Contacts of the helix formed by residues 400 - 405 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B LYS* 5.6 0.8 - - - -
326B PRO* 3.8 19.1 - - + -
330B LEU* 3.7 23.9 - - + +
399B ASP* 1.3 85.1 + - - +
401B ALA* 1.3 64.9 + - - +
402B ASP* 3.3 5.6 - - - -
403B ARG* 2.9 14.8 + - + +
404B MET 3.2 8.1 + - - -
431B PHE 2.9 11.4 + - - -
432B SER* 3.9 6.1 + - - -
551B ARG* 2.9 39.5 + - + +
552B GLY* 3.4 21.3 + - - -
575B HIS* 3.2 15.6 - - - -
2802B MG 3.7 5.7 - - - -
2902B ANP 3.4 16.4 + - - -
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Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B LEU* 3.5 20.0 - - + +
399B ASP 3.0 3.0 - - - -
400B GLU* 1.3 76.4 - - - +
402B ASP* 1.3 57.7 + - - +
404B MET* 2.9 3.6 + - - -
405B LEU* 2.8 32.8 + - - +
430B MET* 3.4 38.6 - - + -
431B PHE 2.9 10.2 + - - +
435B PHE* 3.7 13.0 - - + -
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Residues in contact with ASP 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B GLU 3.6 0.3 - - - +
401B ALA* 1.3 75.4 - - - +
403B ARG* 1.3 59.3 + - - -
405B LEU 3.4 0.7 + - - -
406B ASP* 3.3 10.4 + - - +
432B SER* 2.6 21.8 + - - -
434B THR* 2.5 42.5 + - - +
435B PHE* 3.9 13.5 - - + -
436B PRO* 3.9 22.1 - - + +
439B ILE* 3.2 33.0 - - + +
551B ARG* 2.9 23.7 + - - -
571B ASP* 4.9 1.4 - - - +
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Residues in contact with ARG 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B PRO* 4.0 20.2 - - + -
400B GLU* 2.9 12.3 + - + +
402B ASP* 1.3 77.3 + - - +
404B MET* 1.3 65.9 + - - +
405B LEU 3.1 2.7 + - - -
406B ASP* 3.4 28.2 + - - +
408B GLY* 6.4 3.1 - - - -
409B PHE* 3.5 22.0 + - + +
551B ARG* 3.6 34.8 - - - +
569B LYS* 6.3 0.8 - - - +
2F U 5.9 0.2 - - - +
3F U 2.5 34.1 + - - +
4F U 4.9 9.1 + - - -
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Residues in contact with MET 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B VAL* 3.0 34.3 - - + +
325B SER 3.8 4.3 - - - -
326B PRO* 3.3 42.0 - - + -
376B PRO* 3.4 23.1 - - + -
398B LEU* 4.3 17.3 - - + -
399B ASP 3.3 21.1 - - - +
400B GLU 3.2 3.6 + - - +
401B ALA* 2.9 10.6 + - - +
403B ARG* 1.3 77.6 - - - +
405B LEU* 1.3 60.2 + - - +
406B ASP 3.5 0.2 - - - -
409B PHE* 3.5 24.2 - - + +
413B MET* 3.6 26.3 - - + +
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Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B LEU* 4.2 13.0 - - + -
401B ALA 2.8 16.4 + - - +
402B ASP 3.9 0.7 - - - -
403B ARG 3.1 0.2 - - - -
404B MET* 1.3 83.4 - - - +
406B ASP* 1.3 62.2 + - - +
410B SER* 3.7 15.9 - - - +
413B MET* 4.4 5.6 - - + -
430B MET* 3.8 28.5 - - + -
435B PHE* 4.5 4.0 - - + -
439B ILE* 3.5 26.7 - - + -
442B MET* 4.2 21.3 - - + +
443B ALA* 3.9 22.2 - - + +
446B PHE* 3.5 33.2 - - + -
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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