Contacts of the helix formed by residues 524 - 537 (chain C) in PDB entry 2DB3
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 LEU 524 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522C ASP 5.4 2.0 - - - +
523C ARG* 1.3 73.9 - - - +
525C GLN* 1.3 57.5 + - - +
526C SER* 3.9 14.4 - - - +
527C GLN* 2.7 57.6 + - + +
528C ARG* 3.0 9.9 + - - +
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Residues in contact with GLN 525 (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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202C TYR* 4.1 4.0 - - + -
328C ARG* 2.7 46.9 + - - +
329C GLU* 3.0 23.9 + - - +
332C ILE* 4.8 0.6 - - - +
353C TYR* 4.1 4.2 - - + -
354C GLY 3.9 8.3 - - - +
355C GLY* 3.4 33.2 - - - +
523C ARG 3.5 2.6 + - - -
524C LEU* 1.3 71.6 - - - +
526C SER* 1.3 62.3 + - - +
528C ARG* 3.3 15.0 + - - +
529C GLU* 2.9 56.1 + - - +
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Residues in contact with SER 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C TYR* 3.4 44.4 + - - +
524C LEU* 3.9 17.9 - - - +
525C GLN* 1.3 79.0 - - - +
527C GLN* 1.3 63.6 + - - +
529C GLU* 3.5 2.4 + - - +
530C GLN* 3.0 28.1 + - - +
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Residues in contact with GLN 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523C ARG* 3.6 45.3 + - + +
524C LEU* 2.7 59.3 + - + +
526C SER* 1.3 74.5 + - - +
528C ARG* 1.3 58.9 + - - +
530C GLN* 3.8 6.4 - - - +
531C ALA* 2.9 30.8 + - - +
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Residues in contact with ARG 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C ARG* 3.8 11.5 - - - +
329C GLU* 2.9 45.7 + - - +
519C ILE* 3.7 29.8 - - + +
520C HIS 3.5 22.2 - - - +
521C GLY* 3.9 18.0 + - - -
523C ARG* 4.0 19.2 + - + -
524C LEU 3.0 9.7 + - - +
525C GLN* 3.3 26.1 + - - +
527C GLN* 1.3 77.3 - - - +
529C GLU* 1.3 62.9 + - - +
531C ALA* 3.4 5.3 + - - +
532C LEU* 3.4 17.2 + - - +
548C VAL* 3.5 14.5 - - - +
5G U 3.0 42.4 + - - -
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Residues in contact with GLU 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C TYR* 2.7 29.1 + - - +
204C PRO* 3.6 5.5 - - - +
205C PRO* 4.7 3.1 - - - +
329C GLU* 4.7 7.6 - - + +
332C ILE* 3.5 16.4 - - + +
353C TYR* 2.8 31.2 + - - -
525C GLN* 2.9 40.4 + - - +
526C SER 3.9 4.3 - - - +
528C ARG* 1.3 76.7 - - - +
530C GLN* 1.3 62.1 + - - +
532C LEU* 3.6 5.5 + - - +
533C ARG* 3.1 22.2 + - - +
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Residues in contact with GLN 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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526C SER 3.0 18.2 + - - +
527C GLN* 3.3 8.0 + - - +
529C GLU* 1.3 75.3 - - - +
531C ALA* 1.3 55.7 + - - +
533C ARG* 3.1 28.5 + - - +
534C ASP* 2.7 76.5 + - - +
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Residues in contact with ALA 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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517C THR* 3.5 28.1 - - + +
518C SER 3.4 28.0 - - - +
519C ILE* 4.5 1.8 - - + -
523C ARG* 4.0 1.8 - - - +
527C GLN 2.9 17.3 + - - +
528C ARG* 3.5 7.2 - - - +
530C GLN* 1.3 77.9 - - - +
532C LEU* 1.3 62.2 + - - +
534C ASP* 3.4 3.0 + - - -
535C PHE* 3.0 24.6 + - - +
543C LEU* 4.5 5.3 - - + +
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Residues in contact with LEU 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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329C GLU* 3.6 35.7 - - + -
519C ILE* 4.0 13.5 - - + -
528C ARG 3.4 9.9 + - - +
529C GLU* 4.0 6.7 - - - +
530C GLN 3.3 0.2 - - - -
531C ALA* 1.3 80.4 - - - +
533C ARG* 1.3 57.7 + - - +
535C PHE* 3.3 3.6 + - + +
536C LYS* 2.9 50.3 + - - +
543C LEU* 3.7 29.2 - - + -
553C LEU* 4.1 20.9 - - + -
555C ILE* 3.9 20.2 - - + -
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Residues in contact with ARG 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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205C PRO* 5.2 13.1 - - - +
529C GLU 3.1 18.2 + - - +
530C GLN* 3.1 29.8 + - - +
532C LEU* 1.3 77.6 - - - +
534C ASP* 1.3 61.7 + - - +
536C LYS* 3.3 10.1 + - - +
537C ASN* 3.2 35.5 + - + +
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Residues in contact with ASP 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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517C THR* 5.5 0.9 + - - -
530C GLN* 2.7 56.5 + - - +
531C ALA* 3.9 5.6 - - - +
533C ARG* 1.3 73.1 - - - +
535C PHE* 1.3 60.8 + - - +
537C ASN* 2.8 26.9 + - - +
539C SER* 3.2 25.3 + - - +
540C MET* 3.3 33.7 + - + +
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Residues in contact with PHE 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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491C GLY* 3.9 10.3 - - - -
492C THR 3.5 31.9 - - - -
493C ILE* 4.7 0.7 - - + -
517C THR* 5.0 0.7 - - + -
531C ALA 3.0 17.3 + - - +
532C LEU* 3.6 7.4 - - - +
533C ARG 3.2 0.2 - - - -
534C ASP* 1.3 78.3 - - - +
536C LYS* 1.3 61.5 + - - +
538C GLY* 3.4 7.3 + - - -
540C MET* 3.8 21.5 - - + +
541C LYS 3.2 23.3 - - - -
542C VAL 4.1 3.1 - - - -
543C LEU* 3.6 33.9 - - + -
555C ILE* 4.1 15.7 - - + -
557C ASN* 3.2 27.7 + - + +
558C ILE* 3.6 28.7 - - + -
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Residues in contact with LYS 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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333C GLN* 5.9 1.5 + - - +
532C LEU* 2.9 34.7 + - - +
533C ARG* 3.3 8.0 + - - +
535C PHE* 1.3 79.5 - - + +
537C ASN* 1.3 56.3 + - - +
554C ASP 5.5 1.8 - - - -
555C ILE* 3.9 42.6 - - + -
557C ASN* 2.8 20.1 + - - +
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Residues in contact with ASN 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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533C ARG* 3.2 29.6 + - + +
534C ASP* 2.8 15.3 + - - +
536C LYS* 1.3 75.8 - - + +
538C GLY* 1.3 57.4 + - - +
539C SER* 2.2 32.6 + - - -
557C ASN* 4.5 0.9 - - - -
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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