Contacts of the helix formed by residues 360 - 375 (chain B) in PDB entry 3MYV
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 LEU 360 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242B LEU 5.6 0.2 - - - -
243B ILE* 4.5 12.3 - - + +
246B ALA* 4.2 17.3 - - + -
247B ASP* 5.6 2.7 - - - +
252B TYR* 4.0 5.2 - - + +
253B ALA* 3.5 42.6 - - - +
254B LEU* 3.6 9.4 - - + +
273B GLU* 2.8 25.4 + - + +
275B PHE* 3.6 27.3 - - + -
359B ARG* 1.3 72.9 - - - +
361B SER* 1.3 63.7 + - - +
363B VAL* 3.0 16.7 + - + +
364B TYR* 3.2 38.9 + - + +
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Residues in contact with SER 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LEU* 3.5 10.5 - - - +
273B GLU* 2.5 28.3 + - - -
359B ARG* 3.3 14.8 + - - -
360B LEU* 1.3 75.8 - - - +
362B GLU* 1.3 62.2 + - - +
364B TYR* 3.4 4.3 + - - +
365B LEU* 3.1 26.5 + - - +
389B ILE* 4.1 8.7 - - - +
392B ARG* 2.9 26.8 + - - -
416B GLU* 4.1 13.0 - - - -
417B LEU* 5.3 0.2 - - - -
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Residues in contact with GLU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B ALA* 5.8 1.3 - - - +
224B ARG* 2.7 55.0 + - - +
357B VAL 4.1 2.8 - - - +
358B LEU* 4.0 12.8 - - - +
359B ARG* 3.2 16.8 + - + +
361B SER* 1.3 77.3 - - - +
363B VAL* 1.3 54.6 + - + +
365B LEU* 3.0 7.7 + - - +
366B ILE* 2.8 46.9 + - + +
413B ARG* 4.6 11.7 + - - +
417B LEU* 4.6 17.7 - - + +
422B HIS* 3.5 23.3 + - + +
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Residues in contact with VAL 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B ALA* 3.7 20.2 - - + -
223B ALA* 5.5 1.6 - - + -
239B ALA* 3.6 38.4 - - + +
242B LEU* 3.9 14.8 - - + -
243B ILE* 3.7 11.9 - - + -
275B PHE* 3.6 29.8 - - + -
359B ARG 4.1 2.5 - - - +
360B LEU* 3.0 8.9 + - + +
362B GLU* 1.3 74.7 - - + +
364B TYR* 1.3 65.4 + - - +
366B ILE* 3.2 12.9 + - + +
367B ALA* 3.0 19.6 + - - +
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Residues in contact with TYR 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B ILE* 3.5 37.3 - - + +
247B ASP* 4.3 12.8 + - - -
254B LEU* 3.8 21.2 - - + +
360B LEU* 3.2 42.0 + - + +
361B SER 3.4 7.8 + - - +
363B VAL* 1.3 75.8 - - - +
365B LEU* 1.3 58.9 + - - +
367B ALA* 3.3 4.5 + - - +
368B ALA* 2.9 27.3 + - - +
385B TYR* 3.7 47.1 - + - +
388B GLU* 3.7 26.4 + - + +
389B ILE* 3.6 19.3 - - + -
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Residues in contact with LEU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B SER 3.1 16.8 + - - +
362B GLU* 3.0 9.4 + - - +
364B TYR* 1.3 73.7 - - - +
366B ILE* 1.3 60.7 + - - +
368B ALA* 3.4 4.9 + - + +
369B GLU* 2.8 30.0 + - - +
386B LEU* 4.1 14.8 - - + -
389B ILE* 4.5 13.0 - - + -
409B VAL* 4.0 9.5 - - + +
412B GLU* 3.8 31.2 - - + -
413B ARG* 3.9 40.5 + - + +
416B GLU* 4.0 23.1 - - + -
417B LEU* 4.2 10.8 - - + -
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Residues in contact with ILE 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B ALA 4.4 4.3 - - - +
223B ALA* 3.9 22.7 - - + +
224B ARG* 3.7 27.8 - - + +
227B LEU* 4.3 13.1 - - + +
235B ALA* 4.2 15.3 - - + +
239B ALA* 4.1 12.8 - - + -
362B GLU* 2.8 44.3 + - + +
363B VAL* 3.6 13.0 - - + +
365B LEU* 1.3 69.9 - - - +
367B ALA* 1.3 61.6 + - - +
369B GLU* 3.2 0.9 + - - +
370B ALA* 2.8 30.3 + - - +
413B ARG* 3.7 19.7 - - - +
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Residues in contact with ALA 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B PHE* 3.5 21.2 - - + +
239B ALA* 3.9 16.1 - - + +
240B ASP 4.6 1.3 - - - +
243B ILE* 4.5 2.2 - - + -
363B VAL 3.0 12.5 + - - +
364B TYR 3.5 8.3 - - - +
366B ILE* 1.3 78.1 - - - +
368B ALA* 1.3 57.3 + - - +
370B ALA* 4.6 1.6 - - - -
371B GLY* 2.9 27.2 + - - -
382B GLY* 3.8 3.9 - - - -
385B TYR* 3.6 29.8 - - + -
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Residues in contact with ALA 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B TYR 2.9 17.8 + - - +
365B LEU* 3.6 10.5 - - - +
367B ALA* 1.3 75.2 - - - +
369B GLU* 1.3 62.6 + - - +
372B CYS* 3.2 7.4 + - - +
382B GLY 3.6 24.4 + - - +
386B LEU* 3.9 22.9 - - + +
404B TYR* 2.5 24.6 + - - +
409B VAL* 4.0 14.3 - - + +
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Residues in contact with GLU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B LEU* 3.6 10.8 - - + -
365B LEU 2.8 17.2 + - - +
366B ILE 3.2 2.9 + - - +
368B ALA* 1.3 74.5 - - - +
370B ALA* 1.3 65.6 + - - +
372B CYS* 3.2 6.4 + - - +
373B LYS* 2.9 41.5 + - - +
406B LEU* 3.9 19.3 - - + -
409B VAL* 3.8 13.0 - - + -
410B LEU* 4.2 2.9 - - - -
413B ARG* 2.9 18.5 + - - -
429B ARG* 2.8 46.1 + - - -
430B ASN* 3.1 11.2 + - - +
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Residues in contact with ALA 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B LEU* 3.9 17.1 - - + +
232B ASN* 3.4 30.3 - - - +
235B ALA* 4.2 1.6 - - + -
236B PHE* 3.7 20.0 - - + +
366B ILE 2.8 20.4 + - - +
367B ALA 4.0 0.4 - - - +
369B GLU* 1.3 73.5 - - - +
371B GLY* 1.3 61.7 + - - +
373B LYS* 3.1 4.3 + - - +
374B LEU* 3.0 28.6 + - - +
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Residues in contact with GLY 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B PHE* 4.2 1.9 - - - -
367B ALA 2.9 19.4 + - - -
370B ALA* 1.3 73.8 - - - +
372B CYS* 1.3 54.8 + - - +
374B LEU* 3.2 0.3 + - - -
375B GLY 2.9 28.2 + - - -
378B ALA* 3.5 31.2 - - - -
379B ALA* 3.4 11.5 + - - +
404B TYR* 3.6 7.2 - - - -
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Residues in contact with CYS 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B ALA 3.2 9.9 + - - +
369B GLU* 3.2 10.3 + - - +
371B GLY* 1.3 75.4 - - - +
373B LYS* 1.3 63.1 + - + +
374B LEU 3.6 0.2 + - - -
375B GLY* 4.1 5.0 + - - -
379B ALA* 4.9 0.9 - - - -
404B TYR* 3.1 37.6 + - + -
405B THR* 3.4 11.0 - - - -
406B LEU* 3.4 35.7 - - + +
409B VAL* 4.6 4.3 - - + -
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Residues in contact with LYS 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B THR* 6.2 2.0 - - - +
227B LEU* 4.6 4.0 + - - +
230B ASP* 4.9 7.2 + - - +
232B ASN* 3.4 39.0 - - - +
369B GLU* 2.9 32.8 + - + +
370B ALA 3.1 8.6 + - - +
372B CYS* 1.3 79.9 - - + +
374B LEU* 1.3 59.6 + - - +
406B LEU* 4.0 20.9 - - + -
429B ARG* 4.0 7.9 + - - +
430B ASN* 2.8 29.1 + - - -
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ASN* 3.5 29.4 - - + +
233B ARG* 3.7 42.6 + - + +
236B PHE* 3.7 18.8 - - + -
370B ALA 3.0 17.3 + - - +
371B GLY 3.2 3.1 + - - +
373B LYS* 1.3 80.8 - - - +
375B GLY* 1.3 66.9 + - - +
378B ALA* 3.9 15.5 - - + -
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Residues in contact with GLY 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ARG* 5.1 1.7 + - - -
371B GLY 2.9 8.1 + - - -
372B CYS 4.1 5.1 + - - -
373B LYS 3.7 0.8 - - - -
374B LEU* 1.3 82.5 - - - +
376B GLY* 1.3 67.2 + - - -
378B ALA* 3.5 8.1 + - - +
379B ALA* 3.1 25.1 + - - -
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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