Contacts of the helix formed by residues 83 - 92 (chain C) in PDB entry 3HJW
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 SER 83 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C ALA* 4.1 2.9 - - - -
57C ASP* 3.8 7.8 + - - -
81C VAL* 3.3 3.5 + - - +
82C PRO* 1.3 80.5 - - - +
84C LYS* 1.3 59.9 + - - +
85C LYS* 3.4 8.7 + - - +
86C GLU* 2.9 52.6 + - - +
87C LEU* 3.1 18.7 + - - +
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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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55C ALA* 3.6 16.4 - - + -
57C ASP* 3.2 42.0 + - - +
58C VAL* 4.9 3.1 - - + -
83C SER* 1.3 72.4 + - - +
85C LYS* 1.3 63.6 + - + +
86C GLU 3.4 0.2 - - - -
87C LEU* 3.7 0.4 - - - -
88C GLY 2.9 13.9 + - - -
96C ALA* 3.7 17.9 - - + -
97C ALA 2.8 36.2 + - - +
98C ALA* 4.4 2.2 - - - +
30D U 3.6 38.3 + - + +
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Residues in contact with LYS 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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83C SER* 3.4 6.9 + - - +
84C LYS* 1.3 81.2 - - + +
86C GLU* 1.3 59.2 + - - +
88C GLY* 3.2 2.9 + - - -
89C ALA* 3.0 27.4 + - - +
94C GLU 3.3 24.8 + - - -
95C VAL* 4.0 11.7 - - - +
96C ALA* 3.8 20.4 - - + +
27D C 5.5 2.8 + - - -
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Residues in contact with GLU 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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18C GLU* 4.3 4.5 - - - +
21C LEU* 3.2 39.5 - - + +
81C VAL* 4.0 4.2 - - - +
82C PRO* 4.0 11.7 - - - +
83C SER* 2.9 49.4 + - - +
85C LYS* 1.3 79.2 - - - +
87C LEU* 1.3 58.8 + - - +
89C ALA* 3.4 8.2 + - - +
90C ALA* 3.1 22.3 + - - +
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Residues in contact with LEU 87 (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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21C LEU* 4.0 12.6 - - + -
24C VAL* 4.7 11.2 - - + -
53C ILE* 3.7 39.9 - - + +
55C ALA* 4.1 4.3 - - + +
81C VAL* 4.0 17.5 - - + -
83C SER 3.1 20.0 + - - +
84C LYS 3.8 4.7 - - - +
85C LYS 3.3 0.2 - - - -
86C GLU* 1.3 74.0 - - - +
88C GLY* 1.3 65.1 + - - +
90C ALA* 3.4 3.9 + - + +
91C ALA* 3.1 20.8 + - - +
97C ALA* 3.3 20.6 - - + +
98C ALA 3.9 9.0 - - - +
99C SER* 4.1 4.7 - - - -
100C VAL* 3.8 21.3 - - + -
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Residues in contact with GLY 88 (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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84C LYS 2.9 14.0 + - - -
85C LYS 3.2 3.3 + - - -
87C LEU* 1.3 73.2 - - - +
89C ALA* 1.3 64.5 + - - +
91C ALA* 3.0 13.4 + - - +
92C GLY 3.2 6.1 + - - -
93C ILE* 3.1 20.5 + - - +
95C VAL 3.3 20.2 - - - -
97C ALA* 3.8 14.0 - - - +
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Residues in contact with ALA 89 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C GLU* 3.8 3.5 - - - +
28C ARG* 3.6 6.4 + - - -
85C LYS 3.0 12.3 + - - +
86C GLU* 3.6 11.9 - - - +
88C GLY* 1.3 73.3 - - - +
90C ALA* 1.3 58.0 + - - +
92C GLY* 3.0 20.1 + - - -
93C ILE 3.6 10.2 + - - -
95C VAL 5.4 0.2 - - - -
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Residues in contact with ALA 90 (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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21C LEU* 3.8 31.2 - - + +
24C VAL* 3.8 19.2 - - + +
25C GLU* 3.3 21.5 - - - +
28C ARG* 3.1 22.3 + - - -
86C GLU 3.1 10.4 + - - +
87C LEU* 3.5 13.0 - - + +
88C GLY 3.2 0.2 - - - -
89C ALA* 1.3 79.0 - - - +
91C ALA* 1.3 57.3 + - - +
92C GLY 3.1 0.2 - - - -
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Residues in contact with ALA 91 (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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24C VAL* 4.2 2.4 - - + +
28C ARG* 3.4 13.6 - - - +
33C ILE* 3.8 21.0 - - + +
35C LYS* 4.0 34.3 - - + +
87C LEU 3.1 12.8 + - - +
88C GLY* 3.0 13.2 + - - +
90C ALA* 1.3 76.2 - - - +
92C GLY* 1.3 60.2 + - - +
93C ILE* 3.4 5.8 - - + +
97C ALA* 5.1 0.4 - - + -
100C VAL* 4.2 11.0 - - + -
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Residues in contact with GLY 92 (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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28C ARG* 3.5 22.4 - - - -
89C ALA* 3.0 11.6 + - - -
90C ALA 3.1 1.4 - - - -
91C ALA* 1.3 79.3 - - - +
93C ILE* 1.3 63.7 + - - +
94C GLU* 5.7 1.2 - - - +
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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