Contacts of the helix formed by residues 405 - 418 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A CYS* 3.6 7.6 - - - -
402A ALA 4.6 2.9 - - - +
403A ASP* 3.1 13.9 + - - +
404A TYR* 1.3 76.0 - - - +
406A LEU* 1.3 64.6 + - - +
407A ASP* 3.6 9.2 + - - +
408A ARG* 3.1 29.3 + - - +
409A VAL* 3.2 15.1 + - - +
507A EDO 3.7 17.9 - - - +
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Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A GLU* 3.8 31.2 - - + +
372A CYS* 3.5 14.8 - - - -
373A LYS* 4.0 20.9 - - + -
405A THR* 1.3 72.4 - - - +
407A ASP* 1.3 59.3 + - - +
409A VAL* 3.0 6.5 + - + +
410A LEU* 2.8 44.5 + - + +
430A ASN* 3.6 25.8 - - + +
432A LYS* 4.3 18.2 - - - +
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Residues in contact with ASP 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A THR* 3.3 8.5 + - - +
406A LEU* 1.3 78.4 - - - +
408A ARG* 1.3 57.4 + - - +
410A LEU* 3.3 7.8 + - - +
411A ASP* 2.8 40.8 + - - +
432A LYS* 2.9 38.8 + - - +
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Residues in contact with ARG 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A LEU* 4.6 5.1 - - + +
390A VAL* 3.8 12.9 - - - +
397A ASN* 5.7 2.4 - - - +
398A GLU 4.7 2.6 + - - -
399A VAL* 3.5 36.9 - - + +
403A ASP* 3.4 30.0 - - - +
404A TYR* 5.0 0.2 - - - -
405A THR* 3.1 16.5 + - - +
407A ASP* 1.3 77.1 - - - +
409A VAL* 1.3 63.0 + - + +
411A ASP* 3.5 13.8 + - - +
412A GLU* 2.8 45.1 + - - +
415A LYS* 4.4 14.5 - - - +
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Residues in contact with VAL 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A LEU* 4.0 11.7 - - + +
368A ALA* 4.1 13.5 - - + +
369A GLU* 3.8 35.9 - - + +
372A CYS* 4.5 5.6 - - + -
386A LEU* 4.2 12.3 - - + -
404A TYR* 3.8 29.2 - - + -
405A THR 3.2 13.4 + - - +
406A LEU* 3.0 8.6 + - + +
408A ARG* 1.3 72.6 - - - +
410A LEU* 1.3 61.0 + - - +
412A GLU* 3.1 8.2 + - - +
413A ARG* 2.9 31.4 + - - +
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Residues in contact with LEU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A GLU* 4.1 10.1 - - + +
406A LEU* 2.8 28.0 + - + +
407A ASP* 3.8 8.3 - - - +
409A VAL* 1.3 77.1 - - - +
411A ASP* 1.3 56.2 + - - +
413A ARG* 3.2 26.5 + - - +
414A SER 2.9 23.6 + - - -
423A ARG* 3.4 20.4 + - - +
426A ASP* 4.3 11.4 - - + +
427A LEU* 4.5 9.9 - - + -
430A ASN* 3.6 32.1 - - + +
432A LYS* 4.0 33.0 - - + -
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Residues in contact with ASP 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A LYS* 5.5 1.4 + - - -
312A GLN* 4.1 13.9 - - - +
407A ASP* 2.8 29.6 + - - +
408A ARG* 3.7 19.2 - - - +
409A VAL 3.3 0.2 - - - -
410A LEU* 1.3 71.7 - - - +
412A GLU* 1.3 62.5 + - - +
414A SER* 3.3 8.3 - - - -
415A LYS* 3.1 30.9 + - - +
423A ARG* 4.6 10.6 + - - -
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Residues in contact with GLU 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A ARG* 2.7 37.7 + - - -
365A LEU* 3.8 12.8 - - + -
386A LEU* 3.8 23.8 - - + -
389A ILE* 3.8 8.5 - - + +
390A VAL* 3.4 25.7 - - + +
408A ARG* 2.8 42.6 + - - +
409A VAL 3.1 9.7 + - - +
411A ASP* 1.3 74.7 - - - +
413A ARG* 1.3 58.1 + - - +
415A LYS* 3.2 13.6 + - - +
416A GLU* 2.9 32.7 + - - +
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Residues in contact with ARG 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ARG* 6.3 0.2 - - - +
227A LEU* 3.3 30.1 - - - +
228A TYR* 6.2 0.4 - - - -
362A GLU* 4.6 6.7 + - - +
365A LEU* 3.9 33.2 + - + +
366A ILE* 3.7 25.3 - - - +
369A GLU* 2.9 20.0 + - - +
409A VAL* 2.9 15.1 + - + +
410A LEU* 3.4 26.7 - - - +
412A GLU* 1.3 73.6 - - - +
414A SER* 1.3 66.3 + - - +
417A LEU* 2.9 47.0 + - + +
422A HIS* 4.4 5.1 + - - -
423A ARG* 5.6 1.6 - - - +
426A ASP* 3.0 36.4 + - + +
429A ARG* 3.4 5.5 - - - +
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Residues in contact with SER 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ASP* 2.5 31.0 + - - +
308A LYS* 3.6 1.4 + - - -
309A TYR* 3.3 12.6 - - - -
312A GLN* 3.0 22.4 + - - -
410A LEU 2.9 13.1 + - - -
411A ASP* 3.3 13.7 - - - -
413A ARG* 1.3 77.9 - - - +
415A LYS* 1.3 61.9 - - - +
418A VAL* 3.5 14.4 + - - +
423A ARG* 3.8 22.1 - - - +
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Residues in contact with LYS 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A TYR* 5.3 0.2 + - - -
309A TYR* 2.9 25.6 + - - -
312A GLN* 4.1 25.7 + - - -
313A MSE 3.7 24.0 - - + +
316A ASP* 4.9 10.3 + - - +
319A ASP* 4.5 6.0 + - - +
321A ARG* 3.7 40.6 - - - +
340A LYS* 5.1 0.2 + - - -
397A ASN* 5.2 4.4 - - - +
408A ARG* 4.4 14.1 - - - +
411A ASP* 3.1 18.5 + - - +
412A GLU* 3.2 22.6 + - - +
414A SER* 1.3 79.0 + - - +
416A GLU* 1.3 63.2 + - - +
417A LEU 3.7 0.2 + - - -
418A VAL* 4.1 4.2 - - - +
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A TYR* 2.7 24.9 + - - -
321A ARG* 3.0 28.4 + - - +
340A LYS* 3.1 11.7 + - - -
359A ARG* 2.8 47.4 + - - +
361A SER* 4.1 12.1 - - - -
365A LEU* 3.9 20.6 - - + -
389A ILE* 3.6 7.6 - - + +
392A ARG* 3.1 25.3 + - - -
412A GLU 2.9 16.5 + - - +
413A ARG 4.1 0.2 - - - +
415A LYS* 1.3 80.8 - - - +
417A LEU* 1.3 60.7 + - + +
418A VAL 3.5 0.2 - - - -
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Residues in contact with LEU 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASP* 4.3 1.0 - - - +
359A ARG* 3.8 23.1 - - + +
362A GLU* 4.5 20.6 - - + +
365A LEU* 4.1 13.5 - - + -
413A ARG* 2.9 44.6 + - + +
416A GLU* 1.3 86.8 - - + +
418A VAL* 1.3 67.1 + - - +
420A GLU* 3.0 36.1 + - - +
421A GLY 4.2 1.4 + - - -
422A HIS* 3.7 40.3 + - + +
423A ARG* 5.6 1.2 + - - -
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Residues in contact with VAL 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASP* 4.1 3.6 - - - +
73A ASP* 4.3 11.7 - - + -
74A MSE 3.9 25.6 - - + -
305A VAL* 4.4 7.2 - - + -
309A TYR* 3.3 36.6 - - + +
321A ARG 6.1 0.2 - - - +
324A LEU* 5.9 1.3 - - + -
338A LEU* 3.8 23.1 - - + +
340A LYS* 2.7 39.9 + - - +
414A SER 3.5 17.0 + - - +
415A LYS 4.1 2.9 - - - +
416A GLU 3.5 0.2 - - - -
417A LEU* 1.3 75.4 - - - +
419A GLY* 1.3 62.8 + - - +
420A GLU 3.4 0.2 + - - -
423A ARG* 6.4 1.8 - - - -
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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