Contacts of the helix formed by residues 417 - 427 (chain B) in PDB entry 2VR1
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 ASN 417 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B VAL* 4.8 7.9 - - - +
338B ARG 3.1 19.3 + - - +
339B ILE* 3.3 9.9 - - - +
340B ASN* 2.7 48.1 + - - +
342B GLU* 4.0 17.8 + - + +
344B PRO* 4.2 10.5 - - + -
347B PHE* 5.5 0.2 - - + -
416B THR* 1.3 71.6 - - - +
418B VAL* 1.3 65.6 + - - +
419B ASP 3.3 2.5 - - - -
420B LEU* 3.3 18.2 + - + +
421B GLN* 2.9 31.6 + - - +
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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
----------------------------------------------------------
339B ILE* 4.3 12.1 - - + -
406B LEU* 3.7 31.6 - - + +
409B LEU* 3.7 31.4 - - + +
411B ILE* 5.0 2.7 - - + -
416B THR* 3.2 25.5 - - + +
417B ASN* 1.3 76.7 + - - +
419B ASP* 1.3 68.4 + - - +
421B GLN* 2.9 19.3 + - - +
422B ILE* 2.9 24.7 + - + +
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Residues in contact with ASP 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B PRO* 4.4 18.3 - - + +
416B THR 4.6 2.4 + - - +
417B ASN* 3.3 0.6 - - - +
418B VAL* 1.3 81.9 - - - +
420B LEU* 1.3 61.7 + - - +
422B ILE* 3.4 20.8 + - - +
423B ARG* 3.2 31.6 + - - +
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Residues in contact with LEU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ARG* 6.0 0.4 - - - -
239B VAL* 5.1 11.2 - - + -
344B PRO* 4.0 19.6 - - + +
347B PHE* 3.7 34.1 - - + -
417B ASN* 3.3 16.9 + - + +
418B VAL 3.2 0.6 - - - -
419B ASP* 1.3 77.2 - - - +
421B GLN* 1.3 64.3 + - + +
423B ARG* 3.3 32.1 + - + +
424B ILE* 3.1 40.9 + - + +
440B LEU* 4.6 7.4 - - + -
443B LYS* 6.5 1.1 - - + -
444B LEU* 4.0 17.3 - - + -
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Residues in contact with GLN 421 (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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239B VAL* 3.1 37.7 + - - +
240B VAL* 3.3 21.7 - - - +
337B CYS* 3.4 16.4 - - + +
338B ARG 3.0 31.8 + - - +
339B ILE* 4.8 1.6 - - + -
406B LEU* 3.8 22.2 - - + -
417B ASN* 2.9 22.2 + - - +
418B VAL* 2.9 10.6 + - - +
420B LEU* 1.3 74.7 - - + +
422B ILE* 1.3 65.8 + - - +
424B ILE* 3.3 7.7 + - - +
425B MET* 3.0 28.1 + - - +
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Residues in contact with ILE 422 (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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403B LYS* 5.3 6.7 - - + +
406B LEU* 3.9 32.3 - - + +
407B GLN* 5.0 12.6 - - + +
418B VAL* 2.9 32.9 + - + +
419B ASP* 3.5 22.0 - - - +
421B GLN* 1.3 76.8 - - - +
423B ARG* 1.3 58.6 + - + +
425B MET* 3.4 4.4 + - - +
426B ASN* 3.1 43.1 + - - +
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Residues in contact with ARG 423 (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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344B PRO* 4.3 6.5 + - - +
345B ASN* 4.0 20.7 + - - +
419B ASP* 3.2 15.4 + - - +
420B LEU* 3.7 33.2 - - + +
421B GLN 3.3 0.2 - - - -
422B ILE* 1.3 78.4 - - + +
424B ILE* 1.3 60.1 + - + +
426B ASN* 3.2 11.1 + - - +
427B ASP* 2.9 27.2 + - - +
443B LYS* 3.7 25.8 + - - +
444B LEU* 3.5 29.3 - - - +
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Residues in contact with ILE 424 (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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232B MET* 3.9 26.5 - - + -
239B VAL* 4.0 25.6 - - + -
240B VAL* 4.1 10.3 - - + -
420B LEU* 3.1 25.6 + - + +
421B GLN* 3.3 13.6 + - - +
423B ARG* 1.3 73.2 - - - +
425B MET* 1.3 81.2 + - + +
427B ASP* 3.2 18.6 + - - +
430B PHE* 3.3 14.7 - - + -
440B LEU* 3.6 31.9 - - + -
443B LYS* 5.2 5.4 - - + +
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Residues in contact with MET 425 (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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240B VAL* 4.2 9.2 - - + -
335B VAL* 4.6 4.7 - - + -
337B CYS* 3.8 17.9 - - - -
399B ILE* 4.2 9.3 - - + +
402B MET* 3.6 26.2 - - + -
403B LYS* 3.5 25.9 - - + -
406B LEU* 3.6 19.7 - - + -
421B GLN 3.0 21.0 + - - +
422B ILE* 3.7 6.5 - - - +
423B ARG 3.3 0.2 - - - -
424B ILE* 1.3 90.9 - - + +
426B ASN* 1.3 58.6 + - - +
427B ASP 3.6 0.3 + - - -
430B PHE* 3.5 41.7 - - + -
431B GLN* 3.1 24.6 + - - +
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Residues in contact with ASN 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B LYS* 3.6 24.3 + - - +
422B ILE* 3.1 36.1 + - - +
423B ARG* 3.6 10.5 - - - +
424B ILE 3.2 0.6 - - - -
425B MET* 1.3 77.0 - - - +
427B ASP* 1.3 64.0 + - - +
428B GLU* 3.3 3.5 + - - +
431B GLN* 3.5 14.4 + - - +
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Residues in contact with ASP 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B MET* 5.6 0.7 - - + -
423B ARG 2.9 7.3 + - - +
424B ILE* 3.2 17.6 + - + +
426B ASN* 1.3 75.3 - - - +
428B GLU* 1.3 59.0 + - - +
429B ASN* 2.7 28.4 + - - +
430B PHE* 2.8 15.1 + - + +
431B GLN* 3.0 28.8 + - - +
439B TYR* 2.6 37.6 + - - -
443B LYS* 2.8 33.2 + - + +
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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