Contacts of the strand formed by residues 449 - 453 (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 TRP 449 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PHE* 3.8 29.8 - + - -
15B PHE* 3.7 22.2 - + - -
32B LYS* 3.2 39.4 + - + -
33B VAL* 4.1 7.4 - - + -
34B PRO* 3.1 37.0 - - + +
38B LEU 3.8 2.0 + - - -
39B VAL* 3.9 10.3 - - + -
40B VAL 3.1 24.1 + - - -
447B ALA* 3.8 6.6 - - - +
448B ASP* 1.3 77.7 - - - +
450B LEU* 1.3 69.0 + - - +
451B VAL* 4.7 2.0 - - + -
467B SER* 2.6 28.4 + - - -
468B GLY* 3.3 27.3 - - - +
469B PRO* 3.4 27.1 - - + -
470B PRO* 4.1 2.9 - - - -
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Residues in contact with LEU 450 (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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39B VAL* 5.3 0.2 - - - -
40B VAL* 3.4 15.5 - - + -
42B THR* 3.5 33.9 - - + +
444B ILE* 3.7 23.1 - - + +
449B TRP* 1.3 75.6 - - - +
451B VAL* 1.4 58.3 + - - +
452B ASP* 4.1 1.1 - - + +
466B TYR* 3.6 6.4 - - + +
467B SER* 2.8 33.8 + - - -
468B GLY 2.7 19.4 + - - +
470B PRO* 3.6 36.1 - - + +
473B LEU* 3.8 23.8 - - + -
481B THR* 4.7 1.3 - - - +
485B LEU* 4.5 8.5 - - + -
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Residues in contact with VAL 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL* 4.1 10.1 - - + -
33B VAL* 4.6 13.0 - - + -
39B VAL* 4.9 2.2 - - + -
40B VAL 3.1 10.3 + - - +
41B PHE* 3.3 21.4 - - + -
42B THR* 2.6 35.5 + - - +
52B LEU* 4.1 18.4 - - + -
449B TRP* 4.7 4.5 - - + -
450B LEU* 1.4 73.8 - - - +
452B ASP* 1.3 53.6 + - - +
453B VAL* 3.8 19.1 - - + -
464B ILE* 4.3 12.6 - - + -
466B TYR 3.1 6.5 - - - +
467B SER* 3.8 19.1 - - - +
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Residues in contact with ASP 452 (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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42B THR* 2.1 29.3 + - - +
43B GLY* 3.8 0.7 + - - -
450B LEU* 4.1 1.9 - - + +
451B VAL* 1.3 68.0 - - - +
453B VAL* 1.3 63.9 + - - +
464B ILE* 3.4 6.9 - - - +
465B LEU* 2.9 38.3 + - + +
466B TYR* 2.7 14.4 + - + +
473B LEU* 3.6 20.6 - - + -
479B SER* 2.7 38.3 + - - -
480B GLN 4.4 0.2 + - - -
481B THR* 2.8 20.4 - - - +
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Residues in contact with VAL 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 4.4 6.1 - - + -
42B THR 2.9 20.7 + - - +
43B GLY* 4.5 4.5 - - - -
44B VAL 5.1 0.2 + - - -
47B SER* 3.1 46.6 - - - +
48B GLY* 4.1 9.2 - - - +
49B LYS* 4.3 17.7 - - + +
52B LEU* 5.5 3.1 - - + -
451B VAL* 3.8 22.9 - - + +
452B ASP* 1.3 78.7 + - - +
454B GLY* 1.3 71.6 - - - +
455B PRO 4.3 0.5 - - - +
462B GLY* 4.0 8.3 - - - -
463B GLU 3.0 13.5 - - - +
464B ILE* 4.6 4.9 - - + -
465B LEU* 3.1 5.5 - - - +
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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