Contacts of the helix formed by residues 356 - 372 (chain h) in PDB entry 5M32
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 GLY 356 (chain h).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194h THR* 3.1 15.6 + - - +
320h PRO* 5.5 1.3 - - - -
328h ILE* 3.8 9.5 - - - +
355h SER* 1.3 80.7 + - - +
357h ALA* 1.3 60.5 + - - +
359h VAL* 3.0 17.8 + - - +
360h LYS 3.5 3.1 + - - -
401h ADP 2.5 43.2 + - - -
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Residues in contact with ALA 357 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193h GLY* 4.9 4.4 - - - -
194h THR 4.7 1.0 - - - +
355h SER* 3.2 8.5 + - - +
356h GLY* 1.3 68.9 - - - +
358h GLU* 1.3 55.2 + - - +
359h VAL 2.4 19.1 + - - -
360h LYS* 2.7 23.0 + - - +
361h GLY 2.8 13.2 + - - -
401h ADP 3.8 18.8 + - + +
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Residues in contact with GLU 358 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354h ALA* 4.3 11.7 - - + +
355h SER* 3.0 34.5 + - - +
357h ALA* 1.3 77.4 - - - +
359h VAL* 1.3 59.9 + - - +
361h GLY* 4.4 3.7 - - - +
362h VAL* 3.4 23.9 - - + +
390h VAL* 4.0 32.9 - - + +
391h MET* 4.9 9.0 - - + +
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Residues in contact with VAL 359 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320h PRO* 6.3 0.9 - - + -
325h ARG* 4.2 19.7 - - + -
328h ILE* 3.9 28.0 - - + -
329h LEU* 3.7 43.3 - - + +
332h HIS* 3.9 6.1 - - + +
354h ALA* 4.9 4.0 - - + -
355h SER 3.5 13.9 - - - +
356h GLY 3.0 10.1 + - - +
357h ALA 2.4 15.8 + - - -
358h GLU* 1.3 72.9 - - - +
360h LYS* 1.3 63.1 + - - +
361h GLY 3.2 0.9 - - - -
362h VAL* 3.3 7.3 - - + +
363h CYS* 3.0 24.0 + - + +
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Residues in contact with LYS 360 (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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324e PRO* 5.2 13.1 - - - +
332h HIS* 3.4 31.8 + - + +
335h LYS* 5.9 8.5 - - - -
356h GLY 3.5 1.4 + - - -
357h ALA* 2.7 18.2 + - - +
359h VAL* 1.3 74.0 - - - +
361h GLY* 1.3 59.7 + - - +
363h CYS* 3.4 1.0 + - - +
364h THR* 3.0 35.5 + - + +
401h ADP 2.6 36.1 + - - +
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Residues in contact with GLY 361 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357h ALA 2.8 13.2 + - - -
358h GLU* 5.0 2.0 - - - -
360h LYS* 1.3 78.9 - - - +
362h VAL* 1.3 55.7 + - - +
364h THR* 2.7 21.9 + - - -
365h GLU* 2.9 22.7 + - - +
390h VAL* 5.4 2.9 - - - -
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Residues in contact with VAL 362 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329h LEU* 4.5 14.6 - - + -
347h ILE* 5.6 0.4 - - + -
358h GLU* 3.4 22.3 + - - +
359h VAL* 3.3 17.9 - - - +
361h GLY* 1.3 75.6 - - - +
363h CYS* 1.3 59.6 + - + +
365h GLU* 3.8 6.7 - - - -
366h ALA* 2.9 28.1 + - - +
383h PHE* 4.8 3.7 - - + -
386h ALA* 3.4 6.0 - - + +
387h VAL* 3.7 31.0 - - + +
390h VAL* 3.6 37.0 - - + -
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Residues in contact with CYS 363 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329h LEU* 5.3 4.0 - - + -
332h HIS* 3.2 41.1 - - + -
333h SER* 3.7 11.0 - - - -
336h MET* 3.4 26.6 - - - +
359h VAL* 3.0 18.5 + - + +
360h LYS 4.0 3.4 - - - +
361h GLY 3.2 0.4 - - - -
362h VAL* 1.3 79.5 - - + +
364h THR* 1.3 60.8 + - + +
366h ALA* 3.4 4.5 + - - +
367h GLY 3.0 21.8 + - - -
383h PHE* 4.2 18.6 - - + -
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Residues in contact with THR 364 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196e ILE* 4.3 26.2 - - + +
197e ASP* 6.1 1.1 - - - +
335h LYS* 5.7 7.6 - - + -
336h MET* 5.6 0.9 - - + -
360h LYS* 3.0 24.9 + - + +
361h GLY* 2.7 23.4 + - - -
363h CYS* 1.3 78.0 - - + +
365h GLU* 1.3 60.8 + - - +
367h GLY* 3.2 2.1 + - - -
368h MET* 2.9 27.5 + - - +
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Residues in contact with GLU 365 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329e ARG* 4.4 15.4 + - - -
361h GLY* 2.9 23.2 + - - +
362h VAL* 4.1 4.9 - - - +
364h THR* 1.3 77.1 + - - +
366h ALA* 1.3 60.4 + - - +
368h MET* 3.8 16.4 - - - +
369h TYR* 2.9 55.9 + - + -
386h ALA* 4.1 13.0 - - + -
389h LYS* 5.2 9.8 + - + -
390h VAL* 4.8 13.5 - - + -
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Residues in contact with ALA 366 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336h MET* 5.8 0.2 - - - -
362h VAL 2.9 19.8 + - - +
363h CYS 3.7 4.7 - - - +
365h GLU* 1.3 75.7 - - - +
367h GLY* 1.3 59.9 + - - +
369h TYR 3.4 0.3 + - - -
370h ALA* 3.0 25.1 + - - +
378h VAL* 3.9 7.0 - - + +
382h ASP* 3.4 39.8 - - + +
383h PHE* 3.7 25.6 - - + +
386h ALA* 3.7 0.4 - - - +
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Residues in contact with GLY 367 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194e ILE* 3.9 9.7 - - - +
196e ILE* 4.4 9.8 - - - +
336h MET* 4.0 21.2 - - - -
363h CYS 3.0 14.0 + - - -
364h THR 3.2 3.8 + - - -
366h ALA* 1.3 76.1 - - - +
368h MET* 1.3 56.3 + - - +
370h ALA* 3.2 5.0 + - - +
371h LEU* 2.9 25.6 + - - +
378h VAL* 4.2 6.3 - - - -
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Residues in contact with MET 368 (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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175e GLN* 3.9 10.8 - - - +
176e GLU* 6.6 0.2 - - + -
179e GLU* 3.5 48.0 - - + +
196e ILE* 4.7 10.0 - - + +
364h THR 2.9 15.8 + - - +
365h GLU* 3.9 16.2 - - - +
367h GLY* 1.3 76.1 - - - +
369h TYR* 1.3 79.1 + - - +
371h LEU* 2.8 22.2 + - + +
372h ARG* 2.9 44.3 + - + +
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Residues in contact with TYR 369 (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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365h GLU* 2.9 32.6 + - + +
366h ALA 3.8 3.8 - - - +
367h GLY 3.3 0.2 - - - -
368h MET* 1.3 92.4 - - - +
370h ALA* 1.3 57.8 + - - +
372h ARG* 3.3 34.5 + - - +
373h GLU* 2.8 22.8 - - - +
382h ASP* 3.0 29.7 - - + +
385h MET* 3.5 57.2 - - + +
386h ALA* 3.9 12.1 - - - -
389h LYS* 3.3 33.1 - - + +
198l ASN* 5.5 0.2 - - - -
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Residues in contact with ALA 370 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194e ILE* 4.1 6.7 - - + -
366h ALA 3.0 11.2 + - - +
367h GLY 3.5 8.3 - - - +
368h MET 3.1 0.2 - - - -
369h TYR* 1.3 78.0 - - - +
371h LEU* 1.3 62.8 + - - +
372h ARG 3.3 0.8 + - - -
373h GLU* 3.9 3.5 + - - +
375h ARG* 3.2 35.3 + - - +
377h HIS 4.3 3.4 - - - +
378h VAL* 3.7 28.7 - - + +
382h ASP* 3.3 17.7 - - - +
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Residues in contact with LEU 371 (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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179e GLU* 3.3 27.1 - - - +
183e LEU* 3.7 22.9 - - + -
190e LEU* 3.7 37.0 - - + +
191e TYR* 3.9 18.2 - - + +
194e ILE* 3.7 20.4 - - + -
196e ILE* 5.1 3.8 - - + -
367h GLY 2.9 12.6 + - - +
368h MET* 2.8 15.5 + - + +
370h ALA* 1.3 77.0 - - - +
372h ARG* 1.3 62.5 + - - +
373h GLU 3.3 0.4 - - - -
374h ARG* 3.2 23.2 + - - +
375h ARG 4.5 1.6 - - - +
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Residues in contact with ARG 372 (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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175e GLN* 3.6 19.7 + - - +
179e GLU* 5.4 5.6 - - - +
368h MET* 2.9 37.0 + - + +
369h TYR* 3.3 37.9 + - - +
370h ALA 3.3 0.8 - - - -
371h LEU* 1.3 81.2 - - - +
373h GLU* 1.3 71.7 + - + +
374h ARG* 3.3 16.4 + - - +
385h MET* 4.8 8.9 - - - +
227l THR 5.5 1.0 - - - +
231l TYR* 5.9 5.8 - - + -
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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