Contacts of the helix formed by residues 405 - 418 (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 THR 405 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B CYS* 3.4 9.0 - - - -
402B ALA 4.6 8.3 - - - +
403B ASP* 3.0 13.8 + - - +
404B TYR* 1.3 77.9 - - - +
406B LEU* 1.3 64.9 + - - +
407B ASP* 3.6 7.7 + - - +
408B ARG* 3.0 31.4 + - - +
409B VAL* 3.1 16.5 + - - +
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Residues in contact with LEU 406 (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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369B GLU* 3.9 27.6 - - + +
372B CYS* 3.4 14.4 - - + -
373B LYS* 4.0 17.7 - - + -
405B THR* 1.3 72.0 - - - +
407B ASP* 1.3 59.0 + - - +
409B VAL* 3.0 6.5 + - + +
410B LEU* 2.9 45.0 + - + +
430B ASN* 3.5 35.4 - - + +
432B LYS* 4.5 13.7 - - - +
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Residues in contact with ASP 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B THR* 3.3 7.7 + - - +
406B LEU* 1.3 78.5 - - - +
408B ARG* 1.3 56.0 + - - +
410B LEU* 3.7 7.4 - - - +
411B ASP* 2.8 39.3 + - - +
432B LYS* 2.7 40.9 + - - +
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Residues in contact with ARG 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B LEU* 4.4 5.7 - - + +
390B VAL* 3.6 13.7 - - - +
397B ASN* 5.6 3.6 - - - +
398B GLU 4.8 3.4 + - - -
399B VAL* 3.6 38.8 - - + +
403B ASP* 3.4 30.0 - - - +
404B TYR* 5.0 0.2 - - - -
405B THR* 3.0 17.4 + - - +
407B ASP* 1.3 75.8 - - - +
409B VAL* 1.3 58.6 + - - +
411B ASP* 3.5 13.5 + - - +
412B GLU* 2.8 58.0 + - - +
415B LYS* 4.3 15.3 - - - +
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Residues in contact with VAL 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LEU* 4.0 14.1 - - + +
368B ALA* 4.0 14.8 - - + +
369B GLU* 3.8 36.1 - - + +
372B CYS* 4.6 2.9 - - + -
386B LEU* 4.2 11.4 - - + -
404B TYR* 3.9 26.9 - - + -
405B THR 3.1 14.1 + - - +
406B LEU* 3.0 10.5 + - + +
408B ARG* 1.3 75.4 - - - +
410B LEU* 1.3 60.0 + - - +
412B GLU* 3.2 7.7 + - - +
413B ARG* 2.9 31.5 + - - +
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B GLU* 4.0 7.9 - - - +
406B LEU* 2.9 27.7 + - + +
407B ASP* 3.8 7.4 - - - +
409B VAL* 1.3 76.4 - - - +
411B ASP* 1.3 58.7 + - - +
413B ARG* 3.3 25.5 + - - +
414B SER 2.9 22.7 + - - -
423B ARG* 3.3 20.7 + - - +
426B ASP* 4.2 11.9 - - + +
427B LEU* 4.4 7.2 - - + -
430B ASN* 3.6 35.2 - - + +
432B LYS* 3.9 34.8 - - + -
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Residues in contact with ASP 411 (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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308B LYS* 5.5 1.9 + - - -
312B GLN* 3.9 12.8 - - - +
407B ASP* 2.8 25.8 + - - +
408B ARG* 3.7 17.6 - - - +
409B VAL 3.2 0.2 - - - -
410B LEU* 1.3 76.0 - - - +
412B GLU* 1.3 65.2 + - - +
414B SER* 3.1 9.4 + - - -
415B LYS* 3.0 30.1 + - - +
423B ARG* 4.6 11.1 + - - -
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Residues in contact with GLU 412 (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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321B ARG* 2.8 37.4 + - - -
365B LEU* 3.8 17.9 - - + -
386B LEU* 3.8 18.4 - - + -
389B ILE* 3.7 8.5 - - + +
390B VAL* 3.4 26.1 - - + +
408B ARG* 2.8 39.4 + - - +
409B VAL 3.2 8.5 + - - +
411B ASP* 1.3 76.4 - - - +
413B ARG* 1.3 62.4 + - - +
415B LYS* 3.2 12.3 + - - +
416B GLU* 3.0 22.7 + - - +
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Residues in contact with ARG 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ARG* 6.2 0.8 - - - +
227B LEU* 3.4 21.0 - - - +
228B TYR* 6.0 0.8 - - - -
362B GLU* 4.6 7.3 + - - +
365B LEU* 3.9 33.8 + - + +
366B ILE* 3.7 23.4 - - - +
369B GLU* 2.9 29.5 + - - +
409B VAL* 2.9 15.1 + - + +
410B LEU* 3.4 25.6 - - - +
412B GLU* 1.3 76.6 - - - +
414B SER* 1.3 63.9 + - - +
417B LEU* 2.9 47.6 + - + +
422B HIS* 4.4 6.1 + - - -
423B ARG* 5.6 1.8 - - - +
426B ASP* 3.0 36.5 + - + +
429B ARG* 3.4 7.2 - - - +
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Residues in contact with SER 414 (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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73B ASP* 2.5 31.5 + - - +
308B LYS* 3.7 2.1 + - - -
309B TYR* 3.3 12.6 - - - -
312B GLN* 2.9 21.7 + - - -
410B LEU 2.9 13.1 + - - -
411B ASP* 3.2 13.0 - - - -
413B ARG* 1.3 76.6 - - - +
415B LYS* 1.3 64.6 + - - +
418B VAL* 3.7 12.3 + - - +
423B ARG* 3.8 23.5 - - - +
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Residues in contact with LYS 415 (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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309B TYR* 2.8 28.3 + - - -
312B GLN* 3.8 29.1 + - - -
313B MSE 3.6 24.3 - - + +
316B ASP* 5.4 6.3 + - - +
319B ASP* 4.8 4.8 + - - +
321B ARG* 3.7 32.5 - - - +
397B ASN* 5.5 4.6 - - - +
408B ARG* 4.3 16.1 - - - +
411B ASP* 3.0 16.3 + - - +
412B GLU* 3.2 27.8 + - - +
414B SER* 1.3 77.5 + - - +
416B GLU* 1.3 61.0 + - - +
418B VAL* 4.0 4.2 - - - +
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Residues in contact with GLU 416 (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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260B TYR* 2.7 24.1 + - - -
321B ARG* 3.1 29.9 + - - +
340B LYS* 3.1 12.0 + - - -
359B ARG* 2.9 47.5 + - - +
361B SER* 4.1 10.1 - - - -
365B LEU* 4.0 16.2 - - + -
389B ILE* 3.6 6.9 - - + +
392B ARG* 3.1 26.4 + - - -
412B GLU 3.0 16.5 + - - +
415B LYS* 1.3 76.0 - - - +
417B LEU* 1.3 67.4 + - + +
418B VAL 3.5 0.4 - - - -
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Residues in contact with LEU 417 (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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68B ASP* 4.3 1.6 - - - +
359B ARG* 3.7 23.8 - - + +
362B GLU* 4.6 20.9 - - + +
365B LEU* 4.2 6.5 - - + -
413B ARG* 2.9 55.3 + - + +
414B SER 4.5 0.2 - - - -
416B GLU* 1.3 86.6 - - + +
418B VAL* 1.3 67.8 + - - +
419B GLY 3.3 0.5 + - - -
420B GLU* 3.0 32.4 + - - +
421B GLY 4.2 1.2 + - - -
422B HIS* 3.7 39.6 + - + +
423B ARG* 5.5 1.8 + - - +
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Residues in contact with VAL 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASP* 4.1 3.4 - - - +
73B ASP* 4.3 11.7 - - + -
74B MSE 3.9 25.1 - - + -
305B VAL* 4.3 11.9 - - + -
309B TYR* 3.4 34.8 - - + +
321B ARG 6.0 0.4 - - - +
324B LEU* 6.0 1.3 - - + -
338B LEU* 4.1 19.3 - - + -
340B LYS* 2.9 34.1 + - + +
414B SER 3.7 15.7 + - - +
415B LYS 4.0 3.4 - - - +
416B GLU 3.5 0.4 - - - -
417B LEU* 1.3 76.3 - - - +
419B GLY* 1.3 64.2 + - - +
423B ARG* 6.3 2.2 - - - -
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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