Contacts of the helix formed by residues 403 - 408 (chain A) in PDB entry 1U67
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 SER 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A ASP 5.6 0.2 - - - -
394A SER* 4.9 7.2 - - - -
395A PHE* 5.1 0.2 - - - -
401A ASP 3.7 2.4 + - - -
402A TYR* 1.3 73.1 - - - +
404A TYR* 1.3 69.8 + - - +
405A GLU* 3.3 16.1 + - - +
406A GLN* 2.9 30.1 - - - +
407A PHE* 2.8 19.5 + - - +
443A HIS* 5.3 3.8 + - - -
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Residues in contact with TYR 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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391A MET* 3.7 16.6 - - - +
392A PRO 3.0 17.5 + - - -
393A ASP 2.9 31.8 + - - -
395A PHE* 3.1 29.6 - + - -
403A SER* 1.3 73.4 + - - +
405A GLU* 1.3 53.8 + - - +
407A PHE* 2.7 10.8 + - - -
408A LEU* 2.5 58.6 + - + +
441A ASP* 3.5 15.7 - - - +
443A HIS* 3.1 53.6 + + + +
444A ILE* 3.7 19.2 - - + +
601A COH 5.3 4.3 - - + -
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Residues in contact with GLU 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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403A SER* 3.3 10.6 + - - +
404A TYR* 1.3 80.0 - - - +
406A GLN* 1.3 59.7 + - + +
408A LEU* 3.5 16.0 - - - +
409A PHE* 5.7 0.9 - - - -
443A HIS* 5.9 0.4 - - - -
1D NAG 4.4 5.2 - - - +
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Residues in contact with GLN 406 (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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401A ASP 4.5 3.0 + - - +
402A TYR* 3.4 27.7 - - + -
403A SER* 2.9 44.6 - - - +
405A GLU* 1.3 74.9 - - - +
407A PHE* 1.3 55.2 + - - +
410A ASN* 2.7 31.5 + - - -
413A MET* 3.9 4.8 - - - +
1D NAG 3.1 25.9 - - - +
2D NDG 4.3 11.9 + - - +
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Residues in contact with PHE 407 (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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200A PHE* 3.9 16.2 - + - -
295A LEU* 3.6 26.9 - - + -
296A PRO* 3.3 32.4 - - + +
297A GLY 4.4 0.4 - - - -
395A PHE* 3.3 55.2 - + + -
397A VAL* 5.7 0.7 - - + -
402A TYR* 4.5 5.6 - - + -
403A SER 2.8 14.3 + - - +
404A TYR* 2.7 14.4 + - - +
406A GLN* 1.3 71.8 - - - +
408A LEU* 1.3 70.0 + - + +
409A PHE 3.4 0.5 + - - -
410A ASN* 2.9 17.6 + - - +
413A MET* 3.4 36.3 - - + -
426A PHE* 4.4 11.0 - + - -
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Residues in contact with LEU 408 (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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294A LEU 3.9 5.4 - - - +
295A LEU* 3.3 29.2 - - + -
404A TYR* 2.5 46.1 + - + +
405A GLU* 3.5 15.2 - - - +
406A GLN 4.3 0.2 - - - -
407A PHE* 1.3 73.5 - - + +
409A PHE* 1.3 83.5 + - + +
410A ASN* 2.4 20.2 + - - +
443A HIS* 5.7 2.9 - - + -
444A ILE* 6.2 0.2 - - + -
601A COH 4.5 25.1 - - + -
1D NAG 4.8 1.7 - - - +
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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