Contacts of the strand formed by residues 338 - 342 (chain H) in PDB entry 1P8J
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 ALA 338 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316H SER 3.6 2.6 + - - -
317H ILE* 3.4 14.5 - - + +
318H SER 3.0 21.8 + - - -
336H THR* 3.6 4.0 - - - +
337H LEU* 1.3 81.7 - - - +
339H THR* 1.3 66.9 + - - +
397H VAL* 3.4 26.9 - - + -
401H SER* 3.6 3.1 - - - +
424H TYR 3.5 4.3 - - - -
427H GLY 3.5 10.3 - - - +
429H LEU* 3.5 18.4 - - + -
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Residues in contact with THR 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317H ILE* 4.2 0.7 - - - -
318H SER* 3.2 17.0 - - - +
319H SER 3.4 25.8 - - - +
320H ALA* 3.7 12.3 - - + +
338H ALA* 1.3 74.3 + - - +
340H THR* 1.3 81.0 + - - +
406H LEU* 4.3 4.0 - - + -
423H SER 4.3 0.5 + - - -
424H TYR* 2.8 40.4 + - + +
427H GLY 2.7 18.0 + - - -
428H LEU* 3.4 4.0 - - + -
429H LEU* 2.9 27.6 + - - +
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Residues in contact with THR 340 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H LEU* 3.9 13.0 - - + -
317H ILE* 3.7 10.8 - - + -
318H SER 3.2 3.2 + - - -
319H SER* 3.3 13.0 - - - -
320H ALA 3.4 2.3 + - - -
339H THR* 1.3 82.5 - - - +
341H TYR* 1.3 66.0 + - - +
370H SER* 2.9 53.0 + - - +
373H LEU* 4.1 10.4 - - + +
374H ALA* 3.9 6.7 - - + +
428H LEU* 3.7 10.1 - - - -
429H LEU* 3.8 21.5 - - + -
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Residues in contact with TYR 341 (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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122H TRP* 3.5 27.6 - + + -
123H TYR* 3.9 16.2 - - + -
130H ARG* 3.4 43.7 + - - +
131H ASP* 3.5 15.3 - - - -
132H LEU* 4.1 7.2 - - + +
320H ALA* 3.4 17.3 - - + -
321H THR 3.3 27.4 - - - -
322H GLN 4.2 7.9 - - - -
324H GLY* 4.6 6.3 - - - -
340H THR* 1.3 84.7 + - - +
342H SER* 1.3 61.1 + - - +
351H ILE* 4.0 2.1 - - - +
370H SER* 3.6 0.9 + - - -
373H LEU* 3.5 16.8 - - - +
405H HIS* 5.0 4.5 + - - +
406H LEU* 4.5 8.7 - - + +
428H LEU* 3.3 33.9 - - + +
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Residues in contact with SER 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H TRP* 3.8 15.9 - - - -
319H SER* 3.7 4.5 - - - -
320H ALA 2.9 12.8 + - - +
321H THR* 3.9 3.5 - - - -
322H GLN 4.1 0.2 + - - -
329H TYR* 3.2 15.1 + - - -
341H TYR* 1.3 77.1 - - - +
343H SER* 1.3 72.6 + - - +
349H LYS 4.1 1.4 - - - +
351H ILE* 3.8 16.5 - - - +
365H THR 4.0 0.3 - - - -
366H GLY 2.7 27.0 + - - -
369H ALA* 3.7 10.3 - - - +
370H SER* 3.5 15.7 - - - -
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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
------------------------------------------------------------
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