Contacts of the helix formed by residues 85 - 95 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D MET 2.7 12.1 + - - +
57D THR* 3.3 22.0 - - - +
58D VAL* 2.9 39.8 - - - +
59D GLU* 4.4 2.0 + - - -
83D SER 4.2 4.0 - - - +
84D THR* 1.3 77.0 - - - +
86D ASP* 1.3 64.8 + - - +
87D HIS* 3.3 14.8 - - + -
88D ALA* 2.9 5.3 + - + +
89D ALA* 2.9 20.3 + - - +
347D LEU* 4.6 0.9 - - - +
350D ALA 5.4 1.8 - - - +
351D MET* 3.1 58.0 - - - +
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Residues in contact with ASP 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 5.5 1.6 - - - +
10D ALA* 3.5 27.0 + - + +
11D ASP 4.9 1.4 + - - +
14D LEU* 3.4 21.1 - - + +
84D THR 3.8 0.6 + - - -
85D GLN* 1.3 70.2 - - - +
87D HIS* 1.3 58.7 + - - +
89D ALA* 3.8 6.0 - - - +
90D ALA* 2.9 31.4 + - - +
101D ALA 4.8 0.3 - - - +
102D TRP* 3.4 11.1 - - - +
103D LYS* 3.2 40.2 + - - +
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Residues in contact with HIS 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 3.6 17.9 - - + +
17D TRP* 3.5 59.7 - + + -
18D GLY* 3.1 34.2 - - - +
21D ALA* 4.1 9.9 - - + +
58D VAL* 3.8 15.9 - - + +
85D GLN* 3.7 26.4 - - + +
86D ASP* 1.3 75.5 + - - +
88D ALA* 1.3 61.5 + - - +
90D ALA* 3.5 1.9 + - - +
91D ALA 3.0 21.8 + - - -
351D MET* 3.8 22.4 - - + +
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Residues in contact with ALA 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D GLY* 4.5 3.4 - - - -
22D LEU* 4.8 3.6 - - + -
56D MET* 4.1 3.5 - - + +
57D THR* 3.5 9.9 - - - +
58D VAL* 3.4 45.5 - - + +
61D ALA* 4.3 3.4 - - + +
85D GLN* 2.9 11.7 + - + +
87D HIS* 1.3 79.7 + - - +
89D ALA* 1.3 64.2 + - - +
91D ALA* 3.3 8.1 + - - +
92D ILE* 3.2 25.8 + - - +
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Residues in contact with ALA 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 4.0 16.8 - - + -
56D MET* 3.5 32.0 - - + +
84D THR* 4.1 11.0 - - + -
85D GLN 2.9 12.6 + - - +
86D ASP* 3.8 6.3 - - - +
88D ALA* 1.3 77.1 - - - +
90D ALA* 1.3 57.3 + - - +
92D ILE* 3.4 2.2 + - - +
93D ALA* 2.9 27.9 + - - +
99D VAL* 3.6 9.7 - - + +
101D ALA* 4.3 6.3 - - + +
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Residues in contact with ALA 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 4.2 6.7 - - + +
11D ASP 3.5 20.4 - - - +
12D ILE* 3.9 7.8 - - - +
14D LEU 3.8 1.6 - - - -
15D ALA* 3.4 25.6 - - - +
86D ASP 2.9 18.2 + - - +
87D HIS 3.7 2.2 - - - +
89D ALA* 1.3 74.1 - - - +
91D ALA* 1.3 56.0 + - - +
93D ALA* 3.0 8.5 + - - +
94D LYS* 2.8 36.4 + - - +
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Residues in contact with ALA 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ALA* 3.7 13.2 - - - +
18D GLY 3.8 1.3 - - - -
19D ARG* 3.7 35.8 + - - +
22D LEU* 3.8 18.8 - - + -
87D HIS 3.0 15.8 + - - +
88D ALA 3.3 9.6 + - - +
90D ALA* 1.3 77.8 - - - +
92D ILE* 1.3 62.0 + - - +
94D LYS* 3.3 4.6 + - - +
95D ALA* 3.0 21.0 + - - +
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Residues in contact with ILE 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 4.7 2.9 - - + -
56D MET* 4.1 7.0 - - + -
61D ALA* 3.6 40.8 - - + +
64D ILE* 4.3 11.0 - - + -
65D GLU* 3.7 24.2 - - + +
88D ALA 3.2 12.6 + - - +
89D ALA* 3.6 7.6 - - - +
90D ALA 3.2 0.2 - - - -
91D ALA* 1.3 72.6 - - - +
93D ALA* 1.3 68.1 + - - +
95D ALA* 2.9 20.4 + - - +
96D GLY 3.4 3.1 + - - -
97D ILE* 3.4 28.4 + - + -
99D VAL* 3.2 29.2 - - + -
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Residues in contact with ALA 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D TYR* 4.0 24.8 - - + -
9D VAL* 3.8 14.8 - - + -
12D ILE* 3.9 14.4 - - + -
89D ALA 2.9 14.5 + - - +
90D ALA 3.0 8.5 + - - +
92D ILE* 1.3 76.5 - - - +
94D LYS* 1.3 61.7 + - - +
96D GLY* 2.9 16.3 + - - -
97D ILE 3.8 4.9 + - - +
99D VAL* 3.4 20.8 - - + +
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Residues in contact with LYS 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ILE* 3.9 16.9 - - + +
15D ALA* 3.7 22.2 - - + -
90D ALA 2.8 15.6 + - - +
91D ALA* 3.5 9.9 - - - +
93D ALA* 1.3 72.2 - - - +
95D ALA* 1.3 58.2 + - - +
96D GLY* 3.1 5.2 + - - -
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Residues in contact with ALA 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ARG* 4.0 4.9 - - - +
65D GLU* 3.8 21.5 - - - +
91D ALA 3.0 12.5 + - - +
92D ILE* 2.9 15.3 + - - +
94D LYS* 1.3 75.4 - - - +
96D GLY* 1.3 59.6 + - - +
97D ILE* 4.4 12.0 - - + +
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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