Contacts of the helix formed by residues 95 - 107 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E LYS* 3.8 9.2 - - + +
15E PHE* 3.6 30.3 - - + +
16E ILE* 3.4 29.2 - - + +
50E PHE* 4.6 4.0 - - + -
53E ILE* 4.1 15.7 - - + -
54E LEU* 4.1 10.1 - - + -
57E GLU* 3.8 35.0 - - + +
92E TYR* 2.8 16.4 + - - +
94E PRO* 1.3 70.6 - - + +
96E GLN* 1.3 65.1 + - - +
97E ASN* 3.2 3.1 - - - -
98E ALA* 3.5 8.9 + - + +
99E ILE* 2.9 34.9 + - + +
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Residues in contact with GLN 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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162D PHE* 3.2 29.3 - - + -
92E TYR* 3.1 39.9 + - - +
93E TYR* 3.2 18.4 + - - +
94E PRO 3.4 1.6 - - - -
95E LEU* 1.3 77.0 - - - +
97E ASN* 1.3 69.6 + - - +
99E ILE* 3.0 13.8 + - - +
100E ILE* 2.8 25.8 + - - +
157E ASN* 3.0 41.5 - - - +
161E THR* 3.8 12.8 - - + +
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Residues in contact with ASN 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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97D ASN* 2.8 39.6 + - - +
100D ILE* 3.7 24.6 - - + +
101D GLU* 2.9 38.8 + - - +
15E PHE 5.7 0.9 - - - +
16E ILE 5.5 5.5 + - - +
18E ASN 4.7 0.2 - - - -
19E GLY* 3.7 15.3 - - - +
94E PRO 5.4 3.4 - - - +
95E LEU* 4.9 0.9 - - - -
96E GLN* 1.3 83.4 - - - +
98E ALA* 1.3 64.5 + - - +
100E ILE* 2.7 15.6 + - - +
101E GLU* 3.1 9.8 + - - +
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Residues in contact with ALA 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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15E PHE* 3.6 22.4 + - + +
19E GLY* 3.8 1.1 - - - -
20E TYR* 3.5 31.8 - - + +
50E PHE* 3.7 23.7 - - + -
95E LEU* 3.5 9.6 + - + +
97E ASN* 1.3 79.2 - - - +
99E ILE* 1.3 56.7 + - - +
101E GLU* 3.9 1.6 - - - -
102E PHE* 3.0 30.7 + - - +
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Residues in contact with ILE 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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50E PHE* 4.0 9.2 - - + -
54E LEU* 3.9 33.2 - - + -
92E TYR* 3.8 32.3 - - + +
95E LEU* 2.9 36.0 + - + +
96E GLN* 3.3 16.6 - - - +
97E ASN 2.8 4.2 + - - -
98E ALA* 1.3 73.5 - - - +
100E ILE* 1.3 67.2 + - + +
102E PHE* 3.9 1.4 - - - +
103E TYR* 3.0 24.8 + - + +
116E MET* 4.8 13.2 - - + -
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Residues in contact with ILE 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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97D ASN* 3.0 42.2 - - + +
161D THR* 4.0 19.5 - - - +
162D PHE* 3.7 32.5 - - + -
96E GLN* 2.8 15.5 + - - +
97E ASN* 2.7 19.9 + - - +
99E ILE* 1.3 73.2 - - + +
101E GLU* 1.3 70.4 + - - +
103E TYR* 3.3 4.8 + - - +
104E THR* 2.9 35.2 + - + +
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Residues in contact with GLU 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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18D ASN 3.6 6.1 - - - +
19D GLY* 4.0 0.2 - - - -
97D ASN* 3.0 35.0 - - - +
101D GLU* 2.4 28.0 - - - +
19E GLY* 3.3 4.1 - - - -
20E TYR* 2.5 36.8 + - + -
21E ASN* 2.9 36.5 + - - +
22E ALA 4.8 0.2 + - - -
97E ASN* 3.1 6.6 + - - +
98E ALA 3.7 5.6 - - - +
100E ILE* 1.3 77.8 - - - +
102E PHE* 1.3 63.0 + - - +
104E THR* 2.8 26.8 + - - -
105E GLU* 3.1 8.3 + - - +
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Residues in contact with PHE 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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20E TYR* 3.5 41.7 - + + +
47E GLU* 3.8 28.7 - - + -
50E PHE* 3.4 27.6 - + + -
51E LEU* 3.7 22.2 - - + -
98E ALA 3.0 19.3 + - - +
99E ILE 3.9 1.3 - - - +
101E GLU* 1.3 75.7 - - - +
103E TYR* 1.3 63.7 + - - +
105E GLU* 3.3 3.6 + - - +
106E TYR* 3.0 43.7 + + + +
112E ILE* 4.2 15.7 - - + -
116E MET* 3.5 33.7 - - + -
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Residues in contact with TYR 103 (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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164D HIS* 6.4 1.8 - + + -
165D GLU* 2.7 58.3 - - + +
99E ILE* 3.0 23.2 + - + +
100E ILE* 3.8 6.7 - - - +
101E GLU 3.3 0.2 - - - -
102E PHE* 1.3 81.2 - - - +
104E THR* 1.3 64.0 + - + +
106E TYR* 4.6 1.6 - - - +
107E TYR* 3.0 39.9 + + + +
113E ASN* 3.1 27.0 + - - -
116E MET* 3.3 37.5 - - + -
117E ASN* 3.6 18.5 + - - -
120E GLU* 5.6 4.0 - - - -
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Residues in contact with THR 104 (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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17D LYS 5.2 5.9 + - - -
164D HIS* 4.1 26.2 - - + +
100E ILE* 2.9 26.7 + - + +
101E GLU* 2.8 13.0 + - - -
103E TYR* 1.3 79.5 - - + +
105E GLU* 1.3 70.9 + - - +
107E TYR* 3.0 32.5 - - - -
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Residues in contact with GLU 105 (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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20E TYR* 4.1 12.3 - - - -
21E ASN* 3.4 21.3 - - - +
101E GLU 3.1 11.2 + - - +
102E PHE* 3.9 3.1 - - - +
104E THR* 1.3 82.1 + - - +
106E TYR* 1.3 98.9 + - + +
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Residues in contact with TYR 106 (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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20E TYR* 4.0 16.8 + - - -
47E GLU* 3.9 19.8 + - + +
102E PHE* 3.0 34.3 + + + +
103E TYR* 3.8 2.2 - - - -
105E GLU* 1.3 123.9 + - + +
107E TYR* 1.3 58.1 + - - +
108E LYS 3.1 11.1 + - - +
109E THR* 3.3 26.5 + - - +
112E ILE* 3.5 51.7 - - + +
113E ASN 4.4 0.3 + - - -
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Residues in contact with TYR 107 (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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164D HIS* 6.3 1.1 - + - -
165D GLU* 4.8 12.8 - - - -
280D SO4 3.3 37.9 + - - -
103E TYR* 3.0 34.2 + + + +
104E THR* 3.0 34.5 - - - -
106E TYR* 1.3 75.1 - - - +
108E LYS* 1.3 86.3 + - + +
109E THR 3.4 0.4 - - - -
113E ASN* 3.5 36.4 + - - +
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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