Contacts of the helix formed by residues 531 - 534 (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 ILE 531 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17L ILE* 3.9 9.9 - - + -
18L GLU 2.9 16.0 + - - +
19L GLY* 4.7 0.2 - - - -
20L HIS* 3.1 33.2 - - + +
21L LEU* 3.7 32.5 - - + -
39L SER* 3.7 22.2 - - - +
40L THR 4.7 0.9 - - - +
41L LEU* 5.1 6.5 - - + +
357L MET* 4.2 14.1 - - + -
490L LEU* 4.5 3.1 - - + -
529L PRO* 3.6 29.8 - - + -
530L CYS* 1.3 72.9 - - - +
532L ALA* 1.3 63.9 + - - +
535L VAL* 3.2 26.5 + - + +
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Residues in contact with ALA 532 (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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18L GLU* 2.6 38.2 + - + +
19L GLY* 4.4 2.5 - - - -
41L LEU* 5.9 4.9 - - + -
43L ARG* 2.8 27.9 + - - +
64L ALA 3.1 18.2 - - - +
65L CYS* 4.5 2.2 - - + -
531L ILE* 1.3 71.2 - - - +
533L CYS* 1.3 55.5 + - - +
535L VAL* 5.6 0.2 - - - -
536L HIS* 3.0 19.2 + - - +
16S GLU 4.1 11.4 - - - +
17S CYS* 4.3 4.9 - - - +
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Residues in contact with CYS 533 (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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64L ALA* 3.6 6.0 + - - -
65L CYS* 3.4 7.0 - - - -
68L CYS* 3.0 4.9 - - - -
72L HIS* 3.5 7.2 - - - -
484L VAL* 3.2 21.7 - - + +
530L CYS* 3.6 5.2 + - - +
531L ILE 3.3 0.2 - - - -
532L ALA* 1.3 77.0 - - - +
534L GLY* 1.3 58.0 - - - +
536L HIS* 2.7 28.3 + - - -
537L FCO 2.2 50.5 - - - +
538L NI 2.6 23.8 - - + -
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Residues in contact with GLY 534 (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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357L MET* 3.5 31.1 - - - +
358L LYS 4.9 0.2 + - - -
484L VAL* 4.5 0.2 - - - -
486L SER* 4.2 0.2 - - - -
487L THR* 2.8 44.8 + - - +
530L CYS 3.0 10.7 + - - -
531L ILE 3.4 0.8 + - - -
533L CYS* 1.3 80.7 - - - +
535L VAL* 1.3 55.7 + - - +
536L HIS* 3.6 4.3 - - - -
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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