Contacts of the helix formed by residues 87 - 102 (chain E) in PDB entry 3NBT
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 LYS 87 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47E THR* 5.8 0.2 - - - +
85E ILE* 3.7 2.5 - - - +
86E LYS* 1.3 78.6 - - + +
88E LYS* 1.3 65.3 + - - +
89E THR* 3.0 35.0 + - + +
90E GLU* 3.2 41.6 + - + +
91E ARG* 3.2 15.5 + - - +
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Residues in contact with LYS 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A MET* 3.6 21.6 - - + +
86E LYS 3.3 4.6 + - - -
87E LYS* 1.3 72.8 - - - +
89E THR* 1.3 62.7 + - - +
91E ARG* 3.5 23.2 + - - +
92E GLU* 3.1 51.3 + - - +
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Residues in contact with THR 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS* 6.3 0.2 - - + -
87E LYS* 3.0 23.4 + - + +
88E LYS* 1.3 76.8 - - - +
90E GLU* 1.3 67.8 + - + +
92E GLU* 3.1 16.0 + - - +
93E ASP* 3.0 36.2 + - - +
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Residues in contact with GLU 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 4.7 27.3 - - + +
13A LYS* 3.6 18.8 + - - -
47E THR* 4.6 11.2 + - - -
85E ILE* 3.4 23.1 - - + +
87E LYS* 3.2 36.2 + - + +
89E THR* 1.3 78.1 - - + +
91E ARG* 1.3 54.3 + - - +
93E ASP* 3.6 8.7 - - - +
94E LEU* 2.7 38.2 + - - +
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Residues in contact with ARG 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A MET* 2.7 64.6 + - - +
66A GLU* 4.7 0.2 - - - +
68A LEU* 4.2 8.5 - - + -
69A GLU* 3.5 37.3 + - - +
85E ILE* 3.2 40.4 + - + +
86E LYS 3.3 19.7 + - - -
87E LYS 3.2 2.3 + - - +
88E LYS* 3.5 29.7 - - - +
90E GLU* 1.3 78.7 - - - +
92E GLU* 1.3 57.1 + - - +
94E LEU* 3.5 7.1 + - - +
95E ILE* 2.9 39.2 + - + +
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Residues in contact with GLU 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GLY* 4.2 10.7 - - - -
65A MET* 3.7 18.2 - - + -
88E LYS* 3.1 57.5 + - - +
89E THR* 3.1 13.8 + - - +
91E ARG* 1.3 76.6 - - - +
93E ASP* 1.3 61.1 + - - +
95E ILE* 3.4 4.1 + - - +
96E ALA* 2.8 29.7 + - - +
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Residues in contact with ASP 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GLY* 3.8 3.3 - - - -
2A ASP* 2.9 42.6 + - - +
5A LYS* 3.5 27.8 - - + +
6A GLY* 3.3 17.8 - - - +
9A ILE* 5.3 2.2 - - + -
89E THR* 3.0 26.6 + - - +
90E GLU* 3.6 9.1 - - - +
92E GLU* 1.3 75.3 - - - +
94E LEU* 1.3 66.4 + - - +
96E ALA* 3.1 3.5 + - - +
97E TYR 2.9 19.1 + - - -
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Residues in contact with LEU 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A GLY* 3.7 25.0 - - - +
9A ILE* 4.1 14.1 - - + -
10A PHE* 3.8 33.9 - - + +
14A CYS* 4.3 0.2 - - - -
68A LEU* 4.1 12.6 - - + -
105A HEC 3.5 36.3 - - + -
85E ILE* 4.6 9.6 - - + -
90E GLU 2.7 21.2 + - - +
91E ARG* 3.7 5.6 - - - +
93E ASP* 1.3 72.4 - - - +
95E ILE* 1.3 58.7 + - + +
97E TYR* 3.2 5.0 + - + +
98E LEU* 2.9 41.7 + - + +
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Residues in contact with ILE 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 3.5 15.8 - - + -
61A GLU* 3.8 30.3 - - + +
64A LEU* 3.5 18.4 - - + -
65A MET* 3.4 50.0 - - + +
68A LEU* 3.9 14.4 - - + -
91E ARG* 2.9 27.1 + - + +
92E GLU* 3.7 4.9 - - - +
94E LEU* 1.3 73.4 - - - +
96E ALA* 1.3 66.2 + - - +
98E LEU* 4.3 7.0 - - + -
99E LYS* 2.9 23.1 + - + +
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Residues in contact with ALA 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GLY* 3.6 33.0 - - - +
3A VAL* 3.8 18.7 - - + +
92E GLU 2.8 19.3 + - - +
93E ASP 3.1 5.1 + - - +
95E ILE* 1.3 76.7 - - - +
97E TYR* 1.3 64.0 + - - +
99E LYS* 3.4 9.5 + - - +
100E LYS* 3.3 15.8 + - - +
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Residues in contact with TYR 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A VAL* 3.6 27.1 - - + +
6A GLY* 3.6 7.0 - - - -
7A LYS* 3.4 62.9 + - + +
10A PHE* 3.7 40.8 - + + -
20A VAL* 3.9 12.6 - - + +
93E ASP 2.9 5.5 + - - -
94E LEU 3.4 8.5 - - - +
96E ALA* 1.3 74.9 - - - +
98E LEU* 1.3 68.8 + - + +
100E LYS* 3.2 3.9 + - + +
101E ALA* 2.9 54.0 + - + +
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Residues in contact with LEU 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE* 3.9 32.5 - - + -
20A VAL* 4.3 5.4 - - + -
32A LEU* 4.2 14.1 - - + -
35A LEU* 4.7 13.9 - - + -
36A PHE* 3.7 10.8 - - + -
64A LEU* 5.0 5.4 - - + -
68A LEU* 4.6 8.5 - - + -
105A HEC 4.0 20.6 - - + -
94E LEU* 2.9 26.6 + - + +
95E ILE* 3.8 13.5 - - + +
97E TYR* 1.3 77.0 - - + +
99E LYS* 1.3 62.5 + - - +
101E ALA* 4.5 1.6 - - - +
102E THR* 2.7 48.7 + - + -
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Residues in contact with LYS 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 3.4 33.1 - - + -
61A GLU* 3.0 32.8 - - + +
95E ILE 2.9 18.8 + - - +
96E ALA* 3.4 10.1 - - - +
97E TYR 3.2 0.2 - - - -
98E LEU* 1.3 76.9 - - - +
100E LYS* 1.3 59.4 + - - +
102E THR* 4.1 0.9 + - - -
103E ASN* 3.4 20.6 + - - +
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Residues in contact with LYS 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A VAL* 3.6 38.0 - - + +
96E ALA 3.3 6.8 + - - +
97E TYR* 3.2 8.6 + - + +
98E LEU 3.1 0.6 - - - -
99E LYS* 1.3 79.2 - - - +
101E ALA* 1.3 66.9 + - - +
103E ASN* 3.1 15.3 + - - +
104E GLU* 3.3 19.4 + - - +
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Residues in contact with ALA 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 3.5 28.6 - - + +
21A GLU* 4.8 1.9 + - - -
33A HIS* 4.3 0.2 - - - -
97E TYR* 2.9 54.1 + - + +
98E LEU* 4.3 0.4 - - - +
100E LYS* 1.3 74.6 - - - +
102E THR* 1.3 56.8 + - - +
103E ASN 3.2 0.2 - - - -
104E GLU* 3.1 19.9 + - - +
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Residues in contact with THR 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 3.8 21.3 - - + -
32A LEU* 3.3 39.7 - - + +
33A HIS* 3.1 12.5 + - - +
34A GLY* 2.7 28.3 + - - -
35A LEU* 4.1 8.2 + - + -
36A PHE* 3.7 16.8 + - - +
98E LEU* 2.7 42.1 + - + +
99E LYS 4.1 1.4 + - - -
101E ALA* 1.3 69.8 - - - +
103E ASN* 1.3 57.3 + - - +
104E GLU 3.1 5.2 - - - -
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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