Contacts of the helix formed by residues 89 - 95 (chain E) in PDB entry 4LQL
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 TRP 89 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E VAL* 4.1 20.4 - - + -
14E GLY* 4.5 6.3 - - - -
54E ALA* 4.3 16.7 + - + +
55E THR 5.8 1.4 + - - -
60E ILE* 3.3 42.5 - - + +
64E MET* 5.9 4.9 - - + -
78E THR* 3.8 27.8 - - - -
79E TRP 5.9 0.2 - - - -
80E MET* 4.1 20.8 - - + +
84E SER* 3.9 18.2 - - - -
85E PRO* 4.2 3.8 - - + -
86E ALA* 2.2 52.4 + - + +
88E ASN* 1.3 70.3 - - + +
90E ILE* 1.3 61.4 + - - +
91E ARG 3.7 0.9 - - - -
92E GLY* 3.2 8.6 + - - -
93E THR* 3.2 35.2 + - - +
100E LEU* 6.1 5.8 - - + -
133E TYR* 4.9 14.3 - + + +
136E ILE* 4.8 11.7 - - + -
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Residues in contact with ILE 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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196B VAL* 3.8 22.0 - - + +
199B GLN* 3.7 45.9 - - + +
200B ILE* 4.1 15.3 - - + -
87E LYS* 3.3 27.1 + - - +
88E ASN 3.5 1.2 - - - -
89E TRP* 1.3 71.9 - - - +
91E ARG* 1.3 67.6 + - - +
93E THR* 3.4 6.6 + - - -
94E GLU* 3.2 20.9 + - + +
136E ILE* 3.5 38.6 - - + -
140E LEU* 5.3 5.9 - - + +
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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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174B PHE* 4.7 27.4 - - + +
199B GLN* 5.1 14.8 - - + +
203B GLY* 5.9 1.8 - - - +
57E ALA* 6.3 2.9 - - + -
61E THR* 4.0 25.8 - - + +
89E TRP 3.7 0.2 - - - -
90E ILE* 1.3 75.0 - - + +
92E GLY* 1.3 57.8 + - - +
94E GLU* 2.9 13.8 + - + +
95E LEU* 2.4 45.2 + - + +
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Residues in contact with GLY 92 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60E ILE* 4.0 21.7 - - - +
61E THR* 4.5 7.0 + - - -
64E MET* 3.7 20.2 - - - +
89E TRP 3.2 9.8 + - - -
91E ARG* 1.3 78.4 - - - +
93E THR* 1.3 54.7 + - - +
95E LEU* 3.2 4.7 + - - -
96E LEU* 2.8 30.1 + - - +
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Residues in contact with THR 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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60E ILE* 5.0 0.6 - - - +
64E MET* 4.7 1.3 - - - +
89E TRP* 3.2 24.7 + - - +
90E ILE* 3.4 7.6 + - - -
92E GLY* 1.3 71.2 - - - +
94E GLU* 1.3 57.0 + - - +
96E LEU* 3.6 24.0 - - - +
100E LEU* 4.3 15.8 - - - +
136E ILE* 4.6 17.6 - - - +
137E ASN* 5.9 3.5 - - - +
140E LEU* 5.1 19.3 - - - +
142E VAL* 4.8 14.0 - - - +
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Residues in contact with GLU 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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97B GLN* 5.6 2.1 - - - +
199B GLN 6.1 0.4 - - - +
200B ILE* 5.4 18.8 - - + +
90E ILE* 3.2 10.4 + - + +
91E ARG* 2.9 29.4 + - + +
93E THR* 1.3 75.9 - - - +
95E LEU* 1.3 63.0 + - + +
96E LEU 3.0 11.2 + - - +
140E LEU* 5.6 6.1 - - + -
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Residues in contact with LEU 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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97B GLN* 4.9 21.1 - - + +
61E THR* 4.9 10.8 - - + -
64E MET* 5.3 2.0 - - - +
65E LYS* 4.4 23.3 - - + +
68E ASN* 2.8 30.5 + - - +
91E ARG* 2.4 32.8 + - + +
92E GLY* 3.5 5.2 - - - +
94E GLU* 1.3 74.9 - - + +
96E LEU* 1.3 60.3 + - - +
97E GLN* 4.1 2.9 - - - +
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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