Contacts of the helix formed by residues 385 - 393 (chain A) in PDB entry 2VM8
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 SER 385 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PRO* 3.9 10.6 + - - +
68A GLY 3.3 26.5 + - - -
69A GLY* 4.3 0.2 - - - -
70A ILE* 3.5 16.9 - - - +
381A VAL* 3.0 14.8 + - - +
382A ALA 4.2 0.2 - - - -
384A THR* 1.3 81.2 + - - +
386A THR* 1.3 70.3 + - - -
387A ASN 3.4 2.0 - - - -
388A ALA* 3.2 6.3 + - - +
389A ALA* 2.9 20.6 + - - +
399A GLY* 3.5 20.3 - - - -
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Residues in contact with THR 386 (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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27A ASP* 3.5 20.6 - - - +
381A VAL* 3.1 25.9 + - - +
382A ALA* 4.1 3.1 - - - -
385A SER* 1.3 75.2 + - - +
387A ASN* 1.3 60.9 + - - +
389A ALA* 2.9 8.6 - - - +
390A LYS* 2.8 55.6 + - - +
395A TYR* 3.4 16.6 - - + -
399A GLY* 3.0 26.5 + - - +
400A ARG* 5.3 0.2 - - + -
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Residues in contact with ASN 387 (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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27A ASP* 4.7 4.0 - - - +
327A GLN* 3.4 39.9 + - + +
328A VAL* 4.3 2.0 - - + -
379A GLN* 5.1 3.0 - - - +
382A ALA* 3.0 37.2 + - - +
383A VAL* 4.6 3.6 - - - +
386A THR* 1.3 73.9 - - - +
388A ALA* 1.3 55.6 + - - +
390A LYS* 3.0 17.4 + - - +
391A VAL* 2.6 42.6 + - + +
477A PHE* 4.8 12.3 - - + -
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Residues in contact with ALA 388 (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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70A ILE* 4.3 18.2 - - + +
72A VAL* 3.2 33.7 - - + -
328A VAL* 4.0 16.1 - - + +
329A THR 5.8 0.4 - - - +
382A ALA 4.5 0.8 + - - -
384A THR 5.5 0.9 - - - +
385A SER* 3.2 10.8 + - - +
387A ASN* 1.3 76.7 - - - +
389A ALA* 1.3 64.4 + - - +
391A VAL* 3.3 2.6 + - - -
392A PHE* 3.1 31.9 + - + +
394A LEU* 5.4 0.8 - - - +
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Residues in contact with ALA 389 (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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70A ILE* 4.2 13.4 - - + +
385A SER 2.9 12.8 + - - +
386A THR* 2.9 17.7 - - - +
388A ALA* 1.3 77.8 - - - +
390A LYS* 1.3 59.0 + - - +
392A PHE 3.4 0.3 + - - -
393A ASN* 3.0 5.9 + - - -
394A LEU* 2.9 36.1 + - - +
395A TYR* 3.6 20.4 + - + +
398A LYS 4.1 14.8 - - - +
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Residues in contact with LYS 390 (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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27A ASP* 3.8 23.4 + - - -
386A THR* 2.8 36.6 + - + +
387A ASN* 3.0 14.9 + - - +
389A ALA* 1.3 74.3 - - - +
391A VAL* 1.3 64.1 + - - +
392A PHE 3.4 0.5 + - - -
393A ASN* 3.6 7.0 + - - +
395A TYR* 3.7 37.2 - - + -
475A PRO* 3.9 7.3 - - - +
477A PHE* 3.5 52.8 - - + +
28B ASP* 4.0 26.6 - - - +
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Residues in contact with VAL 391 (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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194A ILE* 3.9 14.8 - - + +
251A TYR* 4.5 13.0 - - + -
275A TYR* 3.8 39.0 - - + -
328A VAL* 4.3 8.7 - - + -
387A ASN* 2.6 25.9 + - + +
388A ALA* 3.8 5.8 - - - +
390A LYS* 1.3 74.5 - - - +
392A PHE* 1.3 84.1 + - + +
475A PRO* 3.5 19.1 - - - +
477A PHE* 4.0 11.2 - - + -
478A VAL* 4.0 8.5 - - + +
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Residues in contact with PHE 392 (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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72A VAL* 4.0 21.8 - - + -
105A ILE* 4.3 12.6 - - + -
138A HIS* 3.8 23.3 - + - -
162A ASN* 3.0 21.1 + - - +
163A SER* 4.1 12.3 - - - -
194A ILE* 4.3 13.0 - - + -
196A GLN* 4.5 1.8 - - - -
251A TYR* 3.5 31.2 - + - -
328A VAL* 5.4 0.4 - - + -
388A ALA* 3.1 27.5 + - - +
391A VAL* 1.3 94.6 - - + +
393A ASN* 1.3 71.1 + - - +
394A LEU* 3.4 9.8 - - + +
471A ARG* 3.4 41.4 - - - +
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Residues in contact with ASN 393 (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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162A ASN* 3.8 1.6 - - - +
389A ALA 3.0 4.9 + - - -
390A LYS* 3.6 4.4 + - - +
391A VAL 3.6 2.8 + - - -
392A PHE* 1.3 83.4 - - - +
394A LEU* 1.3 63.9 + - - +
395A TYR 3.6 7.2 - - - +
471A ARG* 4.8 4.5 - - - -
472A LYS* 2.9 41.8 + - - +
473A PRO 3.5 9.5 + - - -
474A PHE 4.0 1.4 + - - -
475A PRO* 3.5 31.0 - - + +
476A ASP 4.9 1.4 + - - -
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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