Contacts of the helix formed by residues 362 - 372 (chain A) in PDB entry 4UP5
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 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356A ARG* 3.9 2.0 - - - +
360A GLY 4.7 1.6 - - - +
361A MET* 1.3 77.0 - - - +
363A GLU* 1.3 60.5 + - - +
364A SER* 3.6 12.6 + - - -
365A ALA* 3.0 24.9 + - - +
366A TYR* 3.0 27.9 + - - +
1244A ASN* 2.9 29.9 + - + +
1247A ALA* 4.9 0.7 - - - +
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Residues in contact with GLU 363 (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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342A ASP* 4.9 3.7 - - - +
356A ARG* 3.6 36.9 + - - +
362A THR* 1.3 72.3 - - - +
364A SER* 1.3 61.8 + - - +
366A TYR* 3.4 5.2 + - - +
367A GLY* 3.0 19.8 + - - -
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Residues in contact with SER 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A THR* 3.1 11.2 + - - -
363A GLU* 1.3 78.2 - - - +
365A ALA* 1.3 62.2 + - - +
367A GLY* 3.2 3.0 + - - -
368A LEU* 3.0 27.0 + - - +
1247A ALA* 4.1 9.0 - - - -
1251A LEU* 3.9 27.9 - - - +
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Residues in contact with ALA 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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361A MET* 3.8 9.9 - - + -
362A THR* 3.0 16.9 + - - +
364A SER* 1.3 80.9 - - - +
366A TYR* 1.3 56.4 + - - +
368A LEU* 4.1 0.8 - - - +
369A LEU* 2.8 35.7 + - - +
1243A ALA* 3.6 27.8 - - + +
1244A ASN* 3.4 16.4 - - - +
1247A ALA* 3.6 11.8 - - + +
1258A ILE* 6.3 0.2 - - - -
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Residues in contact with TYR 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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342A ASP* 3.7 23.3 + - + -
343A ALA 3.2 47.7 + - - -
344A ILE* 4.4 4.0 - - + -
356A ARG* 3.6 27.4 - - + -
361A MET* 3.7 17.4 - - - -
362A THR 3.0 18.8 + - - +
363A GLU* 3.6 6.5 - - - +
364A SER 3.3 0.2 - - - -
365A ALA* 1.3 75.3 - - - +
367A GLY* 1.3 65.6 + - - +
369A LEU* 4.7 1.1 - - - -
370A THR* 2.8 59.1 + - + +
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Residues in contact with GLY 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 GLU 3.0 14.0 + - - -
364A SER* 3.2 3.1 + - - -
366A TYR* 1.3 82.3 - - - +
368A LEU* 1.3 60.3 + - - +
370A THR* 3.7 3.9 + - - -
371A THR* 2.8 31.4 + - - +
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Residues in contact with LEU 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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364A SER 3.0 15.0 + - - +
365A ALA* 4.1 3.4 - - - +
367A GLY* 1.3 76.2 - - - +
369A LEU* 1.3 63.4 + - - +
371A THR* 3.5 11.6 + - - +
372A GLU* 3.4 19.1 - - - +
1247A ALA* 3.7 35.4 - - + +
1250A VAL* 4.2 21.8 - - + -
1251A LEU* 4.7 13.9 - - + -
1258A ILE* 3.9 24.5 - - + +
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Residues in contact with LEU 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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344A ILE* 3.7 17.5 - - + -
361A MET* 3.7 29.6 - - + -
365A ALA 2.8 20.7 + - - +
366A TYR* 4.2 2.0 - - - +
368A LEU* 1.3 73.8 - - - +
370A THR* 1.3 61.7 + - - +
372A GLU* 3.3 19.8 + - - +
375A ALA* 3.8 27.7 - - + +
376A VAL 4.5 6.5 - - - +
377A TRP* 3.9 16.6 - - + +
1238A PHE* 4.0 21.3 - - + -
1243A ALA* 4.0 13.0 - - + -
1258A ILE* 4.0 12.3 - - + +
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Residues in contact with THR 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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343A ALA 5.0 2.0 - - - +
344A ILE* 3.9 20.9 - - + -
366A TYR* 2.8 57.7 + - + +
367A GLY* 3.7 6.2 + - - -
369A LEU* 1.3 76.8 - - - +
371A THR* 1.3 64.5 + - - +
372A GLU 3.3 1.3 + - - -
373A ALA 5.3 0.2 + - - -
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Residues in contact with THR 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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367A GLY* 2.8 22.8 + - - +
368A LEU* 3.5 12.8 + - - +
370A THR* 1.3 82.5 + - - +
372A GLU* 1.3 57.3 + - - +
373A ALA* 3.3 8.1 + - - +
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Residues in contact with GLU 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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368A LEU 3.4 17.0 + - - +
369A LEU 3.3 9.2 + - - +
370A THR 5.0 1.6 - - - -
371A THR* 1.3 75.4 - - - +
373A ALA* 1.3 58.3 + - - +
374A SER* 3.3 25.5 + - - -
375A ALA* 2.8 41.8 + - + +
1257A SER* 5.0 7.8 + - - -
1258A ILE* 4.4 7.5 - - + +
1259A LEU* 3.5 44.3 - - + +
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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