Contacts of the helix formed by residues 85 - 95 (chain C) in PDB entry 3NJ4
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 GLN 85 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C MET 2.7 13.1 + - - +
57C THR* 3.4 22.3 - - - +
58C VAL* 2.9 39.2 - - - +
59C GLU* 4.3 1.7 + - - +
83C SER 4.0 6.7 - - - +
84C THR* 1.3 75.3 - - - +
86C ASP* 1.3 59.4 + - - +
87C HIS* 3.3 13.2 - - + -
88C ALA* 2.8 23.7 + - + +
89C ALA 3.1 9.5 + - - -
103C LYS* 5.8 0.9 - - - +
347C LEU* 4.9 0.7 - - + +
350C ALA 5.6 1.1 - - - +
351C MET* 3.1 59.3 - - + +
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Residues in contact with ASP 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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9C VAL* 5.3 1.9 - - - +
10C ALA* 3.5 28.1 + - + +
11C ASP 4.8 1.5 + - - +
14C LEU* 3.4 22.1 - - + +
84C THR 3.8 0.6 + - - -
85C GLN* 1.3 70.0 - - - +
87C HIS* 1.3 62.3 + - - +
89C ALA* 3.2 8.0 + - - +
90C ALA* 3.0 24.3 + - - +
102C TRP* 3.6 5.9 - - - -
103C LYS* 3.1 42.9 + - - +
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Residues in contact with HIS 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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14C LEU* 3.5 26.9 - - + +
17C TRP* 3.5 58.8 - + + -
18C GLY* 3.1 30.0 - - - -
21C ALA* 4.3 8.9 - - + +
58C VAL* 3.6 15.6 - - + +
85C GLN* 3.5 39.2 - - + +
86C ASP* 1.3 74.4 - - - +
88C ALA* 1.3 68.2 + - - +
89C ALA 3.4 0.2 - - - -
90C ALA 3.9 0.2 - - - -
91C ALA* 3.2 17.3 + - - +
351C MET* 3.7 14.8 - - + +
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Residues in contact with ALA 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLY* 4.8 2.7 - - - -
22C LEU* 5.8 1.3 - - + -
56C MET* 4.3 3.6 - - + +
57C THR* 3.6 33.9 - - - +
58C VAL* 3.6 19.1 - - + +
61C ALA* 4.3 4.1 - - + +
85C GLN* 2.8 15.8 + - + +
87C HIS* 1.3 81.2 + - - +
89C ALA* 1.3 61.4 + - - +
91C ALA* 3.6 6.3 + - - +
92C ILE* 3.3 27.9 + - - +
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Residues in contact with ALA 89 (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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9C VAL* 3.5 21.0 - - + +
56C MET* 3.8 26.4 - - + +
84C THR* 4.2 4.3 - - + -
85C GLN 3.1 8.6 + - - +
86C ASP* 3.7 8.1 - - - +
88C ALA* 1.3 74.9 - - - +
90C ALA* 1.3 56.0 + - - +
92C ILE* 3.4 2.1 + - - +
93C ALA* 2.7 35.9 + - - +
99C VAL* 4.0 7.6 - - + +
101C ALA 4.0 13.5 - - - +
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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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9C VAL* 4.0 6.2 - - + +
11C ASP 3.4 21.5 - - - +
12C ILE* 3.8 6.8 - - - +
14C LEU 3.6 3.4 - - - -
15C ALA* 3.1 29.5 - - - +
86C ASP 3.0 15.3 + - - +
87C HIS 3.8 0.4 - - - +
89C ALA* 1.3 75.3 - - - +
91C ALA* 1.3 68.0 + - - +
93C ALA* 3.1 7.5 + - - +
94C LYS* 2.8 25.3 + - - +
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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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15C ALA* 3.5 12.5 - - - +
18C GLY 4.0 0.7 - - - -
19C ARG* 3.8 30.2 + - - +
22C LEU* 3.8 25.8 - - + -
87C HIS 3.2 15.5 + - - +
88C ALA* 3.7 6.1 - - - +
90C ALA* 1.3 80.1 - - - +
92C ILE* 1.3 61.5 + - - +
94C LYS* 3.2 4.2 + - - +
95C ALA* 3.1 20.3 + - - +
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Residues in contact with ILE 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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22C LEU* 4.6 3.4 - - + -
56C MET* 4.0 7.0 - - + -
61C ALA* 3.5 44.0 - - + +
64C ILE* 4.3 14.4 - - + -
65C GLU* 3.9 23.6 - - + +
88C ALA 3.3 14.8 + - - +
89C ALA* 3.9 4.3 - - - +
90C ALA 3.2 0.6 - - - -
91C ALA* 1.3 73.9 - - - +
93C ALA* 1.3 66.2 + - - +
95C ALA* 3.0 14.6 + - - +
97C ILE* 3.4 37.0 + - + -
99C VAL* 3.3 22.2 - - + -
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Residues in contact with ALA 93 (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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7C TYR* 3.8 36.1 - - + -
9C VAL* 3.6 20.4 - - + -
12C ILE* 4.0 10.1 - - + -
89C ALA 2.7 23.0 + - - +
90C ALA 3.5 4.5 - - - +
92C ILE* 1.3 73.3 - - - +
94C LYS* 1.3 59.8 + - - +
96C GLY* 3.4 12.0 + - - -
97C ILE 3.9 4.4 + - - +
99C VAL* 3.5 10.1 - - + +
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Residues in contact with LYS 94 (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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12C ILE* 4.1 17.7 - - + +
15C ALA* 3.9 17.7 - - + +
90C ALA 2.8 16.0 + - - +
91C ALA* 3.4 5.6 - - - +
92C ILE 3.0 0.2 - - - -
93C ALA* 1.3 74.0 - - - +
95C ALA* 1.3 58.3 + - - +
96C GLY* 2.9 11.3 + - - -
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Residues in contact with ALA 95 (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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19C ARG* 4.0 6.3 - - - +
65C GLU* 4.0 20.6 - - - +
91C ALA 3.1 11.8 + - - +
92C ILE* 3.0 14.4 + - + +
94C LYS* 1.3 75.0 - - - +
96C GLY* 1.3 60.5 + - - +
97C ILE* 3.5 14.1 - - + +
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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