Contacts of the helix formed by residues 95 - 105 (chain D) in PDB entry 1JT6
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 LEU 95 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D LYS* 4.2 3.8 - - + +
15D PHE* 4.0 23.8 - - + -
16D ILE* 3.7 26.2 - - + +
50D PHE* 4.6 8.5 - - + -
53D ILE* 3.9 12.6 - - + -
54D LEU* 3.7 22.7 - - + -
57D GLU* 3.6 34.8 - - + +
92D TYR* 2.7 18.2 + - + +
94D PRO* 1.3 72.6 - - + +
96D GLN* 1.3 66.9 + - - +
97D ASN 3.2 2.5 - - - -
98D ALA* 2.8 8.0 + - + +
99D ILE* 2.8 33.1 + - + +
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Residues in contact with GLN 96 (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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92D TYR* 3.6 38.1 + - - +
93D TYR* 3.3 16.8 + - - +
94D PRO 3.3 2.2 - - - -
95D LEU* 1.3 76.6 - - - +
97D ASN* 1.3 62.4 + - - +
99D ILE* 3.2 20.2 + - - +
100D ILE* 3.0 30.5 + - - +
123D TYR* 5.3 0.6 - - - -
157D ASN* 2.9 42.5 - - - +
161D THR* 3.5 16.2 - - + -
162E PHE* 3.3 26.6 - - + -
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Residues in contact with ASN 97 (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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16D ILE 6.0 2.5 - - - +
19D GLY* 3.5 13.2 + - - -
94D PRO 4.6 4.5 + - - +
95D LEU 3.2 0.8 - - - -
96D GLN* 1.3 79.2 - - - +
98D ALA* 1.3 63.3 + - - +
100D ILE* 3.5 3.0 + - - -
101D GLU* 3.4 14.0 + - - +
97E ASN* 2.8 33.8 + - - +
100E ILE* 3.0 40.0 - - + +
101E GLU* 3.0 39.0 + - - +
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Residues in contact with ALA 98 (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 PHE* 3.7 23.0 + - + +
16D ILE* 5.7 0.2 - - - -
19D GLY 3.9 0.4 - - - -
20D TYR* 3.6 30.5 - - - +
50D PHE* 3.8 21.9 - - + -
95D LEU* 2.8 12.1 + - + +
97D ASN* 1.3 78.6 + - - +
99D ILE* 1.3 65.4 + - - +
101D GLU* 3.5 0.7 + - - -
102D PHE* 3.0 24.4 + - - +
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Residues in contact with ILE 99 (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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50D PHE* 4.1 7.0 - - + -
54D LEU* 4.0 27.8 - - + -
92D TYR* 4.2 20.2 - - + +
95D LEU* 2.8 28.2 + - + +
96D GLN* 3.2 36.3 + - - +
98D ALA* 1.3 73.1 - - - +
100D ILE* 1.3 70.9 + - + +
102D PHE* 3.2 3.2 + - + +
103D TYR* 2.8 25.7 + - + +
116D MET* 4.5 20.6 - - + -
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Residues in contact with ILE 100 (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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96D GLN* 3.0 22.2 + - + +
97D ASN* 3.6 7.9 - - - +
99D ILE* 1.3 84.3 - - + +
101D GLU* 1.3 64.7 + - - +
103D TYR* 3.0 4.8 + - - +
104D THR* 2.9 35.3 + - + +
97E ASN* 3.7 26.5 - - + +
161E THR* 4.2 24.0 - - - +
162E PHE* 3.5 38.1 - - + -
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Residues in contact with GLU 101 (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 ASN 4.5 0.7 - - - +
19D GLY* 3.5 2.4 - - - -
20D TYR* 2.8 33.9 + - + -
21D ASN* 3.2 36.0 + - - +
22D ALA 4.7 0.3 + - - -
97D ASN* 3.4 12.5 + - - +
98D ALA 3.9 5.2 - - - +
99D ILE 3.4 0.2 - - - -
100D ILE* 1.3 80.0 - - - +
102D PHE* 1.3 61.2 + - - +
104D THR* 3.4 12.1 + - - -
105D GLU* 3.4 21.5 + - - +
17E LYS 6.0 0.9 - - - -
18E ASN 3.3 8.1 - - - +
22E ALA 5.9 0.2 + - - -
97E ASN* 2.9 30.1 + - - +
101E GLU* 2.4 30.1 - - - +
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Residues in contact with PHE 102 (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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20D TYR* 3.4 29.6 - + + +
47D GLU* 3.5 36.3 - - + -
50D PHE* 3.4 30.1 - + + -
51D LEU* 3.9 15.0 - - + -
98D ALA 3.0 18.7 + - - +
99D ILE* 3.6 3.4 - - - +
101D GLU* 1.3 73.8 - - - +
103D TYR* 1.3 67.1 + - - +
105D GLU* 3.2 10.7 + - - -
106D TYR* 3.3 43.0 + + + +
112D ILE* 3.9 13.0 - - + -
116D MET* 3.5 32.8 - - + -
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Residues in contact with TYR 103 (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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99D ILE* 2.8 20.7 + - + +
100D ILE* 3.6 5.8 - - - +
102D PHE* 1.3 82.1 - - - +
104D THR* 1.3 67.6 + - + +
105D GLU 3.0 1.0 + - - -
106D TYR* 3.1 1.0 + - - -
107D TYR* 3.1 48.1 + + + +
113D ASN* 3.6 19.7 + - - -
116D MET* 4.0 38.1 - - + -
117D ASN* 4.6 9.7 + - - -
120D GLU* 5.9 1.1 - - - -
164E HIS 6.1 0.2 - - - -
165E GLU* 3.1 54.2 - - + +
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Residues in contact with THR 104 (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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100D ILE* 2.9 32.0 + - + +
101D GLU* 3.4 10.4 + - - +
102D PHE 3.3 0.2 - - - -
103D TYR* 1.3 80.5 - - + +
105D GLU* 1.3 59.3 + - - +
106D TYR 3.4 0.2 - - - -
107D TYR* 3.5 27.2 - - - -
16E ILE 5.7 0.6 + - - +
17E LYS 4.4 12.6 + - - -
164E HIS* 6.6 0.4 - - + -
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Residues in contact with GLU 105 (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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20D TYR* 3.9 5.4 - - - -
21D ASN* 3.3 22.6 + - - +
101D GLU 3.4 12.1 + - - +
102D PHE* 3.2 5.6 + - - +
103D TYR 3.0 1.2 - - - -
104D THR* 1.3 81.4 + - - +
106D TYR* 1.3 79.4 + - + +
107D TYR* 5.3 0.2 - - - -
108D LYS* 5.6 3.5 - - - +
999D SO4 3.0 36.1 + - - -
18E ASN* 5.5 3.3 + - - -
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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