Contacts of the helix formed by residues 83 - 91 (chain D) in PDB entry 1NUE
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 VAL 83 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D GLU* 3.4 26.8 + - + +
6D ARG* 3.9 9.0 - - - -
7D THR* 3.7 17.7 - - + +
28D PHE* 5.6 1.6 - - + -
33D PHE* 3.8 43.3 - - + -
78D TRP* 3.8 19.1 - - + +
80D GLY 3.1 20.7 + - - +
81D LEU 3.1 0.8 + - - -
82D ASN* 1.3 77.0 - - - +
84D VAL* 1.3 57.1 + - - +
87D GLY* 2.6 32.6 + - - -
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Residues in contact with VAL 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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5D GLU* 2.9 24.6 + - + +
6D ARG 3.6 24.0 - - - +
7D THR* 3.8 15.2 + - - +
83D VAL* 1.3 76.4 - - - +
85D LYS* 1.3 64.1 + - + +
87D GLY* 3.8 0.9 - - - -
88D ARG* 3.1 27.6 + - + +
120D SER 3.7 10.9 - - - +
121D ASP 3.9 3.6 - - - +
122D SER* 3.6 35.4 - - - +
123D VAL* 4.1 13.7 - - + +
126D ALA* 4.2 8.5 - - + -
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Residues in contact with LYS 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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5D GLU* 4.3 0.4 + - - -
82D ASN* 3.4 24.2 + - - +
84D VAL* 1.3 81.6 - - + +
86D THR* 1.3 64.8 + - - +
88D ARG* 3.2 12.7 + - + +
89D VAL* 3.1 35.4 + - + +
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Residues in contact with THR 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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31D LYS* 3.8 31.9 - - - +
33D PHE* 3.9 18.1 - - + -
81D LEU 4.7 0.9 + - - -
82D ASN* 3.0 26.1 + - - +
85D LYS* 1.3 74.7 - - - +
87D GLY* 1.3 67.6 + - - +
89D VAL* 3.1 10.9 + - + +
90D MET* 2.9 29.8 + - + +
97E ALA* 5.3 11.7 + - - +
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Residues in contact with GLY 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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7D THR* 5.5 0.9 - - - -
9D ILE* 5.1 8.7 - - - -
28D PHE* 4.3 21.7 - - - -
33D PHE* 5.0 0.6 - - - -
83D VAL* 2.6 26.0 + - - +
84D VAL 3.8 1.1 - - - -
86D THR* 1.3 71.4 - - - +
88D ARG* 1.3 57.6 + - - +
90D MET* 3.3 6.3 + - - +
91D LEU* 3.1 35.8 + - - +
119D GLY* 6.2 0.4 - - - -
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Residues in contact with ARG 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 VAL* 3.1 18.2 + - + +
85D LYS* 3.3 16.4 - - + +
86D THR 3.1 0.4 - - - -
87D GLY* 1.3 76.0 - - - +
89D VAL* 1.3 66.1 + - + +
91D LEU* 3.3 13.7 + - - +
92D GLY* 3.2 26.3 + - - +
94D THR* 4.7 2.0 + - - +
105D ARG* 5.4 3.4 - - - +
118D HIS* 5.0 0.2 - - - -
119D GLY* 2.8 35.4 + - - +
120D SER 3.5 13.6 + - - +
121D ASP* 3.7 27.2 - - - +
160D GDP 2.5 45.2 + - - -
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Residues in contact with VAL 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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85D LYS* 3.1 35.4 + - + +
86D THR* 3.1 12.3 + - + +
88D ARG* 1.3 76.4 - - + +
90D MET* 1.3 63.8 + - + +
91D LEU 3.4 0.2 + - - -
92D GLY* 3.4 8.2 + - - -
103D THR* 3.5 13.7 - - - +
97E ALA 5.7 4.3 - - - +
99E SER 5.0 4.7 - - - +
100E LYS* 4.5 21.5 - - + +
101E PRO* 3.8 24.9 - - + +
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Residues in contact with MET 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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27D ARG* 3.6 39.3 - - + +
28D PHE* 4.1 24.0 - - + -
31D LYS* 4.2 15.9 - - + -
33D PHE* 4.0 23.6 - - - -
86D THR* 2.9 26.8 + - + +
87D GLY* 3.5 7.9 - - - +
89D VAL* 1.3 77.9 - - + +
91D LEU* 1.3 58.7 + - - +
103D THR* 3.4 6.2 - - - -
104D ILE* 2.9 33.8 + - + +
101E PRO* 4.2 16.8 - - + +
106E GLY 5.3 3.6 - - - +
107E ASP* 5.9 0.4 - - - +
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Residues in contact with LEU 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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9D ILE* 4.8 3.4 - - + -
28D PHE* 4.3 9.6 - - + -
87D GLY 3.1 23.5 + - - +
88D ARG* 3.7 15.9 - - - +
89D VAL 3.3 0.4 - - - -
90D MET* 1.3 77.4 - - - +
92D GLY* 1.3 59.9 + - - +
103D THR* 3.9 0.4 - - - -
104D ILE* 3.7 13.8 + - + -
105D ARG* 3.0 56.1 + - - +
117D ILE* 3.5 40.6 - - + -
118D HIS 3.9 3.4 - - - -
119D GLY* 3.5 36.6 - - - +
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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