Contacts of the helix formed by residues 384 - 389 (chain B) in PDB entry 1U0E
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 THR 384 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ILE* 3.5 6.9 - - - +
185A ASN* 3.0 13.3 + - - -
186A ILE* 3.6 20.6 - - + -
216A GLU* 2.8 35.4 + - - +
340B TYR* 3.9 2.0 - - + -
383B GLY* 1.3 68.9 + - - -
385B ASN* 1.3 64.8 + - - +
386B GLY 3.2 2.7 - - - -
387B GLN* 2.9 44.9 + - - +
388B HIS* 3.6 4.3 - - - -
424B LEU* 3.9 8.3 - - + -
427B ASN* 3.7 19.1 - - + -
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Residues in contact with ASN 385 (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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156A ILE* 3.8 15.5 - - - +
157A GLY* 5.2 2.0 + - - +
160A ASP* 4.2 7.3 + - - -
161A LEU* 5.9 4.8 - - + +
184A SER* 2.7 36.9 + - - -
185A ASN* 3.2 33.1 + - - +
342B GLN* 3.6 6.7 - - - +
381B GLU* 5.3 4.9 - - + +
382B PRO* 3.2 15.0 + - + +
384B THR* 1.3 76.6 + - - +
386B GLY* 1.3 63.7 + - - +
388B HIS* 2.9 18.4 + - - +
389B ALA* 3.5 10.0 + - - +
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Residues in contact with GLY 386 (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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381B GLU* 4.7 3.7 - - - +
382B PRO 3.2 10.8 + - - -
383B GLY* 4.5 0.2 - - - -
384B THR 3.1 0.8 + - - -
385B ASN* 1.3 77.5 - - - +
387B GLN* 1.3 58.0 + - - +
389B ALA* 3.0 2.6 + - - -
390B PHE* 2.9 56.4 + - - -
391B TYR* 3.1 17.5 - - - -
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Residues in contact with GLN 387 (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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216A GLU* 4.1 4.2 - - - +
357A GLU* 4.6 0.3 - - - +
514A VAL* 3.7 24.3 - - - +
517A GLY 5.9 0.2 - - - -
518A LYS* 5.9 2.8 - - - +
340B TYR* 2.7 39.0 + - - +
384B THR* 2.9 23.6 + - - +
386B GLY* 1.3 77.9 - - - +
388B HIS* 1.3 65.1 + - + +
389B ALA 3.3 1.2 + - - -
391B TYR* 3.4 39.4 + - + +
427B ASN* 3.0 28.7 - - - +
431B GLN* 3.5 24.3 + - - +
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Residues in contact with HIS 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ILE* 3.5 36.9 - - + +
157A GLY* 3.5 22.6 - - - +
214A THR* 3.9 12.2 - - + +
216A GLU* 2.8 34.3 + - - -
353A GLN* 2.8 27.5 + - - -
357A GLU* 3.5 8.6 - - - +
514A VAL* 5.4 1.5 - - - +
518A LYS* 4.5 22.5 + - + -
1201A SO4 5.0 5.9 + - - -
384B THR 3.6 10.8 - - - -
385B ASN 2.9 6.8 + - - +
387B GLN* 1.3 83.8 + - + +
389B ALA* 1.3 57.5 + - - +
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Residues in contact with ALA 389 (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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157A GLY* 5.6 0.2 - - - -
161A LEU* 4.0 23.3 - - + -
349A ALA 5.4 0.2 - - - +
352A GLN* 5.3 1.3 - - + +
353A GLN* 3.3 29.4 - - + +
357A GLU* 3.3 21.7 + - - +
381B GLU* 6.2 1.3 - - + -
385B ASN 3.9 8.1 - - - +
386B GLY* 3.0 7.3 + - - +
387B GLN 3.3 0.8 - - - -
388B HIS* 1.3 80.9 - - - +
390B PHE* 1.3 75.1 + - + +
391B TYR 3.8 0.4 - - - -
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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