Contacts of the helix formed by residues 78 - 86 (chain C) in PDB entry 4X4U
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 ARG 78 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU* 4.0 30.1 + - - +
40C VAL* 6.0 2.0 - - + +
66C PHE* 4.3 23.1 - - + -
70C PHE* 5.6 9.0 - - + -
74C GLU 3.8 4.5 + - - +
77C GLU* 1.3 84.4 - - + +
79C GLY* 1.3 65.2 + - - +
80C LEU 3.3 2.0 - - - -
81C GLU* 3.0 42.7 + - - +
82C ILE* 3.3 38.6 + - + +
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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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64C LEU* 3.7 19.0 - - - +
66C PHE* 4.2 23.0 - - - -
74C GLU 4.6 1.0 + - - -
75C LEU* 3.1 17.4 + - - -
78C ARG* 1.3 80.6 - - - +
80C LEU* 1.3 62.4 + - - +
82C ILE 3.6 5.9 + - - -
83C GLY* 3.7 5.7 + - - -
100C VAL* 5.4 0.3 - - - +
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Residues in contact with LEU 80 (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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75C LEU* 3.4 16.7 + - + +
76C ARG* 3.7 38.3 - - + +
78C ARG 3.3 0.2 - - - -
79C GLY* 1.3 77.9 - - - +
81C GLU* 1.3 64.6 + - + +
82C ILE 3.3 0.2 - - - -
83C GLY* 3.5 8.1 + - - -
84C LYS* 3.7 25.2 + - - +
98C PRO* 3.8 37.2 - - + +
99C TYR* 5.2 1.1 - - - -
100C VAL* 4.3 21.6 - - + +
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Residues in contact with GLU 81 (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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38C LEU* 5.6 0.4 - - - +
76C ARG 5.7 1.1 - - - +
77C GLU* 2.9 33.7 - - - +
78C ARG* 3.0 40.6 + - - +
80C LEU* 1.3 78.1 - - + +
82C ILE* 1.3 64.2 + - - +
83C GLY 3.6 0.2 + - - -
84C LYS* 4.1 3.0 + - - +
85C ALA* 3.4 20.1 + - - +
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Residues in contact with ILE 82 (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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35C LEU* 3.3 34.1 - - + -
38C LEU* 3.6 26.9 - - + -
40C VAL* 4.6 16.6 - - + -
64C LEU* 3.8 27.1 - - + -
66C PHE* 5.2 1.1 - - + -
78C ARG* 3.3 43.7 + - + +
79C GLY 3.9 0.2 - - - +
80C LEU 3.3 0.4 - - - -
81C GLU* 1.3 76.3 - - - +
83C GLY* 1.3 64.6 + - - +
85C ALA* 3.2 4.8 + - - +
86C VAL* 3.1 27.4 + - + +
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Residues in contact with GLY 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LEU* 5.3 1.1 - - - +
79C GLY 3.7 5.9 + - - -
80C LEU 3.5 6.2 + - - -
81C GLU 3.3 1.0 - - - -
82C ILE* 1.3 81.1 - - - +
84C LYS* 1.3 61.9 + - - +
85C ALA 3.2 0.5 + - - -
86C VAL* 3.3 10.6 + - - +
87C LEU* 3.2 29.8 - - - +
100C VAL* 4.0 20.0 - - - -
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Residues in contact with LYS 84 (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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80C LEU* 3.7 19.5 + - - +
81C GLU* 4.7 3.1 - - - +
82C ILE 3.5 0.4 - - - -
83C GLY* 1.3 74.5 - - - +
85C ALA* 1.3 61.1 + - - +
86C VAL 3.5 0.2 + - - -
87C LEU* 3.6 16.7 - - - +
90C TYR* 4.1 51.1 - - + +
92C ILE* 5.7 9.4 - - - +
100C VAL* 4.3 11.4 - - + +
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Residues in contact with ALA 85 (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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34C ARG* 4.5 9.0 + - - +
38C LEU* 4.5 15.9 - - + -
81C GLU 3.4 17.3 + - - +
82C ILE* 3.4 8.1 - - - +
83C GLY 3.1 1.2 - - - -
84C LYS* 1.3 80.7 - - - +
86C VAL* 1.3 58.9 + - + +
87C LEU 3.4 2.5 + - - +
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Residues in contact with VAL 86 (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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31C LEU* 3.4 34.9 - - + +
34C ARG* 2.8 52.1 + - + +
35C LEU* 3.9 16.4 - - + -
38C LEU* 5.3 1.3 - - + -
82C ILE* 3.3 24.5 - - + +
83C GLY* 3.4 12.6 - - - +
85C ALA* 1.3 79.2 - - + +
87C LEU* 1.3 64.4 + - + +
104C VAL* 3.9 5.5 - - - +
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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