Contacts of the helix formed by residues 400 - 406 (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 GLU 400 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295C LYS* 5.7 1.2 - - - -
326C PRO* 3.8 17.0 - - + -
330C LEU* 3.6 25.1 - - + +
399C ASP* 1.3 84.8 + - - +
401C ALA* 1.3 64.8 + - - +
402C ASP* 3.3 5.2 - - - -
403C ARG* 2.9 13.7 + - - +
404C MET* 3.1 9.0 + - - +
431C PHE 2.9 8.4 + - - -
432C SER* 4.0 5.8 + - - -
551C ARG* 2.9 42.6 + - + +
552C GLY* 3.3 21.3 + - - -
575C HIS* 3.3 14.5 - - - -
2803C MG 3.8 4.9 - - - -
2903C ANP 3.4 17.8 + - - -
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Residues in contact with ALA 401 (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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398C LEU* 3.4 27.6 - - + +
399C ASP 2.9 5.3 - - - -
400C GLU* 1.3 73.3 - - - +
402C ASP* 1.3 66.0 + - - +
404C MET* 3.0 2.7 + - - -
405C LEU* 3.0 28.8 + - - +
430C MET* 3.5 29.6 - - + -
431C PHE 2.9 9.5 + - - +
432C SER* 4.0 0.4 - - - -
435C PHE* 3.9 11.7 - - + -
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Residues in contact with ASP 402 (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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400C GLU 3.7 0.3 - - - +
401C ALA* 1.3 75.7 - - - +
403C ARG* 1.3 60.5 + - - -
405C LEU 3.4 0.3 + - - -
406C ASP* 3.2 19.1 + - - +
432C SER* 2.7 19.3 + - - -
434C THR* 2.5 43.3 + - - +
435C PHE* 4.0 12.5 - - + -
436C PRO* 3.9 23.2 - - + +
439C ILE* 3.5 23.7 - - + +
551C ARG* 3.0 22.5 + - - -
571C ASP* 4.6 1.9 - - - +
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Residues in contact with ARG 403 (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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326C PRO* 4.0 20.8 - - + +
400C GLU* 2.9 13.2 + - + +
402C ASP* 1.3 78.3 + - - +
404C MET* 1.3 63.7 + - - +
405C LEU 3.1 2.9 + - - -
406C ASP* 3.4 28.0 + - - +
408C GLY* 6.2 2.8 - - - -
409C PHE* 3.5 22.7 + - + +
551C ARG* 3.6 36.8 - - - +
569C LYS* 6.2 1.6 - - - +
3G U 2.7 33.9 + - - +
4G U 4.9 9.5 + - - -
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Residues in contact with MET 404 (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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324C VAL* 3.2 33.7 - - + +
325C SER 3.6 5.2 - - - +
326C PRO* 3.3 41.7 - - + -
376C PRO* 3.4 21.5 - - + -
398C LEU* 4.5 10.1 - - + -
399C ASP 3.3 22.4 - - - +
400C GLU 3.1 2.7 + - - +
401C ALA* 3.0 9.7 + - - +
403C ARG* 1.3 75.8 - - - +
405C LEU* 1.3 57.5 + - - +
406C ASP 3.6 0.2 - - - -
409C PHE* 3.3 27.2 - - + +
413C MET* 3.3 35.6 - - + +
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Residues in contact with LEU 405 (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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398C LEU* 4.2 17.5 - - + -
401C ALA 3.0 20.3 + - - +
402C ASP 3.8 0.2 - - - -
404C MET* 1.3 80.7 - - - +
406C ASP* 1.3 66.1 + - - +
410C SER* 3.7 9.5 - - - +
413C MET* 4.4 8.7 - - + -
417C MET* 4.9 0.7 - - + -
430C MET* 3.9 13.9 - - + -
435C PHE* 4.5 2.5 - - + -
439C ILE* 3.6 22.7 - - + -
442C MET* 3.6 28.1 - - + +
443C ALA* 3.6 33.7 - - + +
446C PHE* 4.1 29.2 - - + -
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Residues in contact with ASP 406 (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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402C ASP 3.2 15.0 + - - +
403C ARG* 3.4 26.3 + - - +
405C LEU* 1.3 78.8 - - - +
407C MET* 1.3 95.2 + - - +
408C GLY 3.3 3.4 - - - +
409C PHE 3.2 3.9 + - - -
410C SER* 2.9 21.2 + - - -
439C ILE* 3.6 22.1 - - - +
442C MET* 5.5 2.0 - - - -
569C LYS* 5.3 10.4 + - - +
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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