Contacts of the helix formed by residues 364 - 372 (chain A) in PDB entry 1UOU
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 364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A GLY* 1.3 72.2 - - - -
365A PRO* 1.3 77.7 - - - +
366A ALA* 3.8 8.6 + - - +
367A GLU* 2.9 35.5 + - - +
368A ARG* 2.9 21.1 + - - +
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Residues in contact with PRO 365 (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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288A GLU* 5.2 0.5 - - - +
292A LEU* 3.9 27.1 - - + -
295A ASP* 4.7 4.7 - - - +
363A GLY 4.5 1.6 - - - +
364A SER* 1.3 83.7 - - - +
366A ALA* 1.3 62.3 + - - +
368A ARG* 3.1 21.5 + - - +
369A ARG* 3.0 42.0 + - - +
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Residues in contact with ALA 366 (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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364A SER* 3.1 8.5 + - - +
365A PRO* 1.3 77.3 - - - +
367A GLU* 1.3 65.0 + - + +
369A ARG* 3.2 37.2 + - - +
370A GLN* 3.3 17.4 + - - +
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Residues in contact with GLU 367 (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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363A GLY* 3.4 13.6 - - - -
364A SER* 2.9 36.7 + - - +
366A ALA* 1.3 79.7 - - + +
368A ARG* 1.3 61.3 + - - +
370A GLN* 3.5 7.7 + - - +
371A LEU* 3.2 36.7 + - + +
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Residues in contact with ARG 368 (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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288A GLU* 4.3 19.4 + - + -
291A LEU* 3.4 41.0 - - + +
292A LEU* 3.9 5.7 - - - +
295A ASP* 2.8 40.3 + - - -
340A LEU* 4.6 2.0 - - - +
359A ALA 5.0 0.2 - - - +
360A LEU* 2.7 38.5 + - + +
361A CYS* 2.8 27.5 + - - +
363A GLY* 3.5 19.2 + - - +
364A SER 2.9 16.1 + - - +
365A PRO* 3.1 15.6 + - - +
367A GLU* 1.3 77.5 - - - +
369A ARG* 1.3 61.5 + - - +
371A LEU* 3.2 2.2 + - - -
372A LEU* 3.2 29.6 + - + +
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Residues in contact with ARG 369 (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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285A LEU* 5.9 2.9 - - - -
288A GLU* 3.4 29.7 - - + +
365A PRO* 3.0 32.4 + - - +
366A ALA* 3.2 35.0 + - - +
368A ARG* 1.3 75.7 - - - +
370A GLN* 1.3 58.3 + - - +
371A LEU 3.5 0.2 - - - -
372A LEU 3.3 5.4 - - - +
374A ARG* 3.2 35.8 + - + +
422A GLU* 5.6 6.3 - - - -
441A HIS* 6.3 3.4 - - - -
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Residues in contact with GLN 370 (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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366A ALA 3.3 12.9 + - - +
367A GLU* 4.0 8.3 - - - +
368A ARG 3.3 0.6 - - - -
369A ARG* 1.3 77.2 - - - +
371A LEU* 1.3 65.3 + - + +
372A LEU 3.3 0.9 - - - -
374A ARG* 3.1 50.0 + - - +
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Residues in contact with LEU 371 (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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162A PRO* 4.3 13.7 - - - +
356A LEU* 3.8 23.3 - - + +
359A ALA* 3.8 42.0 - - + +
360A LEU* 3.8 21.8 - - + +
367A GLU* 3.2 26.5 + - + +
368A ARG 3.2 0.8 + - - +
370A GLN* 1.3 78.5 - - + +
372A LEU* 1.3 65.7 + - - +
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Residues in contact with LEU 372 (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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160A SER* 4.0 7.9 - - - +
161A ILE* 4.1 9.4 - - + -
162A PRO* 4.0 19.5 - - + -
284A ALA* 4.3 6.7 - - + +
287A VAL* 3.8 33.7 - - + -
288A GLU* 3.4 31.0 - - + +
291A LEU* 5.2 1.8 - - + -
360A LEU* 3.7 30.1 - - + -
368A ARG 3.2 10.5 + - - +
369A ARG 3.3 5.2 - - - +
371A LEU* 1.3 86.2 - - - +
373A PRO* 1.3 74.6 - - + +
374A ARG* 3.1 18.2 + - - -
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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