Contacts of the strand formed by residues 326 - 332 (chain H) in PDB entry 3QS7
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 GLY 326 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287H LEU* 4.9 1.1 - - - -
288H GLU* 4.1 14.4 - - - -
324H ASP 3.6 2.9 + - - -
325H THR* 1.3 73.0 - - - +
327H TYR* 1.4 57.3 + - - -
328H TYR* 3.3 15.9 - - - -
341H LEU* 4.4 2.5 - - - -
342H VAL* 2.8 36.5 + - - +
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Residues in contact with TYR 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286H GLU 3.8 0.2 - - - +
287H LEU 3.0 24.8 - - - +
288H GLU* 3.5 11.2 + - + +
326H GLY* 1.4 68.9 - - - -
328H TYR* 1.4 62.1 + - - +
329H THR* 5.2 1.9 - - - +
339H SER* 5.8 4.0 - - - -
340H ALA 5.3 0.7 - - - -
341H LEU* 4.0 19.0 - - + +
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Residues in contact with TYR 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247H ILE* 6.1 0.2 - - + -
268H LEU* 4.0 19.0 - - + +
270H ILE* 4.6 16.2 - - + -
285H TRP* 4.1 21.1 - + + -
286H GLU 3.3 6.7 - - - -
287H LEU* 3.4 44.8 - - + +
315H ALA* 5.6 4.0 - - + -
317H VAL* 4.6 5.2 - - + +
324H ASP* 2.7 36.2 + - - +
326H GLY 3.3 18.4 - - - -
327H TYR* 1.4 70.3 - - - +
329H THR* 1.3 60.8 + - - +
339H SER* 3.3 4.0 - - - -
340H ALA* 2.9 39.9 + - + +
342H VAL* 3.6 26.0 - - + -
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Residues in contact with THR 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284H THR 3.7 1.4 - - - +
285H TRP* 3.3 8.3 - - - -
286H GLU* 2.9 54.7 + - + +
287H LEU 5.1 2.7 - - - +
327H TYR 5.2 1.6 - - - +
328H TYR* 1.3 74.4 - - - +
330H CYS* 1.3 65.6 + - - +
331H SER* 5.9 1.6 - - - +
337H SER* 4.1 13.1 - - - -
338H GLN 3.3 8.4 + - - -
339H SER* 2.7 26.0 + - - -
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Residues in contact with CYS 330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247H ILE* 4.6 2.7 - - + -
249H LEU* 3.4 11.8 - - + +
272H CYS* 2.0 49.8 - - - -
283H LEU* 4.0 11.7 - - - -
284H THR 3.3 12.6 - - - -
285H TRP* 3.7 21.2 - - + -
313H LEU* 5.0 0.7 - - - -
329H THR* 1.3 75.0 + - - +
331H SER* 1.3 61.8 + - - +
337H SER* 3.2 2.5 - - - -
338H GLN 2.9 35.4 + - - +
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Residues in contact with SER 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249H LEU* 4.1 2.9 - - - -
283H LEU* 3.4 2.1 - - - +
284H THR* 2.9 38.9 + - - -
329H THR* 4.2 2.0 + - - -
330H CYS* 1.3 75.0 - - - +
332H SER* 1.3 61.7 + - - +
333H SER 4.4 0.2 + - - -
335H HIS 5.3 0.7 - - - -
337H SER* 3.5 24.2 - - - +
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Residues in contact with SER 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249H LEU* 3.7 14.0 - - - +
274H ALA* 4.5 0.2 - - - -
281H PHE* 4.5 0.9 - - - -
282H GLY 3.1 13.5 - - - -
283H LEU* 4.0 9.6 - - - -
331H SER* 1.3 75.9 - - - +
333H SER* 1.4 52.6 + - - +
334H LYS 2.8 14.9 + - - -
335H HIS* 2.9 57.5 + - - +
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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