Contacts of the helix formed by residues 400 - 405 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A LYS* 5.9 0.9 - - - -
326A PRO* 3.7 19.7 - - + -
330A LEU* 3.6 25.5 - - + +
399A ASP* 1.3 86.3 + - - +
401A ALA* 1.3 64.2 + - - +
402A ASP* 3.3 5.4 - - - -
403A ARG* 3.0 13.3 + - - +
404A MET* 3.2 8.5 + - - +
431A PHE 2.9 9.0 + - - -
432A SER* 4.0 5.8 + - - -
551A ARG* 2.8 45.1 + - + +
552A GLY* 3.4 20.1 + - - -
575A HIS* 3.3 11.4 + - - -
2801A MG 3.9 4.5 - - - -
2901A ANP 3.4 17.8 + - - -
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Residues in contact with ALA 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A LEU* 3.3 30.5 - - + +
399A ASP 2.9 3.0 - - - -
400A GLU* 1.3 76.5 - - - +
402A ASP* 1.3 63.1 + - - +
404A MET* 2.9 12.8 + - - +
405A LEU* 3.0 19.6 + - - +
430A MET* 3.5 30.1 - - + -
431A PHE 2.9 10.2 + - - +
435A PHE* 4.1 9.9 - - + -
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Residues in contact with ASP 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A GLU 3.7 0.5 - - - -
401A ALA* 1.3 73.4 - - - +
403A ARG* 1.3 58.7 + - - -
405A LEU 3.6 0.3 + - - -
406A ASP* 3.3 10.7 + - - +
432A SER* 2.5 14.2 + - - -
434A THR* 2.6 40.3 + - - +
435A PHE* 4.0 22.9 - - + -
436A PRO* 4.1 8.2 - - + +
439A ILE* 3.3 36.7 - - + +
551A ARG* 2.4 36.8 + - - -
571A ASP* 4.4 2.9 - - - +
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Residues in contact with ARG 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A PRO* 4.0 22.0 - - + -
400A GLU 3.0 10.5 + - - +
402A ASP* 1.3 79.2 - - - +
404A MET* 1.3 66.9 + - - +
405A LEU 3.1 1.0 + - - -
406A ASP* 3.3 32.0 + - - +
408A GLY* 6.2 3.6 - - - -
409A PHE* 3.7 21.1 + - + +
551A ARG* 3.6 35.2 - - - +
569A LYS* 5.2 9.7 - - - +
2E U 5.9 0.2 - - - +
3E U 2.8 32.5 + - - +
4E U 4.9 8.7 + - - -
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Residues in contact with MET 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A VAL* 3.5 12.6 - - + +
325A SER* 3.7 1.8 - - - +
326A PRO* 3.4 40.2 - - - -
376A PRO* 3.3 24.2 - - + -
398A LEU* 4.4 11.7 - - + -
399A ASP 3.5 11.4 - - - +
400A GLU 3.5 12.6 - - - +
401A ALA* 2.9 9.3 + - - +
403A ARG* 1.3 77.7 - - - +
405A LEU* 1.3 59.5 + - - +
406A ASP 3.5 0.2 - - - -
409A PHE* 3.0 37.4 - - + +
413A MET* 3.2 48.9 - - + +
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Residues in contact with LEU 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A LEU* 4.1 19.7 - - + -
401A ALA 3.0 16.4 + - - +
402A ASP 3.9 0.9 - - - -
404A MET* 1.3 77.9 - - - +
406A ASP* 1.3 63.0 + - - +
410A SER* 3.8 14.7 - - - +
413A MET* 4.1 7.9 - - + -
417A MET* 4.1 18.2 - - + -
430A MET* 3.9 13.5 - - - -
435A PHE* 4.5 1.3 - - + -
439A ILE* 4.1 18.8 - - + +
442A MET* 3.7 25.1 - - + +
443A ALA* 3.5 37.5 - - + +
446A PHE* 4.3 15.7 - - + -
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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