Contacts of the helix formed by residues 307 - 315 (chain K) in PDB entry 5XTE
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 SER 307 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292K VAL 4.6 1.3 - - - -
293K LEU 3.0 21.7 + - - -
294K GLY* 3.3 13.6 - - - +
304K ASN* 3.0 33.4 + - - +
305K THR 3.6 0.3 - - - +
306K THR* 1.3 83.4 - - - +
308K HIS* 1.3 62.3 + - - +
309K LEU* 3.4 5.9 + - - +
310K HIS* 3.4 20.0 + - - -
311K GLN* 3.4 24.3 + - - +
377K LYS* 5.5 0.4 - - - +
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Residues in contact with HIS 308 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292K VAL* 3.2 42.5 + - + +
293K LEU* 4.5 2.8 - - + -
306K THR 3.5 7.8 + - - -
307K SER* 1.3 74.3 + - - +
309K LEU* 1.3 62.4 + - + +
311K GLN* 3.7 3.1 + - - +
312K ALA* 2.9 30.3 + - - +
357K GLN* 3.4 37.4 + - + +
361K ILE* 4.5 8.5 - - + -
366K LEU* 4.6 3.6 - - + +
367K SER* 5.2 0.9 - - - -
370K ASP* 2.9 33.9 + - + +
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Residues in contact with LEU 309 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293K LEU* 3.5 50.5 - - + +
307K SER* 3.3 1.4 + - - +
308K HIS* 1.3 74.7 - - - +
310K HIS* 1.3 66.3 + - - +
311K GLN 3.2 1.8 - - - -
312K ALA* 3.2 5.0 + - - +
313K VAL* 2.9 31.2 + - - +
323K VAL* 3.6 36.6 - - + +
324K SER 4.4 0.7 - - - -
325K ALA 4.3 13.0 - - - +
338K ILE* 3.7 23.6 - - + -
354K ALA* 4.3 15.5 - - + +
357K GLN* 3.9 17.5 - - + -
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Residues in contact with HIS 310 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B GLN* 3.9 17.8 + - + -
294K GLY 4.1 8.3 + - - -
303K SER* 4.8 4.7 - - - +
304K ASN* 3.5 43.2 + - + +
307K SER* 3.4 22.1 + - - -
309K LEU* 1.3 76.4 - - + +
311K GLN* 1.3 58.2 + - - +
313K VAL 3.6 0.2 + - - -
314K ALA* 2.9 30.2 + - - +
321K PHE* 3.7 20.9 - - + -
322K ASP* 3.3 22.4 - - - -
323K VAL* 2.9 34.9 + - - -
324K SER* 5.0 0.4 - - - -
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Residues in contact with GLN 311 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303K SER* 3.2 26.3 + - - -
304K ASN 3.8 2.5 + - - +
305K THR* 3.3 48.1 - - - +
307K SER 3.4 11.1 + - - +
308K HIS* 3.7 3.1 + - - +
309K LEU 3.2 0.8 - - - -
310K HIS* 1.3 76.2 + - - +
312K ALA* 1.3 64.3 + - - +
313K VAL 3.2 0.8 + - - -
314K ALA* 3.4 13.0 + - - +
315K LYS* 3.4 27.0 + - - +
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Residues in contact with ALA 312 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308K HIS 2.9 20.3 + - - +
309K LEU* 3.2 5.6 + - - +
311K GLN* 1.3 77.9 - - - +
313K VAL* 1.3 59.0 + - + +
315K LYS* 4.1 14.7 + - - +
316K ALA* 3.3 21.0 + - - +
353K ALA* 3.9 16.8 - - + +
354K ALA* 5.1 0.2 - - - -
357K GLN* 3.4 30.5 - - + +
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Residues in contact with VAL 313 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309K LEU 2.9 20.3 + - - +
312K ALA* 1.3 78.1 - - - +
314K ALA* 1.3 58.6 + - - +
315K LYS 3.2 2.5 - - - -
316K ALA* 2.9 5.2 + - + -
317K THR* 2.8 46.0 + - - +
321K PHE* 3.5 32.3 - - + -
323K VAL* 3.9 20.6 - - + -
350K VAL* 3.7 34.1 - - + +
353K ALA* 4.8 0.7 - - + -
354K ALA* 4.5 10.5 - - + +
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Residues in contact with ALA 314 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310K HIS 2.9 19.4 + - - +
311K GLN* 3.4 18.1 + - - +
313K VAL* 1.3 77.2 - - - +
315K LYS* 1.3 58.5 + - - +
317K THR 2.9 16.5 - - - +
321K PHE* 3.6 17.9 - - + -
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Residues in contact with LYS 315 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311K GLN* 3.4 20.9 - - + +
312K ALA* 4.1 13.4 + - - +
314K ALA* 1.3 77.7 - - - +
316K ALA* 1.3 62.0 + - - +
317K THR 5.2 0.2 - - - -
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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