Contacts of the strand formed by residues 470 - 475 (chain A) in PDB entry 5VLR
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 ALA 470 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A GLY* 3.5 2.6 - - - -
331A SER* 2.9 41.6 + - - +
332A LYS* 6.4 0.2 - - + -
333A VAL* 5.3 0.3 - - - +
438A CYS* 4.1 15.5 - - - -
439A LEU 3.4 16.4 - - - +
440A TYR* 3.9 23.6 - - + -
441A MET* 3.9 10.6 - - - +
468A ALA 4.7 0.7 - - - +
469A ALA* 1.3 77.0 - - - +
471A LEU* 1.3 61.9 + - - +
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Residues in contact with LEU 471 (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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327A LEU* 4.1 17.7 - - + -
329A GLN 3.6 11.7 - - - +
330A GLY* 4.6 4.0 - - - -
343A VAL* 5.3 7.9 - - + -
371A TRP* 5.2 4.9 - - + -
392A PHE* 5.8 10.8 - - + -
394A LEU* 5.8 4.9 - - + -
421A ALA* 6.1 0.7 - - + -
437A ARG 3.7 1.4 - - - +
438A CYS* 3.7 1.2 - - - -
439A LEU* 2.9 41.0 + - + +
441A MET* 4.2 21.5 - - + -
470A ALA* 1.3 77.4 - - - +
472A LEU* 1.4 63.7 + - - +
473A ILE* 3.8 7.9 + - + +
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Residues in contact with LEU 472 (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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327A LEU* 4.0 1.0 - - - +
328A ILE* 3.1 35.3 + - + -
329A GLN* 2.7 44.5 + - + +
330A GLY* 4.7 0.2 - - - -
331A SER* 4.5 15.0 - - - +
436A GLU* 3.4 36.3 - - + +
437A ARG 3.6 5.6 - - - +
438A CYS* 4.0 26.9 - - + -
470A ALA 4.4 0.2 - - - -
471A LEU* 1.4 68.6 - - - +
473A ILE* 1.3 62.4 + - - +
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Residues in contact with ILE 473 (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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325A ILE* 4.8 11.0 - - + -
326A GLU 3.5 10.3 - - - +
327A LEU* 4.3 17.0 - - + +
328A ILE* 5.1 1.6 - - - -
392A PHE* 3.7 32.3 - - + -
423A LEU* 5.0 5.6 - - + -
436A GLU* 3.2 8.1 - - - +
437A ARG* 2.8 53.2 + - + +
439A LEU* 4.1 20.9 - - + -
471A LEU* 4.7 6.5 - - + +
472A LEU* 1.3 77.7 - - - +
474A CYS* 1.3 62.4 + - - +
475A LEU* 4.3 1.8 - - + +
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Residues in contact with CYS 474 (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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325A ILE* 4.0 1.7 - - - -
326A GLU* 3.0 45.6 + - + +
328A ILE* 4.5 10.1 - - + -
435A GLY* 3.6 7.9 - - - -
436A GLU* 3.5 32.1 - - + +
473A ILE* 1.3 78.0 - - - +
475A LEU* 1.3 69.7 + - - +
476A PRO* 3.8 6.4 - - - +
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Residues in contact with LEU 475 (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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323A PHE* 5.0 11.2 - - + -
325A ILE* 4.0 19.5 - - + -
390A LEU* 5.4 0.2 - - + -
423A LEU* 4.8 18.2 - - + -
425A LEU* 6.1 1.6 - - - +
433A LYS* 3.5 30.5 - - + +
434A THR* 4.2 1.1 - - - -
435A GLY* 2.7 38.5 + - - +
437A ARG* 5.3 5.8 - - + +
473A ILE* 5.6 2.4 - - + +
474A CYS* 1.3 75.3 - - - +
476A PRO* 1.3 66.9 - - + +
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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