574C SER* 1.3 62.9 + - - +
575C THR 3.2 1.4 + - - -
576C ILE* 3.3 38.0 + - - +
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Residues in contact with SER 574 (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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570C GLU 3.1 14.1 + - - -
571C TRP* 2.7 26.3 + - - -
573C GLN* 1.3 77.2 - - - +
575C THR* 1.3 58.6 + - - +
576C ILE 3.4 1.6 + - - -
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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