Contacts of the helix formed by residues 82 - 94 (chain D) in PDB entry 3NZG
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 GLU 82 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78D ARG* 3.2 29.0 + - - +
79D LEU* 2.9 29.0 + - + +
81D ILE* 1.3 86.1 - - + +
83D ILE* 1.3 57.3 + - - +
84D ASN 3.3 2.7 - - - -
85D ALA* 3.3 15.1 + - + +
86D ILE* 2.9 33.6 + - + +
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Residues in contact with ILE 83 (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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80D PRO 3.1 18.4 - - - +
81D ILE* 3.1 9.0 + - - +
82D GLU* 1.3 72.2 - - - +
84D ASN* 1.3 56.3 + - - +
86D ILE* 3.8 1.2 - - - +
87D TRP* 2.9 28.9 + - - +
111D ASP* 3.3 11.4 - - - +
114D LEU* 3.9 38.6 - - + +
115D TYR* 3.5 44.0 - - + +
118D ALA* 4.3 7.0 - - + -
129D LEU* 5.0 4.3 - - + -
295D THR* 3.2 24.9 - - - +
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Residues in contact with ASN 84 (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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82D GLU 3.3 0.8 - - - -
83D ILE* 1.3 79.5 - - - +
85D ALA* 1.3 63.8 + - - +
87D TRP* 3.4 6.4 + - - +
88D ASP* 3.2 32.6 + - - +
295D THR* 3.8 12.2 - - + +
299D ARG* 2.7 34.1 - - - +
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Residues in contact with ALA 85 (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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78D ARG* 3.8 20.5 + - - +
82D GLU* 3.3 18.0 + - + +
84D ASN* 1.3 79.9 + - - +
86D ILE* 1.3 57.8 + - - +
88D ASP* 3.2 9.6 + - - +
89D ALA* 2.9 27.8 + - - +
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Residues in contact with ILE 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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12D ILE* 4.3 8.5 - - + -
74D LYS 4.6 1.6 - - - +
75D ALA* 4.0 22.9 - - + -
78D ARG* 3.6 35.2 - - + +
79D LEU 3.6 23.3 - - - +
80D PRO* 4.4 2.0 - - + -
82D GLU* 2.9 24.2 + - + +
83D ILE 3.8 3.8 - - - +
85D ALA* 1.3 73.4 - - - +
87D TRP* 1.3 60.9 + - - +
89D ALA* 3.1 7.4 + - - +
90D MSE 2.9 47.9 + - + +
114D LEU* 4.0 20.0 - - + -
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Residues in contact with TRP 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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83D ILE 2.9 18.1 + - - +
84D ASN* 3.4 9.2 - - - +
85D ALA 3.2 0.2 - - - -
86D ILE* 1.3 77.0 - - - +
88D ASP* 1.3 67.8 - - - +
90D MSE 3.3 11.9 + - + +
91D TYR* 2.9 63.4 + + + +
104D MSE 3.9 19.3 - - + -
107D LEU* 3.3 22.2 - - + +
111D ASP* 3.5 23.6 - - + +
268D THR* 5.6 0.4 - - + -
269D ARG* 3.7 23.3 - - - -
270D PHE* 5.8 0.2 - + - -
292D GLY 2.9 19.7 + - - -
295D THR* 3.7 11.3 - - + -
296D GLU* 3.6 22.6 - - + +
299D ARG* 3.5 20.0 - - - +
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Residues in contact with ASP 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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84D ASN* 3.2 24.5 + - - +
85D ALA* 3.2 10.4 + - - +
87D TRP* 1.3 95.2 - - - +
89D ALA* 1.3 66.3 + - - +
91D TYR* 3.9 2.2 - - - +
92D ASP* 3.0 28.8 + - - +
269D ARG* 5.3 4.3 + - - -
299D ARG* 4.5 8.0 + - - -
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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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74D LYS* 3.6 24.2 - - + +
78D ARG* 4.0 19.3 - - - +
85D ALA 2.9 13.9 + - - +
86D ILE* 3.1 9.4 + - - +
88D ASP* 1.3 77.8 - - - +
90D MSE 1.3 61.7 + - - +
92D ASP* 4.2 3.4 - - - +
93D ALA* 3.3 25.1 + - - +
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Residues in contact with MSE 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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71D ILE* 3.6 37.0 - - + +
74D LYS* 4.2 14.6 - - + -
75D ALA* 4.4 8.5 - - + -
86D ILE* 2.9 38.1 + - + +
87D TRP* 3.7 13.9 - - + +
89D ALA* 1.3 73.6 - - - +
91D TYR* 1.3 57.9 + - - +
93D ALA* 3.5 1.6 + - - -
94D THR* 2.6 38.0 + - - +
107D LEU* 4.0 20.0 - - + +
110D ILE* 3.7 42.8 - - + -
111D ASP* 4.6 6.3 - - + +
114D LEU* 4.7 4.5 - - + -
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Residues in contact with TYR 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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244B ASP* 2.7 30.6 + - - -
87D TRP* 2.9 51.5 + + + +
88D ASP* 3.9 4.0 - - - +
90D MSE 1.3 78.2 - - - +
92D ASP* 1.3 68.6 + - - +
94D THR* 3.1 19.4 + - - -
95D GLN* 3.3 21.5 + - + +
98D GLY 5.0 1.0 - - - -
99D MSE 3.4 31.2 - - + +
100D ARG* 3.2 20.3 + - - -
104D MSE 3.9 27.6 - - - -
107D LEU* 3.9 6.2 - - + +
268D THR* 4.4 4.9 - - + -
270D PHE* 3.9 8.4 - + - -
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Residues in contact with ASP 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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242B GLN* 4.4 7.6 + - - -
66D LYS* 4.2 21.6 + - - +
67D TRP* 3.7 9.4 + - - -
88D ASP 3.0 17.7 + - - +
89D ALA* 4.2 4.2 - - - +
91D TYR* 1.3 79.3 - - + +
93D ALA* 1.3 61.7 + - - +
95D GLN* 2.9 50.0 + - - +
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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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66D LYS 3.6 10.3 - - - +
67D TRP 3.2 8.4 - - - -
69D THR* 3.0 43.6 + - - +
74D LYS* 3.5 28.5 - - + -
89D ALA 3.3 17.2 + - - +
90D MSE 4.0 3.4 - - - +
91D TYR 3.2 0.8 - - - -
92D ASP* 1.3 80.2 - - - +
94D THR* 1.3 60.2 + - + +
95D GLN 3.7 0.4 - - - -
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Residues in contact with THR 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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58D TYR* 4.0 15.7 - - - +
67D TRP 3.3 3.4 - - - -
68D LEU* 5.0 0.7 - - - +
69D THR* 3.4 27.1 - - - +
70D ASN 4.6 0.7 - - - +
71D ILE* 4.0 27.6 - - + +
90D MSE 2.6 25.1 + - - +
91D TYR* 3.1 9.3 + - - -
93D ALA* 1.3 81.6 - - + +
95D GLN* 1.3 58.7 + - - +
96D TRP 3.0 5.2 + - - -
97D GLN* 3.1 4.7 + - - +
98D GLY* 2.8 34.8 + - - -
107D LEU* 5.0 2.3 - - - +
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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