Contacts of the strand formed by residues 313 - 320 (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 TYR 313 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272F GLU* 4.2 18.3 + - - +
271G GLU* 3.7 21.4 + - - -
274G PHE* 3.5 37.9 - + + -
275G PHE* 3.2 42.0 - + + +
278G VAL* 3.9 32.0 - - + +
287G SER 5.1 0.5 - - - +
288G ILE* 5.6 0.2 - - - -
289G PHE* 3.5 22.5 + - + +
311G SER* 3.1 21.0 - - - +
312G ILE* 1.3 104.1 - - + +
314G THR* 1.3 57.7 + - - +
315G LEU* 5.5 1.0 - - - +
390G TRP* 4.0 11.7 - + - +
394G GLN* 4.4 5.0 + - - -
571G TYR* 5.0 2.9 + - - -
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Residues in contact with THR 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G PHE* 3.6 29.6 - - + -
289G PHE* 3.2 10.3 - - + -
291G TRP* 3.7 23.3 - - + +
308G TYR 2.8 29.7 + - - +
309G THR* 3.6 9.9 + - - +
311G SER* 3.4 17.4 + - - +
312G ILE 4.0 4.7 - - - +
313G TYR* 1.3 85.4 - - - +
315G LEU* 1.3 63.3 + - - +
316G SER 3.5 4.5 + - - -
337G LEU* 5.5 0.7 - - - +
394G GLN* 4.1 7.2 + - - +
486G HIS* 6.0 0.2 - - - -
534G MET* 5.5 1.9 - - - +
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Residues in contact with LEU 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288G ILE* 3.7 31.0 - - + -
289G PHE 2.8 17.4 + - - +
290G VAL* 3.7 5.2 - - + -
291G TRP 2.9 22.1 + - - +
313G TYR 5.5 0.9 - - - +
314G THR* 1.3 71.9 - - - +
316G SER* 1.3 62.7 + - - +
317G ILE* 3.5 15.5 + - + +
337G LEU* 3.8 20.4 - - + -
378G ILE* 4.0 16.2 - - + -
390G TRP 5.3 1.6 - - - +
393G MET* 4.6 7.0 - - + -
394G GLN* 3.7 27.6 - - + +
397G VAL* 3.6 30.7 - - + -
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Residues in contact with SER 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G TRP* 3.5 7.9 - - - -
293G SER* 3.3 25.3 - - - -
303G CYS* 5.3 0.3 - - - +
309G THR* 3.4 38.4 - - - -
314G THR 3.5 4.6 + - - -
315G LEU* 1.3 71.8 - - - +
317G ILE* 1.3 63.9 + - - +
335G SER* 4.1 15.2 + - - -
336G THR* 3.6 8.6 + - - +
337G LEU* 3.0 29.2 + - - +
338G ALA 3.7 0.3 + - - -
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Residues in contact with ILE 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G VAL* 4.0 7.2 - - + -
291G TRP 2.8 15.9 + - - +
292G ALA* 3.9 2.8 - - - -
293G SER* 3.0 22.7 + - - -
315G LEU* 3.6 25.1 - - + +
316G SER* 1.3 83.0 + - - +
318G SER* 1.3 74.5 + - - +
337G LEU* 5.1 0.9 - - + -
338G ALA* 3.4 26.7 - - + +
339G THR* 4.2 0.2 - - - -
340G THR* 4.1 15.5 - - + +
367G THR* 4.4 4.0 - - - -
370G SER* 3.9 23.6 - - - +
371G ALA* 4.4 5.8 - - - -
374G ALA* 3.7 22.7 - - + -
378G ILE* 6.0 0.9 - - + -
397G VAL* 5.6 0.2 - - + -
429G LEU* 5.0 3.8 - - + -
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Residues in contact with SER 318 (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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293G SER* 2.9 21.0 + - - -
317G ILE* 1.3 75.1 - - - +
319G SER* 1.3 65.0 + - - +
330G SER* 5.0 4.4 + - - -
331G GLU 4.3 7.4 + - - -
336G THR* 3.4 23.9 + - - +
338G ALA 2.9 8.1 + - - -
339G THR* 3.6 7.6 - - - -
340G THR 3.2 21.7 + - - -
367G THR* 4.6 1.3 - - - -
370G SER* 3.5 6.2 + - - -
423G SER 3.2 25.1 + - - -
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Residues in contact with SER 319 (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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318G SER* 1.3 76.1 - - - +
320G ALA* 1.3 62.1 + - - +
327G PRO* 3.2 17.2 - - - +
329G TYR* 3.4 31.1 + - - -
330G SER* 4.8 4.1 + - - -
339G THR* 3.4 4.7 - - - +
340G THR 3.3 5.2 - - - -
342G SER* 3.7 4.5 - - - -
367G THR* 3.4 26.7 - - - +
370G SER* 2.6 20.7 + - - -
423G SER 4.5 1.2 - - - +
424G TYR* 3.5 15.1 - - - -
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Residues in contact with ALA 320 (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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319G SER* 1.3 76.8 - - - +
321G THR* 1.3 64.0 + - - +
324G GLY* 4.9 0.2 - - - -
325G ASN 3.6 7.9 - - - +
327G PRO* 3.8 4.3 - - - -
339G THR* 3.8 14.4 - - + -
340G THR 3.3 5.3 + - - +
341G TYR* 3.4 14.2 - - + -
342G SER 2.9 24.3 + - - +
406G LEU* 3.9 28.3 - - + -
424G TYR* 3.9 7.2 - - + -
428G LEU* 4.9 0.9 - - + -
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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