Contacts of the helix formed by residues 63 - 67 (chain L) in PDB entry 4FAO
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 ASP 63 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29H PRO* 3.9 18.7 - - + +
31H GLU 4.1 4.2 - - - +
32H TYR* 4.6 6.1 - - + -
33H GLU* 5.3 1.7 + - - +
82H ILE* 6.4 1.6 - - + -
40L HIS* 3.4 11.0 + - - -
60L TRP* 3.2 25.5 + - + +
61L LEU 2.6 14.3 + - - +
62L ASP* 1.3 71.8 - - - +
64L PHE* 1.3 67.6 + - - +
65L ASN* 3.0 39.2 + - - +
66L CYS* 3.0 24.7 + - - +
67L TYR* 4.4 1.1 - - - -
83L PHE* 5.6 0.7 - - - -
85L CYS* 4.4 1.7 - - - -
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Residues in contact with PHE 64 (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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14H ARG* 3.1 60.1 - - - +
31H GLU* 3.6 28.3 - - + -
32H TYR* 3.7 10.3 - - - -
33H GLU* 3.6 27.9 - - + +
62L ASP* 4.2 1.2 + - - -
63L ASP* 1.3 74.8 + - - +
65L ASN* 1.3 82.8 + - - +
66L CYS 3.1 0.7 - - - -
67L TYR* 3.1 52.1 + - + +
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Residues in contact with ASN 65 (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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29H PRO* 4.2 5.1 - - - +
30H LYS 5.3 0.6 + - - -
31H GLU* 3.2 23.6 + - - +
63L ASP* 3.0 29.0 + - - +
64L PHE* 1.3 100.2 - - - +
66L CYS* 1.3 58.1 + - - +
67L TYR 3.8 1.1 + - - +
69L ARG* 3.3 29.1 + - - -
85L CYS* 4.3 8.4 - - - -
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Residues in contact with CYS 66 (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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40L HIS* 2.9 29.7 + - + +
60L TRP* 4.0 9.6 - - - -
63L ASP* 3.0 17.1 + - - -
65L ASN* 1.3 75.9 - - - +
67L TYR* 1.3 67.9 + - - +
68L ASP 3.2 2.4 + - - -
69L ARG* 3.3 20.3 + - - +
85L CYS* 2.0 56.5 - - + -
86L CYS 3.9 6.5 - - - +
87L GLU* 3.8 8.5 + - - +
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Residues in contact with TYR 67 (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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35H TYR* 5.1 5.4 + - - -
38L ARG* 3.3 53.8 + - + +
40L HIS* 3.7 15.3 - + - -
62L ASP* 2.6 33.3 + - - -
63L ASP 4.3 0.2 - - - -
64L PHE* 3.1 44.3 + - + +
65L ASN 3.4 1.4 - - - +
66L CYS* 1.3 78.9 - - - +
68L ASP* 1.3 70.4 + - + +
69L ARG* 3.2 5.4 + - - +
87L GLU* 3.7 0.9 - - - -
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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