Contacts of the helix formed by residues 565 - 574 (chain C) in PDB entry 3GJN
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 THR 565 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468C ALA* 2.8 27.4 + - + +
469C GLY* 3.9 7.4 - - - +
533C ASP* 3.8 37.0 - - + +
541C PHE* 4.1 18.7 - - + -
564C VAL* 1.3 74.9 - - - +
566C PRO* 1.3 64.6 - - - +
567C LYS* 3.6 2.6 + - - +
568C ARG* 3.0 23.7 + - - +
569C HIS* 2.8 31.0 + - - +
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Residues in contact with PRO 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529C THR* 3.7 11.2 - - + -
533C ASP 3.5 15.7 - - - +
534C VAL* 4.8 0.2 - - - -
535C SER* 4.1 7.6 - - - +
538C ARG* 3.1 47.3 - - + +
539C THR 4.3 0.2 - - - +
540C SER 3.3 27.1 - - - +
542C GLU* 3.8 17.3 - - + +
564C VAL 3.7 1.8 - - - +
565C THR* 1.3 84.9 - - - +
567C LYS* 1.3 58.0 + - - +
569C HIS* 3.9 0.8 - - + +
570C ILE* 3.1 33.2 + - - +
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Residues in contact with LYS 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C GLN 3.0 23.3 + - - +
533C ASP* 3.8 13.7 + - - +
534C VAL 3.2 26.4 + - - +
535C SER* 3.9 12.6 - - - +
565C THR* 3.3 4.3 + - - +
566C PRO* 1.3 73.0 - - - +
568C ARG* 1.3 66.0 + - - +
570C ILE* 3.3 8.5 + - - +
571C ASP* 3.2 28.6 + - - +
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Residues in contact with ARG 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C ALA 3.9 10.5 - - - +
469C GLY 3.7 27.4 - - - +
470C LYS* 4.0 1.8 - - - +
471C ASP* 3.0 48.0 + - - +
564C VAL* 4.3 3.6 - - + -
565C THR* 3.0 21.8 + - - +
567C LYS* 1.3 73.4 - - - +
569C HIS* 1.3 65.8 + - - +
570C ILE 3.0 1.5 + - - -
571C ASP* 3.1 34.6 + - - +
572C ILE* 3.1 34.2 + - + +
576C LYS 3.3 24.3 + - - -
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Residues in contact with HIS 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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538C ARG* 4.0 7.1 + - - +
542C GLU* 2.6 33.3 + - + +
543C LEU 3.6 20.6 - - - -
544C HIS* 3.3 13.1 + + + -
564C VAL* 3.6 20.3 - - + +
565C THR 2.8 19.8 + - - +
566C PRO 3.9 2.5 - - - +
568C ARG* 1.3 73.3 - - - +
570C ILE* 1.4 62.6 + - - +
572C ILE* 3.3 5.8 + - + +
573C HIS* 3.2 42.5 + + - -
600C ZN 2.2 36.2 - - - -
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Residues in contact with ILE 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535C SER* 4.4 15.0 - - - +
538C ARG* 3.0 47.3 - - - +
566C PRO 3.1 20.3 + - - +
567C LYS* 3.4 10.5 - - - +
568C ARG 3.0 1.0 - - - -
569C HIS* 1.4 74.5 - - - +
571C ASP* 1.3 64.1 + - - +
573C HIS* 3.1 9.1 + - + +
574C ARG* 3.0 56.1 + - - +
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Residues in contact with ASP 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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567C LYS 3.2 14.3 + - - +
568C ARG* 3.1 32.7 + - - +
570C ILE* 1.3 76.0 - - - +
572C ILE* 1.3 64.5 + - - +
574C ARG* 2.8 27.9 + - - -
575C GLY 2.8 20.3 + - - -
576C LYS* 2.8 25.7 + - + +
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Residues in contact with ILE 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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471C ASP 3.3 26.9 - - - +
472C LEU* 4.4 15.7 - - + -
544C HIS* 3.6 39.7 - - + +
546C GLU* 5.0 2.2 - - - +
564C VAL* 4.1 20.9 - - + -
568C ARG* 3.1 30.7 + - - +
569C HIS* 3.6 8.3 - - - +
570C ILE 3.2 0.2 - - - -
571C ASP* 1.3 78.1 - - - +
573C HIS* 1.3 67.7 + - + +
575C GLY* 3.2 12.3 + - - -
576C LYS 4.1 7.2 - - - -
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Residues in contact with HIS 573 (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 ARG* 6.2 0.7 - - - -
544C HIS* 3.6 10.3 + + - -
545C ALA 5.6 1.6 - - - -
569C HIS* 3.2 29.6 + + - +
570C ILE* 3.1 12.1 + - + +
571C ASP 3.1 0.6 - - - -
572C ILE* 1.3 83.7 - - + +
574C ARG* 1.3 57.5 + - + +
575C GLY 3.2 2.2 + - - -
600C ZN 2.2 36.9 - - - -
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Residues in contact with ARG 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570C ILE* 3.0 41.3 + - - +
571C ASP* 2.8 27.6 + - - +
573C HIS* 1.3 75.9 - - - +
575C GLY* 1.3 55.4 + - - +
576C LYS* 3.3 45.5 + - + +
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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