Contacts of the helix formed by residues 501 - 506 (chain H) in PDB entry 2FRV
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 501 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277H THR* 4.0 7.9 - - + +
366H ALA* 5.0 3.2 - - - +
367H PHE 3.8 22.1 + - - +
368H GLU* 4.1 15.0 - - + +
488H TRP 4.4 2.8 + - - -
489H ASN* 3.6 8.7 + - - +
500H SER* 1.3 73.8 - - - +
502H VAL* 1.3 57.3 + - - +
504H GLN* 3.8 3.8 - - - -
505H ALA 2.9 22.9 + - - -
527H TYR* 3.1 33.6 + - + +
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Residues in contact with VAL 502 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H ILE* 5.1 2.2 - - + -
37H SER* 3.7 32.1 - - - +
489H ASN 2.9 23.8 + - - +
490H LEU* 3.9 20.0 - - + -
500H SER* 3.8 3.8 - - - +
501H ALA* 1.3 70.5 - - - +
503H GLU* 1.3 71.1 + - - +
505H ALA* 3.2 2.1 + - - +
506H LEU* 3.0 29.1 + - + +
523H THR* 4.9 1.6 - - + -
524H VAL* 4.2 28.3 - - + -
527H TYR* 4.1 27.1 + - + -
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Residues in contact with GLU 503 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H ALA* 3.6 21.0 - - + +
36H TRP* 3.5 0.7 - - - -
37H SER* 2.9 35.5 + - - +
354H TYR* 2.7 32.6 + - - -
491H GLY 4.0 3.4 - - - -
492H PRO* 3.8 1.7 - - - +
493H ARG* 3.9 12.9 + - - -
499H LEU* 3.7 23.1 - - + -
500H SER* 3.2 31.7 + - - +
502H VAL* 1.3 81.4 - - + +
504H GLN* 1.3 61.7 + - - +
506H LEU* 3.0 16.3 + - + +
507H ILE* 3.2 17.5 - - - +
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Residues in contact with GLN 504 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276H LYS 4.3 13.9 - - - +
277H THR* 5.4 5.8 - - + -
499H LEU* 4.0 29.6 + - + +
500H SER 3.1 16.8 + - - +
501H ALA* 4.0 5.6 - - - +
503H GLU* 1.3 75.4 - - - +
505H ALA* 1.3 65.7 + - - +
506H LEU 3.2 0.7 + - - -
507H ILE* 3.5 27.0 + - - +
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Residues in contact with ALA 505 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H GLY* 3.2 40.9 + - - +
276H LYS 4.4 3.8 - - - -
277H THR* 4.4 1.3 - - + +
501H ALA 2.9 19.5 + - - +
502H VAL 3.2 5.6 + - - +
504H GLN* 1.3 77.6 - - - +
506H LEU* 1.3 62.0 + - - +
507H ILE 3.9 3.5 - - - +
509H THR* 3.7 5.9 + - - -
523H THR* 3.6 21.3 - - + +
527H TYR* 3.5 16.4 - - + +
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Residues in contact with LEU 506 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H ILE* 3.9 35.0 - - + -
25H VAL* 4.0 4.9 - - + -
32H ILE* 3.1 30.9 - - + +
35H ALA* 3.8 24.7 - - + -
36H TRP 5.6 0.7 - - - +
502H VAL* 3.0 19.5 + - + +
503H GLU* 3.0 11.8 + - + +
505H ALA* 1.3 77.2 - - - +
507H ILE* 1.3 63.2 - - - +
509H THR* 2.7 25.0 + - - +
520H ILE* 4.3 16.6 - - + +
523H THR* 3.9 26.7 - - + -
524H VAL* 4.6 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