Contacts of the helix formed by residues 501 - 506 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277L THR* 4.0 7.6 - - + +
366L ALA* 5.0 4.3 - - - +
367L PHE 3.8 22.6 + - - +
368L GLU* 4.1 14.6 - - + +
488L TRP 4.4 3.2 + - - -
489L ASN* 3.6 8.1 + - - +
500L SER* 1.3 72.8 - - - +
502L VAL* 1.3 57.6 + - - +
504L GLN* 4.7 4.3 - - - -
505L ALA* 2.9 23.4 + - - +
527L TYR* 3.1 32.8 + - + +
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Residues in contact with VAL 502 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L ILE* 5.1 2.7 - - + -
37L SER* 3.7 32.1 - - - +
489L ASN 2.9 24.9 + - - +
490L LEU* 3.9 19.3 - - + -
500L SER* 3.8 4.0 - - - +
501L ALA* 1.3 69.5 - - - +
503L GLU* 1.3 72.3 + - + +
505L ALA* 3.2 2.4 + - - +
506L LEU* 3.0 28.9 + - + +
523L THR* 4.9 2.0 - - + -
524L VAL* 4.2 28.0 - - + -
527L TYR* 4.1 26.0 + - + -
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Residues in contact with GLU 503 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L ALA* 3.6 20.6 - - + +
36L TRP* 3.5 0.7 - - - +
37L SER* 2.9 35.1 + - - +
354L TYR* 2.7 33.7 + - - -
491L GLY 4.0 2.7 - - - -
492L PRO* 3.8 1.4 - - - +
493L ARG* 3.9 13.6 + - - +
499L LEU* 3.7 22.2 - - + -
500L SER* 3.2 33.3 + - - +
502L VAL* 1.3 81.2 - - - +
504L GLN* 1.3 61.6 + - - +
506L LEU* 3.0 16.2 + - + +
507L ILE* 3.2 17.7 - - - +
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Residues in contact with GLN 504 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276L LYS 4.3 14.4 - - - +
277L THR* 5.4 5.6 - - + -
499L LEU* 4.0 29.9 - - + +
500L SER 3.1 16.4 + - - +
501L ALA* 4.0 5.2 - - - +
503L GLU* 1.3 75.1 - - - +
505L ALA* 1.3 64.8 + - - +
506L LEU 3.2 0.5 + - - -
507L ILE* 3.5 26.0 + - - +
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Residues in contact with ALA 505 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275L GLY* 3.2 42.2 + - - +
276L LYS 4.4 3.8 - - - -
277L THR* 4.4 1.7 - - + +
410L ARG* 4.4 0.2 - - - +
501L ALA 2.9 19.3 + - - +
502L VAL 3.2 5.6 + - - +
504L GLN* 1.3 77.8 - - - +
506L LEU* 1.3 60.3 + - - +
507L ILE 3.9 3.8 - - - +
509L THR* 3.7 5.7 + - - -
523L THR* 3.6 20.6 - - + +
527L TYR* 3.5 16.8 - - + +
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Residues in contact with LEU 506 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L ILE* 3.9 34.8 - - + -
25L VAL* 4.0 5.6 - - + -
32L ILE* 3.1 30.7 - - + +
35L ALA* 3.8 24.5 - - + -
36L TRP 5.6 0.7 - - - +
502L VAL* 3.0 18.1 + - + +
503L GLU* 3.0 12.5 + - + +
505L ALA* 1.3 77.2 - - - +
507L ILE* 1.3 64.7 - - - +
509L THR* 2.7 23.6 + - - +
520L ILE* 4.3 16.4 - - + +
523L THR* 3.9 26.7 - - + -
524L VAL* 4.6 4.0 - - + -
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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