Contacts of the helix formed by residues 528 - 539 (chain C) in PDB entry 2A19
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 ASN 528 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406C HIS* 6.1 0.8 + - - -
467C LYS* 5.6 8.7 - - - +
471C LEU* 4.3 13.8 - - - +
526C ARG 3.8 3.4 + - - -
527C PRO* 1.3 77.4 - - - +
529C THR* 1.3 67.7 + - - +
530C SER* 3.2 17.6 + - - +
531C GLU* 3.1 14.3 + - + +
532C ILE* 3.0 18.8 + - - +
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Residues in contact with THR 529 (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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399C THR* 3.6 17.8 - - + +
402C VAL* 3.6 25.8 - - + -
403C ASP* 2.6 35.8 + - - +
406C HIS* 4.0 11.6 + - - +
471C LEU* 3.5 22.8 - - + +
474C LEU* 3.8 8.7 - - + -
528C ASN* 1.3 73.2 - - - +
530C SER* 1.3 49.2 + - - +
532C ILE* 3.0 13.4 + - - +
533C LEU* 2.7 34.8 + - - +
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Residues in contact with SER 530 (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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403C ASP* 3.3 7.8 + - - -
528C ASN* 3.6 14.9 + - - +
529C THR* 1.3 75.5 + - - +
531C GLU* 1.3 58.1 + - - +
533C LEU* 2.8 15.2 + - - +
534C ARG* 2.6 47.5 + - - +
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Residues in contact with GLU 531 (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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514C LEU* 5.9 0.4 - - - -
527C PRO* 3.7 29.0 - - + +
528C ASN* 3.1 19.1 + - + +
530C SER* 1.3 81.4 + - - +
532C ILE* 1.3 52.4 + - - +
534C ARG* 3.5 24.3 - - - +
535C THR* 2.4 38.9 + - - +
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Residues in contact with ILE 532 (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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395C PHE* 3.7 30.5 - - + -
399C THR* 3.8 11.9 - - + +
471C LEU* 4.1 14.8 - - + +
474C LEU* 4.2 16.6 - - + -
514C LEU* 4.7 18.0 - - + +
518C LEU* 6.0 2.9 - - + -
527C PRO* 3.8 25.6 - - + +
528C ASN 3.0 15.6 + - - +
529C THR* 3.1 19.5 - - - +
531C GLU* 1.3 75.0 - - - +
533C LEU* 1.3 57.5 + - + +
535C THR* 3.3 6.5 + - - -
536C LEU* 3.0 30.5 + - + +
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Residues in contact with LEU 533 (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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396C GLU* 4.2 13.7 - - + +
399C THR* 3.5 28.0 - - + -
400C LYS* 4.1 26.7 - - + -
403C ASP* 3.4 35.7 - - + +
529C THR 2.7 20.9 + - - +
530C SER* 2.8 11.5 + - - +
532C ILE* 1.3 71.7 - - + +
534C ARG* 1.3 65.0 + - - +
535C THR 3.2 0.2 + - - -
536C LEU* 3.3 6.0 + - + +
537C THR* 2.9 29.8 + - - +
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Residues in contact with ARG 534 (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 SER* 2.6 23.5 + - - +
531C GLU* 3.5 31.7 - - - +
533C LEU* 1.3 72.0 - - - +
535C THR* 1.3 58.5 + - - +
537C THR* 3.3 7.0 + - - -
538C VAL* 3.0 33.6 + - + +
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Residues in contact with THR 535 (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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510C LYS 6.0 0.2 - - - +
514C LEU* 4.6 22.7 - - + +
531C GLU* 2.4 27.1 + - - +
532C ILE* 3.7 6.6 - - - -
533C LEU 3.2 0.4 - - - -
534C ARG* 1.3 75.4 - - - +
536C LEU* 1.3 65.0 + - - +
538C VAL* 3.2 18.1 + - + +
539C TRP* 3.3 45.2 - - + +
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Residues in contact with LEU 536 (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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392C LEU* 3.9 25.6 - - + +
395C PHE* 3.9 19.1 - - + -
396C GLU* 3.7 55.0 - - + +
399C THR* 6.3 0.4 - - - -
514C LEU* 6.0 2.2 - - + +
532C ILE* 3.0 18.3 + - + +
533C LEU* 4.0 5.6 - - + +
535C THR* 1.3 76.9 - - - +
537C THR* 1.3 57.6 + - - +
539C TRP* 3.0 53.6 + - + +
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Residues in contact with THR 537 (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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396C GLU* 5.5 5.2 + - - -
533C LEU 2.9 15.1 + - - -
534C ARG* 3.5 9.6 - - - -
536C LEU* 1.3 73.8 - - - +
538C VAL* 1.3 65.3 + - - +
539C TRP 3.0 13.9 + - - +
540C LYS* 3.8 13.3 + - + +
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Residues in contact with VAL 538 (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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534C ARG* 3.0 23.1 + - + +
535C THR* 3.2 13.7 + - + +
537C THR* 1.3 74.6 - - - +
539C TRP* 1.3 64.7 + - + +
540C LYS* 3.4 7.7 + - - +
541C LYS* 5.9 1.0 - - - +
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Residues in contact with TRP 539 (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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392C LEU* 3.8 26.5 - - + -
478C LEU* 5.3 8.1 - - + -
482C LEU* 6.0 0.4 - - + -
510C LYS* 3.3 52.0 - - + +
511C GLU* 4.3 26.5 - - + -
514C LEU* 4.2 19.7 - - + -
535C THR* 3.3 36.9 + - + +
536C LEU* 3.0 45.5 - - + +
537C THR* 3.0 4.6 - - - +
538C VAL* 1.3 85.7 - - + +
540C LYS* 1.3 57.6 + - - +
541C LYS 4.0 0.2 - - - -
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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