Contacts of the strand formed by residues 338 - 342 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316G SER 3.7 2.4 + - - -
317G ILE* 3.4 14.7 - - + +
318G SER 2.9 22.3 + - - -
336G THR* 3.6 3.5 - - - +
337G LEU* 1.3 80.4 - - - +
339G THR* 1.3 67.2 + - - +
397G VAL* 3.4 25.8 - - + -
401G SER* 3.7 3.1 - - - +
424G TYR 3.6 4.7 - - - -
427G GLY 3.5 12.3 - - - +
429G LEU* 3.6 18.4 - - + -
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Residues in contact with THR 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317G ILE* 4.2 0.7 - - - -
318G SER* 3.2 18.0 - - - +
319G SER 3.4 26.9 - - - +
320G ALA* 3.7 12.3 - - + +
338G ALA* 1.3 76.3 + - - +
340G THR* 1.3 81.6 + - - +
406G LEU* 4.7 0.9 - - + -
424G TYR* 2.9 38.7 + - + +
427G GLY 2.7 18.5 + - - -
428G LEU* 3.4 5.8 - - + -
429G LEU* 2.9 27.1 + - - +
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Residues in contact with THR 340 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G LEU* 4.3 9.9 - - + -
317G ILE* 4.1 2.5 - - + -
318G SER 3.2 4.6 + - - -
319G SER* 3.3 1.0 - - - -
320G ALA 3.3 15.3 + - - -
339G THR* 1.3 82.5 - - - +
341G TYR* 1.3 66.8 + - - +
370G SER* 3.0 51.3 + - - +
373G LEU* 4.0 11.2 - - + +
374G ALA* 4.1 10.8 - - + +
377G ILE* 4.9 1.8 - - + -
428G LEU* 3.8 7.9 - - - -
429G LEU* 3.7 27.1 - - + -
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Residues in contact with TYR 341 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G TRP* 3.6 29.2 - + + -
123G TYR* 3.9 17.5 - - + -
130G ARG* 2.5 41.4 + - - +
131G ASP* 4.3 11.4 - - - -
132G LEU* 4.2 15.4 - - + +
320G ALA* 3.4 16.6 - - + -
321G THR 3.3 27.6 - - - -
322G GLN 4.2 10.8 + - - -
324G GLY* 4.6 2.9 - - - -
340G THR* 1.3 85.2 + - - +
342G SER* 1.3 61.5 + - - +
351G ILE* 4.0 3.0 - - - +
370G SER* 3.6 1.6 + - - -
373G LEU* 3.5 16.6 - - - +
404G ALA 4.5 0.3 + - - -
406G LEU* 4.3 12.8 - - + +
428G LEU* 3.4 23.7 - - + +
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Residues in contact with SER 342 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G TRP* 3.8 16.7 - - - -
319G SER* 3.7 4.0 - - - -
320G ALA 2.9 12.4 + - - +
321G THR* 3.9 3.1 - - - -
322G GLN 4.1 0.3 + - - -
329G TYR* 3.3 14.7 + - - -
341G TYR* 1.3 77.3 - - - +
343G SER* 1.3 72.8 + - - +
349G LYS 4.1 1.1 - - - +
351G ILE* 3.7 16.8 - - - +
365G THR 4.0 0.3 - - - -
366G GLY 2.7 26.9 + - - -
369G ALA* 3.6 11.3 - - - +
370G SER* 3.6 15.3 - - - -
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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