Contacts of the helix formed by residues 531 - 534 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17J ILE* 3.9 10.1 - - + -
18J GLU 2.9 16.6 + - - +
19J GLY* 4.7 0.4 - - - -
20J HIS* 3.1 33.0 - - + +
21J LEU* 3.7 32.5 - - + -
39J SER* 3.7 22.7 - - - +
40J THR 4.7 1.3 - - - +
41J LEU* 5.1 6.5 - - + +
357J MET* 4.2 13.9 - - + -
490J LEU* 4.5 3.1 - - + -
529J PRO* 3.6 29.2 - - + -
530J CYS* 1.3 73.0 - - - +
532J ALA* 1.3 64.5 + - - +
535J VAL* 3.2 25.6 + - + +
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Residues in contact with ALA 532 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I GLU 4.1 11.7 - - - +
17I CYS* 4.3 5.2 - - - +
18J GLU* 2.6 37.8 + - - +
19J GLY* 4.4 2.1 - - - -
41J LEU* 5.9 4.0 - - - -
43J ARG* 2.8 26.9 + - - +
64J ALA 3.1 18.5 - - - +
65J CYS* 4.5 2.0 - - + -
531J ILE* 1.3 72.8 - - - +
533J CYS* 1.3 53.8 + - - +
535J VAL* 5.6 0.2 - - - -
536J HIS* 3.0 19.6 + - - +
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Residues in contact with CYS 533 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64J ALA* 4.1 5.6 - - - -
65J CYS* 3.4 6.5 - - - -
68J CYS* 3.0 4.3 - - - -
72J HIS* 3.5 8.7 - - - -
484J VAL* 3.2 23.2 - - + +
530J CYS* 3.6 5.5 + - - +
531J ILE 3.3 0.2 - - - -
532J ALA* 1.3 77.8 - - - +
534J GLY* 1.3 57.2 + - - +
536J HIS* 2.7 27.6 + - - -
537J FCO 2.2 50.5 - - - +
538J NI 2.6 24.2 - - + -
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Residues in contact with GLY 534 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357J MET* 3.5 29.5 - - - +
484J VAL* 4.5 0.4 - - - -
486J SER* 4.2 0.6 - - - -
487J THR* 2.8 44.1 + - - +
530J CYS 3.0 10.3 + - - -
531J ILE 3.4 1.2 + - - -
533J CYS* 1.3 81.4 - - - +
535J VAL* 1.3 55.3 + - - +
536J HIS* 3.6 4.6 - - - -
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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