Contacts of the helix formed by residues 395 - 399 (chain B) in PDB entry 4DTZ
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 395 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B ALA 5.0 0.2 + - - -
62B CYS* 3.1 50.1 + - - +
64B GLU* 4.0 11.2 - - - +
331B PHE* 4.2 13.5 - - + -
333B LEU* 5.6 6.6 - - + +
388B HIS* 3.5 7.3 - - - -
391B LYS* 3.0 24.4 + - - +
394B GLY* 1.3 75.8 - - - +
396B GLY* 1.3 76.8 + - - +
398B ARG* 3.2 11.9 + - - +
399B ALA* 3.1 16.9 + - - +
500B HEM 5.4 1.0 + - - +
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Residues in contact with GLY 396 (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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64B GLU* 3.4 20.0 - - - -
391B LYS* 5.1 0.4 - - - +
395B ASN* 1.3 79.5 + - - +
397B GLN* 1.3 59.3 + - - -
399B ALA* 3.0 24.8 + - - +
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Residues in contact with GLN 397 (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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64B GLU* 2.8 25.2 + - - +
68B ASP* 4.8 3.1 - - - +
91B THR* 3.4 19.0 - - - +
96B TRP* 3.4 44.6 - - + -
97B LYS* 5.1 9.7 - - - +
100B HIS* 3.9 18.6 + - + +
396B GLY* 1.3 70.5 - - - -
398B ARG* 1.3 67.2 + - + +
399B ALA 3.3 5.0 + - - +
500B HEM 4.4 1.6 - - - +
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Residues in contact with ARG 398 (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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64B GLU* 4.5 0.6 + - - +
68B ASP* 4.5 3.4 - - - +
69B LYS* 3.6 47.1 - - + +
86B LEU 2.8 29.1 + - - -
87B PHE 4.2 0.2 + - - -
89B SER 3.0 26.8 + - - -
90B TRP* 3.6 1.6 - - - +
91B THR* 3.0 38.7 + - - +
96B TRP* 3.3 34.0 - - - +
395B ASN 3.2 10.5 + - - +
396B GLY 3.1 1.4 - - - -
397B GLN* 1.3 83.5 - - + +
399B ALA* 1.3 65.1 + - - +
500B HEM 2.8 48.1 + - - +
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Residues in contact with ALA 399 (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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393B PHE* 3.4 15.3 - - + +
394B GLY 4.2 1.3 - - - +
395B ASN* 3.1 16.9 + - - +
396B GLY 3.0 19.6 + - - +
397B GLN 3.3 3.4 - - - +
398B ARG* 1.3 83.8 - - - +
400B CYS* 1.3 70.3 + - - +
401B ILE* 3.1 5.5 + - - +
403B GLN* 5.8 2.0 - - - +
500B HEM 3.5 10.8 - - - +
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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