Contacts of the helix formed by residues 356 - 368 (chain M) in PDB entry 5M64
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 LYS 356 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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822B THR* 3.7 33.2 + - + +
823B GLN* 4.4 6.3 - - - +
865B THR* 2.9 30.6 + - - +
355M LEU* 1.3 73.1 - - - +
357M PRO* 1.3 79.0 - - + +
358M SER* 3.2 27.4 - - - +
359M LYS* 3.0 21.1 + - + +
360M VAL* 3.2 12.9 + - - +
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Residues in contact with PRO 357 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820B PRO* 5.3 17.0 - - + -
822B THR* 4.8 10.3 - - + -
864B ASP* 4.3 17.9 - - - +
865B THR* 5.0 2.5 - - - -
346M ILE* 4.6 13.9 - - + -
347M THR* 5.6 9.0 - - + -
350M ALA* 3.8 22.0 - - + -
351M HIS* 6.1 0.7 - - + -
355M LEU 3.6 4.5 - - - +
356M LYS* 1.3 92.4 - - + +
358M SER* 1.3 60.1 + - - +
360M VAL* 3.4 4.5 + - + +
361M VAL* 3.1 30.4 + - - +
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Residues in contact with SER 358 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819B ASP* 5.9 2.9 - - - -
356M LYS* 3.2 26.4 - - - +
357M PRO* 1.3 78.2 - - - +
359M LYS* 1.3 63.7 + - - +
361M VAL* 3.6 5.5 + - - +
362M SER* 3.0 28.8 + - - -
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Residues in contact with LYS 359 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 3.4 48.3 + - + +
42A GLY* 5.3 0.4 - - - -
326M ASP* 5.9 1.8 - - - +
329M LEU* 5.1 10.3 - - + -
355M LEU* 5.0 18.4 - - + -
356M LYS* 3.0 19.8 + - + +
358M SER* 1.3 80.7 + - - +
360M VAL* 1.3 65.1 + - - +
362M SER* 3.5 5.3 + - - -
363M LEU* 3.3 21.5 + - + +
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Residues in contact with VAL 360 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333M LEU* 3.7 16.3 - - + +
346M ILE* 4.8 8.1 - - + +
349M LEU* 4.4 18.4 - - + +
350M ALA* 4.1 19.7 - - + -
353M LEU* 5.5 1.3 - - + -
355M LEU* 3.9 26.0 - - + -
356M LYS 3.2 15.1 + - - +
357M PRO* 3.8 6.7 - - + +
358M SER 3.3 0.4 - - - -
359M LYS* 1.3 75.2 - - - +
361M VAL* 1.3 65.8 + - + +
363M LEU* 3.2 15.0 + - - +
364M PHE* 3.1 33.5 + - + -
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Residues in contact with VAL 361 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346M ILE* 3.7 33.2 - - + -
357M PRO 3.1 18.8 + - - +
358M SER* 4.0 5.4 - - - +
359M LYS 3.4 0.2 - - - -
360M VAL* 1.3 76.7 - - - +
362M SER* 1.3 62.6 + - - +
364M PHE* 3.1 24.6 + - - +
365M ARG* 3.6 21.5 + - - +
371M VAL* 3.7 31.9 - - + -
393M LYS* 5.9 4.7 - - + -
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Residues in contact with SER 362 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.6 20.0 - - - +
358M SER 3.0 18.6 + - - -
359M LYS* 3.9 9.4 - - - -
360M VAL 3.3 0.4 - - - -
361M VAL* 1.3 77.1 - - - +
363M LEU* 1.3 60.1 + - - +
364M PHE 3.3 0.2 - - - -
365M ARG* 3.4 27.5 + - - +
366M VAL* 3.6 11.1 + - - +
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Residues in contact with LEU 363 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.7 18.6 - - + -
187M PRO* 6.4 0.9 - - + -
326M ASP* 4.3 17.9 - - - +
329M LEU* 3.4 45.1 - - + +
330M CYS* 4.3 2.2 - - - -
333M LEU* 3.7 16.8 - - + -
359M LYS* 3.3 12.3 + - + +
360M VAL* 3.2 12.1 + - - +
361M VAL 3.1 1.0 - - - -
362M SER* 1.3 75.3 - - - +
364M PHE* 1.3 65.0 + - - +
366M VAL* 3.2 28.8 - - + +
367M LEU* 3.4 25.0 - - + +
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Residues in contact with PHE 364 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333M LEU* 3.5 38.4 - - + -
337M MET* 4.5 12.8 - - - -
344M VAL* 3.9 15.0 - - + -
345M GLU 5.5 0.2 - - - -
346M ILE* 3.6 23.3 - - + -
349M LEU* 5.5 0.2 - - + -
360M VAL* 3.1 33.8 + - + -
361M VAL* 3.1 16.2 + - + +
363M LEU* 1.3 79.3 - - - +
365M ARG* 1.3 60.4 + - + +
367M LEU* 3.3 6.4 + - + +
368M GLY 3.2 5.0 + - - -
369M ALA* 2.9 48.2 + - + +
371M VAL* 4.9 12.6 - - + -
395M ALA* 3.4 29.4 - - + -
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Residues in contact with ARG 365 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361M VAL* 3.8 23.2 - - - +
362M SER* 3.4 17.0 + - - +
363M LEU 3.2 0.8 - - - -
364M PHE* 1.3 77.3 - - - +
366M VAL* 1.3 59.4 + - - +
368M GLY* 3.8 8.4 + - - -
369M ALA 4.3 9.4 - - - +
371M VAL* 3.8 28.5 - - + +
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Residues in contact with VAL 366 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 5.5 8.3 - - + -
43A HIS* 6.3 0.2 - - + -
186M ARG* 5.3 9.0 - - - +
187M PRO* 3.7 35.2 - - + -
188M THR* 3.3 22.1 - - + +
330M CYS* 5.7 1.3 - - - -
362M SER 3.6 5.8 + - - +
363M LEU* 3.2 38.8 - - + +
365M ARG* 1.3 77.0 - - - +
367M LEU* 1.3 70.1 + - + +
368M GLY 3.3 0.6 + - - -
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Residues in contact with LEU 367 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188M THR* 3.4 31.0 + - - +
189M PRO* 4.7 1.6 - - + -
191M ALA* 5.2 5.2 - - - +
330M CYS* 4.0 30.1 - - + +
333M LEU* 3.9 32.8 - - + +
334M ALA* 4.4 9.2 - - + -
363M LEU* 3.4 29.8 - - + +
364M PHE* 3.3 11.5 + - + +
366M VAL* 1.3 78.5 - - + +
368M GLY* 1.3 56.1 + - - +
369M ALA* 4.7 3.6 - - + +
397M MET* 5.1 0.2 - - - +
401M PHE* 3.6 15.8 - - - -
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Residues in contact with GLY 368 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364M PHE 3.2 2.8 + - - -
365M ARG 3.8 7.0 + - - -
366M VAL 3.3 4.0 - - - -
367M LEU* 1.3 78.3 - - - +
369M ALA* 1.3 58.4 - - - +
370M ILE* 4.6 5.5 - - - +
397M MET* 2.2 26.3 - - - +
401M PHE* 3.5 21.3 - - - -
402M LYS* 5.0 8.6 + - - +
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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