Contacts of the strand formed by residues 313 - 320 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272C GLU* 4.0 15.5 + - - +
271D GLU* 3.7 21.9 + - - -
274D PHE* 3.5 37.2 - + + -
275D PHE* 3.5 48.6 - + + -
278D VAL* 3.9 32.8 - - + +
287D SER 5.1 0.5 - - - +
289D PHE* 3.6 22.4 + - + +
311D SER* 3.1 20.5 + - - +
312D ILE* 1.3 103.2 - - + +
314D THR* 1.3 56.7 + - - +
315D LEU* 5.4 1.0 - - - +
390D TRP* 4.1 12.2 - + - +
394D GLN* 4.4 5.2 + - - -
571D TYR* 5.1 2.1 + - - -
4012D SO4 5.7 0.2 - - - -
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Residues in contact with THR 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D PHE* 3.6 29.2 - - + -
289D PHE* 3.1 10.8 - - + -
291D TRP* 3.6 23.6 - - + -
308D TYR 2.8 28.9 + - - +
309D THR* 3.6 9.0 + - - +
311D SER* 3.3 18.6 + - - +
312D ILE* 3.2 5.2 - - - +
313D TYR* 1.3 85.7 - - - +
315D LEU* 1.3 63.1 + - - +
316D SER 3.5 4.0 + - - -
335D SER 5.8 0.2 - - - +
337D LEU* 5.6 0.2 - - - +
394D GLN* 4.2 6.8 + - - +
486D HIS* 5.6 0.2 + - - -
534D MET* 5.5 2.1 - - - +
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Residues in contact with LEU 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D ILE* 3.6 31.4 - - + -
289D PHE 2.7 19.8 + - - +
290D VAL* 3.6 4.8 - - + -
291D TRP 2.9 23.1 + - - +
313D TYR 5.4 0.4 - - - +
314D THR* 1.3 72.7 - - - +
316D SER* 1.3 62.3 + - - +
317D ILE* 3.5 15.6 + - + +
337D LEU* 4.0 18.2 - - + -
378D ILE* 3.7 22.9 - - + -
390D TRP 5.4 1.3 - - - +
393D MET* 4.5 7.4 - - + -
394D GLN* 3.9 24.9 - - + +
397D VAL* 3.8 26.2 - - + -
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Residues in contact with SER 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D TRP* 3.5 8.3 - - - -
293D SER* 3.4 17.0 - - - -
303D CYS* 5.3 0.5 - - - +
309D THR* 3.4 44.5 - - - +
314D THR* 3.5 5.2 + - - -
315D LEU* 1.3 71.5 - - - +
317D ILE* 1.3 65.6 + - - +
335D SER* 4.0 15.4 + - - -
336D THR* 3.6 9.1 + - - +
337D LEU* 3.0 29.2 + - - +
338D ALA 3.7 0.2 + - - -
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Residues in contact with ILE 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D VAL* 4.0 6.3 - - + -
291D TRP 2.8 14.9 + - - +
292D ALA* 3.8 2.8 - - - -
293D SER* 2.9 25.2 + - - -
315D LEU* 3.6 26.0 - - + +
316D SER* 1.3 82.9 + - - +
318D SER* 1.3 76.3 + - - +
337D LEU* 5.2 1.1 - - + -
338D ALA* 3.4 27.1 - - + +
339D THR* 4.2 0.2 - - - -
340D THR* 3.9 23.8 - - + +
367D THR* 4.5 4.2 - - - -
370D SER* 3.9 14.3 - - - +
371D ALA* 4.5 5.6 - - - -
374D ALA* 3.7 22.9 - - + -
378D ILE* 6.0 0.4 - - + -
397D VAL* 5.6 0.4 - - + -
429D LEU* 4.9 4.3 - - + -
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Residues in contact with SER 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D SER* 3.0 20.1 + - - -
317D ILE* 1.3 76.7 - - - +
319D SER* 1.3 65.1 + - - +
330D SER* 5.1 4.7 - - - -
331D GLU 4.4 5.5 + - - -
336D THR* 3.1 26.1 + - - +
338D ALA 3.0 7.9 + - - -
339D THR* 3.2 8.1 - - - +
340D THR 3.1 23.0 + - - -
367D THR* 4.6 1.1 - - - -
370D SER* 3.4 5.5 + - - -
423D SER 3.3 25.3 + - - -
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Residues in contact with SER 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D SER* 1.3 74.7 - - - +
320D ALA* 1.3 61.5 + - - +
327D PRO* 3.2 17.2 - - - +
329D TYR* 3.3 30.0 + - - -
330D SER* 4.9 4.2 + - - -
339D THR* 3.4 5.0 - - - +
340D THR 3.3 4.7 - - - -
342D SER* 3.6 5.9 - - - -
367D THR* 3.4 25.3 - - - +
370D SER* 2.6 21.3 + - - -
423D SER 4.5 2.3 - - - +
424D TYR* 3.4 15.4 - - - -
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Residues in contact with ALA 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D SER* 1.3 76.4 - - - +
321D THR* 1.3 67.3 + - - +
324D GLY* 4.9 1.3 - - - -
325D ASN 3.5 9.0 - - - +
327D PRO* 3.9 4.9 - - - -
339D THR* 3.8 14.8 - - + -
340D THR 3.3 5.5 + - - +
341D TYR* 3.4 12.3 - - + -
342D SER 2.9 23.9 + - - +
406D LEU* 4.1 19.3 - - + -
424D TYR* 3.8 13.7 - - + +
428D LEU* 4.9 1.1 - - + -
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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