Contacts of the helix formed by residues 73 - 79 (chain C) 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 HIS 73 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B LEU 6.1 0.4 - - - -
51B PRO* 3.7 35.3 + - + +
53B LYS* 3.0 40.1 + - + +
56B ILE* 4.3 21.0 - - + +
50C TRP* 3.8 7.5 - - - -
72C LEU* 1.3 111.2 + - + +
74C ARG* 1.3 66.2 + - - +
75C GLU* 2.9 19.9 + - + +
76C LEU* 2.9 33.0 + - + +
77C CYS* 5.3 0.2 - - - -
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Residues in contact with ARG 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C TRP* 3.3 48.5 - - + +
72C LEU 3.8 1.6 + - - -
73C HIS* 1.3 72.2 - - - +
75C GLU* 1.3 68.3 + - - +
77C CYS* 2.9 33.7 + - + +
78C ARG* 4.3 5.2 + - - +
89C CYS* 3.7 29.1 + - - +
91C ASP* 2.7 33.3 + - - +
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Residues in contact with GLU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A TRP* 5.0 9.0 - - + -
25A TRP* 3.6 34.4 + - + -
99A TYR* 2.6 28.6 + - - +
53B LYS* 2.8 30.9 + - - -
72C LEU 4.8 0.5 - - - +
73C HIS* 2.9 23.2 + - + +
74C ARG* 1.3 79.1 + - - +
76C LEU* 1.3 67.5 + - + +
77C CYS 2.8 1.6 + - - -
78C ARG* 2.9 29.7 + - - +
79C GLY 3.8 1.4 + - - -
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Residues in contact with LEU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A TRP* 3.6 35.0 - - + +
43B PHE* 4.3 20.6 - - + -
44B PRO* 6.3 0.7 - - + -
56B ILE* 4.3 29.4 - - + -
60B LEU* 4.6 4.7 - - + -
73C HIS* 2.9 30.4 + - + +
75C GLU* 1.3 77.2 - - + +
77C CYS* 1.3 57.0 + - - +
79C GLY* 3.0 21.3 + - - -
87C HIS* 3.6 44.2 - - + +
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Residues in contact with CYS 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C TRP* 4.1 9.2 - - - -
73C HIS 5.3 0.2 - - - -
74C ARG* 2.9 33.3 + - + +
75C GLU 2.8 4.6 + - - -
76C LEU* 1.3 70.6 - - - +
78C ARG* 1.3 62.0 + - + +
79C GLY 3.0 13.5 + - - +
87C HIS* 3.7 15.4 - - - +
88C TYR* 5.3 0.5 - - - -
89C CYS* 2.0 58.7 + - + +
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Residues in contact with ARG 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A SER* 2.6 25.7 + - - -
25A TRP* 3.4 47.2 - - + +
86A TYR* 4.1 13.7 - - - -
87A LYS* 3.0 29.5 + - - +
88A ASP 3.8 12.9 + - - -
89A ASP* 3.7 29.0 + - - +
74C ARG* 4.7 5.2 - - + +
75C GLU* 2.9 21.0 + - - +
77C CYS* 1.3 75.1 - - + +
79C GLY* 1.3 61.5 + - - +
80C ARG* 3.0 0.7 + - - -
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Residues in contact with GLY 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ILE 5.4 0.4 - - - -
21A GLY 3.4 10.8 - - - -
22A TRP* 4.2 13.5 - - - -
24A SER* 4.3 0.7 - - - -
25A TRP* 4.2 1.0 - - - +
75C GLU 3.8 1.6 + - - -
76C LEU 3.0 19.0 + - - -
77C CYS 3.6 6.9 - - - +
78C ARG* 1.3 78.4 - - - +
80C ARG* 1.3 66.0 + - - -
81C PRO* 3.7 5.0 - - - +
87C HIS* 4.2 12.9 + - - +
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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