Contacts of the helix formed by residues 402 - 408 (chain B) in PDB entry 1U2X
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 ASP 402 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A ARG* 2.7 34.3 + - - +
390B ALA* 3.4 10.0 - - - +
394B LEU* 3.6 17.9 - - + +
397B ILE* 3.8 14.2 - - + -
398B ARG* 2.7 51.3 + - - +
399B GLY 2.9 17.7 + - - +
401B ASP* 1.3 75.5 - - - +
403B TYR* 1.3 64.4 + - - +
404B LYS 3.0 0.2 - - - -
405B VAL* 3.1 19.7 + - - +
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Residues in contact with TYR 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B MSE 4.9 10.6 + - - -
24B ILE* 4.2 13.7 - - + -
130B LEU* 4.8 6.1 - - + +
382B GLU 4.8 0.3 - - - -
383B PHE* 3.3 66.3 + + - -
386B THR* 3.5 27.7 + - + +
387B LEU* 4.0 20.6 - - + -
390B ALA* 4.4 5.6 - - - -
397B ILE* 5.3 1.2 - - - +
399B GLY 4.4 0.4 + - - -
400B PRO 3.1 15.2 + - - +
401B ASP 3.1 0.4 - - - -
402B ASP* 1.3 78.9 - - - +
404B LYS* 1.3 66.5 + - + +
406B GLY* 3.1 12.7 + - - -
407B LEU* 3.5 38.0 + - + +
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Residues in contact with LYS 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B PRO 5.5 0.2 - - - +
401B ASP* 3.1 39.4 + - + +
402B ASP 3.0 1.2 - - - -
403B TYR* 1.3 80.0 - - + +
405B VAL* 1.3 65.8 + - + +
407B LEU* 3.1 26.5 + - + +
408B LYS* 2.9 39.2 + - - +
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Residues in contact with VAL 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LEU* 4.2 21.2 - - + +
398A ARG* 3.5 46.9 - - - +
390B ALA* 4.5 2.2 - - + -
393B SER* 3.9 27.4 - - - +
394B LEU* 4.1 17.7 - - + -
401B ASP 4.8 0.7 - - - +
402B ASP* 3.3 13.9 - - - +
403B TYR 3.1 0.6 - - - -
404B LYS* 1.3 78.4 - - + +
406B GLY* 1.3 60.1 + - - +
408B LYS* 3.3 22.8 + - + +
409B VAL* 3.8 8.2 - - + +
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Residues in contact with GLY 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B THR* 3.5 28.7 - - - -
389B ALA* 4.1 5.4 - - - -
390B ALA* 3.6 14.6 - - - +
403B TYR 3.1 7.1 + - - -
405B VAL* 1.3 73.8 - - - +
407B LEU* 1.3 56.3 + - - +
408B LYS 3.0 5.2 - - - -
409B VAL* 2.9 21.5 + - - +
442B ARG* 3.4 16.1 - - - -
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Residues in contact with LEU 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B THR* 3.5 14.8 - - + +
403B TYR* 3.5 33.2 + - + +
404B LYS* 3.1 30.3 + - + +
406B GLY* 1.3 75.7 - - - +
408B LYS* 1.3 64.9 + - + +
409B VAL 3.3 2.0 - - - +
442B ARG* 3.4 33.3 + - - +
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Residues in contact with LYS 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLU* 5.7 5.9 - - - +
394A LEU 5.6 4.9 - - - +
396A ASP* 6.5 0.9 - - + -
448A VAL* 4.5 8.3 - - - +
404B LYS* 2.9 41.5 + - - +
405B VAL* 3.3 13.7 + - - +
406B GLY 3.0 1.2 - - - -
407B LEU* 1.3 87.9 - - - +
409B VAL* 1.3 64.3 + - + +
410B PRO* 3.7 6.9 - - - +
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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