Contacts of the helix formed by residues 479 - 487 (chain B) in PDB entry 2VF8
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 479 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452B ASP* 2.7 27.5 + - - -
465B LEU* 4.6 7.1 - - - +
473B LEU* 3.2 18.9 - - - +
476B VAL* 2.8 20.9 + - - +
477B PRO 3.3 0.4 - - - +
478B GLU* 1.3 74.9 - - - +
480B GLN* 1.3 60.0 + - - +
482B GLY* 2.6 38.4 + - - -
483B GLN* 3.2 16.6 + - - +
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Residues in contact with GLN 480 (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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44B VAL* 3.9 24.8 - - + +
455B PRO 3.5 25.4 + - - +
456B GLU* 4.2 17.8 - - - +
465B LEU* 5.8 0.2 - - - +
478B GLU 3.3 4.9 + - - +
479B SER* 1.3 68.6 - - - +
481B THR* 1.3 70.3 + - + +
483B GLN* 2.9 31.3 + - - +
484B TYR* 3.2 19.6 + - + -
765B HIS* 3.9 5.2 - - + -
767B ALA* 3.5 24.4 - - + +
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Residues in contact with THR 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B THR* 3.5 18.3 + - - +
43B GLY* 3.9 7.9 - - - +
44B VAL 5.4 0.2 - - - +
441B LEU* 4.9 5.3 - - - +
444B ILE* 5.5 5.0 - - - +
450B LEU* 4.7 1.4 - - - +
452B ASP* 2.8 34.8 - - - +
473B LEU* 3.6 11.8 - - - +
480B GLN* 1.3 77.3 - - + +
482B GLY* 1.3 62.6 + - - -
484B TYR* 3.1 3.9 + - - +
485B LEU* 2.9 30.9 + - - +
765B HIS* 3.0 30.2 + - - +
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Residues in contact with GLY 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B LEU* 3.8 19.7 - - - +
476B VAL 5.7 0.4 - - - -
479B SER* 2.6 27.9 + - - -
481B THR* 1.3 76.0 + - - +
483B GLN* 1.3 62.8 + - - +
484B TYR 3.1 0.2 + - - -
485B LEU* 3.2 2.6 + - - -
486B PHE* 3.1 32.2 + - - +
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Residues in contact with GLN 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B PRO 3.6 19.5 + - - +
478B GLU* 4.5 3.4 + - - +
479B SER 3.2 23.9 + - - +
480B GLN* 2.9 24.4 + - - +
482B GLY* 1.3 73.8 - - - +
484B TYR* 1.3 67.8 + - + +
486B PHE* 4.0 0.9 - - - +
487B ALA* 3.1 31.1 + - - +
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Residues in contact with TYR 484 (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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441B LEU* 3.7 20.2 - - + +
445B ARG* 5.7 0.2 + - - -
480B GLN* 3.2 24.8 + - + +
481B THR* 3.1 7.8 + - - +
483B GLN* 1.3 83.9 - - + +
485B LEU* 1.3 59.3 + - - +
486B PHE 3.2 5.7 + - - -
487B ALA* 4.1 10.9 + - + +
490B HIS* 5.5 11.1 - + - -
765B HIS* 4.2 3.4 - + - -
766B PRO* 3.5 46.4 + - + -
767B ALA* 3.5 27.9 - - + +
770B GLU* 3.7 20.3 - - + +
794B GLN* 4.3 10.1 - - - -
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Residues in contact with LEU 485 (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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441B LEU* 3.8 36.5 - - + +
444B ILE* 3.9 20.6 - - + -
445B ARG* 3.3 53.6 + - + +
450B LEU* 4.5 11.9 - - + -
470B PRO* 5.2 4.5 - - + +
473B LEU* 5.0 5.8 - - + -
481B THR* 2.9 21.7 + - - +
482B GLY 3.2 3.5 + - - +
484B TYR* 1.3 77.5 - - - +
486B PHE* 1.3 85.9 + - + +
487B ALA 5.1 1.1 - - - +
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Residues in contact with PHE 486 (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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470B PRO 4.1 9.2 - - - -
471B GLU* 3.8 31.4 - - - -
473B LEU* 4.0 7.6 - - + -
474B LYS* 3.4 51.6 - - + -
482B GLY 3.1 25.7 + - - +
483B GLN* 4.0 0.9 - - - +
484B TYR 3.2 0.2 - - - -
485B LEU* 1.3 107.1 - - + +
487B ALA* 1.3 66.5 + - - +
488B ASP* 3.3 2.9 + - - +
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Residues in contact with ALA 487 (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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483B GLN 3.1 20.1 + - - +
484B TYR* 4.1 9.4 + - + +
485B LEU 3.8 0.7 - - - -
486B PHE* 1.3 80.7 + - - +
488B ASP* 1.3 62.0 + - - +
489B ARG 4.1 0.2 + - - -
490B HIS* 2.4 44.7 - - + +
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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