Contacts of the strand formed by residues 449 - 453 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE* 3.9 18.6 - + + -
15A PHE* 3.6 28.9 - + - -
32A LYS* 3.7 22.6 + - + -
33A VAL* 3.9 1.0 - - + +
34A PRO* 3.4 31.8 - - + +
38A LEU 3.0 4.3 + - - +
39A VAL* 3.0 30.0 - - + +
40A VAL* 2.9 26.0 + - - +
447A ALA* 3.2 6.1 - - - -
448A ASP* 1.3 81.1 - - + +
450A LEU* 1.3 77.0 + - - +
451A VAL* 3.6 4.1 - - + +
467A SER* 3.0 38.3 + - - -
468A GLY* 3.4 15.3 - - - -
469A PRO* 3.7 25.1 - - + -
470A PRO* 5.1 0.2 - - - -
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Residues in contact with LEU 450 (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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40A VAL* 3.4 18.4 - - + -
42A THR* 3.3 41.7 - - + +
444A ILE* 3.5 17.0 - - + +
447A ALA* 6.0 0.4 - - + -
449A TRP* 1.3 75.7 - - - +
451A VAL* 1.3 78.5 + - - +
452A ASP* 3.7 11.7 - - + -
466A TYR* 4.0 13.5 - - + -
468A GLY 2.6 37.7 + - - +
469A PRO* 4.4 0.8 - - - +
470A PRO* 4.2 19.0 - - + -
473A LEU* 3.7 29.2 - - + -
481A THR* 5.3 0.2 - - - +
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Residues in contact with VAL 451 (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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31A VAL* 4.2 1.6 - - + -
33A VAL* 3.9 17.5 - - + -
39A VAL* 4.5 1.6 - - + -
40A VAL 3.0 4.2 + - - +
41A PHE* 3.4 31.4 - - + -
42A THR* 2.7 32.5 + - - +
52A LEU* 4.2 7.9 - - + -
449A TRP* 3.6 10.1 - - + +
450A LEU* 1.3 85.3 - - - +
452A ASP* 1.3 56.5 + - - +
453A VAL* 4.4 3.9 - - + +
464A ILE* 4.1 24.5 - - + -
466A TYR 3.1 6.7 - - - +
467A SER* 3.5 23.6 - - - +
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Residues in contact with ASP 452 (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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42A THR* 2.6 30.4 + - - +
43A GLY* 3.9 0.6 - - - -
450A LEU* 3.7 11.7 - - + -
451A VAL* 1.3 75.6 - - - +
453A VAL* 1.3 68.9 + - - +
463A GLU 3.7 0.3 - - - +
464A ILE* 3.9 2.1 - - - -
465A LEU* 2.9 43.5 + - + +
466A TYR 2.9 12.2 + - - +
473A LEU* 4.9 2.5 - - + -
479A SER* 3.3 14.8 + - - +
480A GLN 5.1 0.7 + - - -
481A THR* 2.5 39.3 - - - +
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Residues in contact with VAL 453 (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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26A LEU* 4.6 5.4 - - + -
41A PHE* 5.1 1.8 - - + -
42A THR 2.8 21.5 + - - +
43A GLY* 3.6 9.9 - - - -
44A VAL 4.0 1.6 + - - -
47A SER* 3.1 23.9 + - - +
48A GLY* 3.3 36.3 - - - +
49A LYS* 3.8 18.4 - - + +
52A LEU* 4.9 10.1 - - + -
451A VAL* 4.4 14.4 - - + +
452A ASP* 1.3 82.0 - - - +
454A GLY* 1.3 71.0 + - - +
455A PRO 4.1 2.3 - - - +
462A GLY* 4.5 5.4 - - - -
463A GLU 3.7 7.0 - - - +
464A ILE* 5.0 3.6 - - + -
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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