Contacts of the helix formed by residues 354 - 362 (chain A) in PDB entry 5UQ9
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 ASN 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A TRP 5.8 3.6 - - - +
174A VAL* 4.6 4.6 + - - +
352A THR 3.9 2.2 + - - +
353A LEU* 1.3 70.5 - - - +
355A TYR* 1.3 61.9 + - - +
356A GLY* 3.7 8.0 + - - -
357A GLY* 3.0 20.9 + - - +
358A ILE* 2.9 33.8 + - - +
380A PHE* 5.8 0.2 - - - +
384A PRO* 5.2 9.4 - - - +
38H LYS* 4.8 21.4 + - - +
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Residues in contact with TYR 355 (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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339A PHE* 3.4 34.7 - + + -
342A LEU* 4.4 4.5 - - + -
343A ARG* 3.3 59.2 + - + +
346A ALA* 3.9 12.3 - - - +
353A LEU* 3.6 39.6 + - + -
354A ASN* 1.3 73.7 + - - +
356A GLY* 1.3 62.2 + - - +
358A ILE* 3.5 9.7 + - + +
359A ALA* 3.2 18.9 + - - +
380A PHE* 3.6 33.5 - + + -
384A PRO 4.1 16.7 + - - +
385A GLU* 6.0 0.2 - - - -
386A LEU 5.2 0.4 - - - -
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Residues in contact with GLY 356 (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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354A ASN* 3.2 6.7 + - - -
355A TYR* 1.3 76.4 - - - +
357A GLY* 1.3 63.6 + - - +
359A ALA* 3.4 6.3 + - - +
360A LEU* 3.1 16.1 + - - +
377A LYS* 3.7 22.9 - - - +
380A PHE* 3.5 28.8 - - - +
381A ASP* 4.9 5.2 - - - -
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Residues in contact with GLY 357 (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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172A ASP* 6.3 2.5 - - - -
354A ASN* 3.0 28.4 + - - +
356A GLY* 1.3 73.8 - - - +
358A ILE* 1.3 58.8 + - - +
360A LEU* 3.0 13.0 + - - +
361A MET* 2.8 38.0 + - - +
377A LYS* 6.0 0.9 - - - -
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Residues in contact with ILE 358 (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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174A VAL* 5.1 6.5 - - + -
183A VAL* 3.9 31.2 - - + -
339A PHE* 4.8 1.6 - - + -
342A LEU* 4.1 17.7 - - + -
353A LEU* 4.2 23.3 - - + -
354A ASN 2.9 23.2 + - - +
355A TYR* 3.7 9.6 - - + +
356A GLY 3.3 0.2 - - - -
357A GLY* 1.3 74.8 - - - +
359A ALA* 1.3 62.0 + - - +
361A MET* 3.2 17.2 + - - +
362A TRP* 3.0 62.1 + - + +
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Residues in contact with ALA 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PHE* 4.4 2.6 - - + -
355A TYR 3.2 13.4 + - - +
356A GLY 3.6 8.7 - - - +
357A GLY 3.2 0.2 - - - -
358A ILE* 1.3 76.6 - - - +
360A LEU* 1.3 58.0 + - - +
362A TRP* 3.3 5.7 + - - +
363A ARG* 2.9 30.1 + - - +
373A LEU* 3.9 28.2 - - + +
376A ILE* 3.8 26.7 - - + -
377A LYS* 4.1 7.6 - - - +
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Residues in contact with LEU 360 (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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164A VAL* 4.0 27.8 - - + -
168A GLU* 3.8 28.3 - - + +
169A PRO 4.0 20.9 - - - +
170A CYS* 3.7 9.9 - - - -
172A ASP* 6.4 2.0 - - + -
356A GLY 3.1 12.2 + - - +
357A GLY* 3.0 14.8 + - - +
359A ALA* 1.3 74.6 - - - +
361A MET* 1.3 61.5 + - + +
363A ARG* 2.9 30.3 + - + +
377A LYS* 4.1 26.4 - - + +
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Residues in contact with MET 361 (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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140A SER* 3.2 27.9 + - - -
141A LEU 3.2 23.6 - - - +
142A MET* 3.5 23.8 - - + -
169A PRO 5.5 0.2 - - - +
170A CYS* 3.8 15.2 - - - +
171A CYS 4.2 5.2 - - - +
172A ASP* 3.2 45.3 - - + +
173A TRP 5.5 0.4 - - - +
174A VAL* 3.8 12.6 - - + -
183A VAL* 5.9 1.8 - - + -
357A GLY 2.8 22.6 + - - +
358A ILE* 3.2 20.4 + - + +
360A LEU* 1.3 77.5 - - + +
362A TRP* 1.3 63.4 + - + +
364A GLY 3.7 4.0 - - - +
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Residues in contact with TRP 362 (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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142A MET* 3.3 35.7 - - + +
183A VAL* 3.4 33.9 - - + +
186A VAL* 4.3 8.5 - - + -
187A HIS* 3.6 28.6 - + + +
190A ILE* 4.0 13.5 - - + -
335A TYR* 5.0 0.7 - + - -
339A PHE* 4.0 22.2 - + - -
342A LEU* 4.1 13.2 - - + -
358A ILE* 3.0 33.5 + - + +
359A ALA 3.5 3.1 - - - +
360A LEU 3.1 0.4 - - - -
361A MET* 1.3 79.9 - - + +
363A ARG* 1.3 55.5 + - - +
364A GLY 3.1 8.7 + - - -
366A CYS* 3.1 24.4 - - - -
368A ILE* 4.1 13.2 - - + -
369A ARG* 3.5 3.8 - - - -
373A LEU* 3.2 39.0 - - + +
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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