Contacts of the helix formed by residues 91 - 98 (chain E) in PDB entry 4JCQ
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 SER 91 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60E GLN 3.9 12.3 + - - -
61E GLY* 4.3 2.5 - - - -
62E GLY 5.2 1.6 - - - -
90E ALA* 1.3 74.4 - - - +
92E ALA* 1.3 61.4 + - - -
94E ILE* 2.9 20.5 + - - +
95E THR* 3.3 3.5 + - - -
114E MET* 3.0 18.6 + - - +
116E HIS* 2.7 33.4 + - - -
117E GLN* 3.1 22.0 + - - +
118E PRO* 4.1 17.9 - - - +
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Residues in contact with ALA 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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30E ILE* 4.3 9.2 - - + -
61E GLY* 3.9 1.9 - - - -
62E GLY 3.8 24.7 - - - +
63E HIS 4.3 18.8 - - - +
64E VAL* 4.9 4.9 - - - -
67E GLY* 4.6 5.8 - - - -
90E ALA 3.2 0.2 + - - -
91E SER* 1.3 78.7 - - - +
93E GLY* 1.3 62.8 + - - +
95E THR* 3.3 12.0 + - - -
96E ILE* 3.2 28.2 + - - +
117E GLN* 3.8 4.3 + - - +
118E PRO* 5.5 0.6 - - - +
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Residues in contact with GLY 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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30E ILE* 4.3 0.6 - - - +
57E ILE* 4.4 5.9 - - - +
59E SER* 4.5 18.4 - - - -
61E GLY* 3.8 4.0 - - - -
89E VAL* 3.5 12.9 - - - +
90E ALA 2.8 13.5 + - - -
92E ALA* 1.3 77.4 - - - +
94E ILE* 1.3 58.8 + - - +
96E ILE* 3.5 11.5 + - - +
97E TYR* 2.9 27.5 + - - +
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Residues in contact with ILE 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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89E VAL* 3.5 24.7 - - + +
90E ALA* 3.6 2.9 + - - -
91E SER 2.9 13.2 + - - +
93E GLY* 1.3 74.8 - - - +
95E THR* 1.3 58.8 + - - +
97E TYR* 3.2 2.6 + - + +
98E LEU* 2.9 49.6 + - + +
113E TYR* 3.8 25.1 - - + -
114E MET 3.3 24.9 - - - +
115E ILE* 4.0 23.6 - - + -
117E GLN* 4.4 1.1 - - - +
147E ILE* 4.3 12.3 - - + -
178E ILE* 4.1 15.5 - - + -
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Residues in contact with THR 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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67E GLY 4.7 6.1 - - - +
68E ASP* 4.4 13.5 - - - +
71E HIS* 3.1 34.1 - - + -
91E SER 3.3 10.0 + - - -
92E ALA* 3.3 12.5 + - - -
94E ILE* 1.3 80.8 - - - +
96E ILE* 1.3 61.4 + - - +
98E LEU* 3.4 8.1 + - - +
99E ALA 3.5 0.5 + - - -
117E GLN* 4.0 14.6 + - - -
143E ILE* 4.2 15.0 - - + +
146E LEU* 4.0 33.2 - - + +
147E ILE* 4.9 2.1 - - - +
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Residues in contact with ILE 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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26E ILE* 4.1 9.9 - - + -
30E ILE* 3.6 37.2 - - + -
57E ILE* 4.0 19.0 - - + +
67E GLY* 3.7 18.6 - - - +
70E ILE* 3.7 41.7 - - + -
71E HIS* 4.3 7.2 - - - +
74E ILE* 3.9 13.6 - - + +
83E VAL* 4.8 1.0 - - - +
92E ALA 3.2 14.0 + - - +
93E GLY* 3.7 7.4 - - - +
95E THR* 1.3 73.6 - - - +
97E TYR* 1.3 66.7 + - - +
99E ALA* 3.0 20.8 + - - +
100E ALA 4.4 0.7 + - - -
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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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57E ILE* 3.8 19.9 - - + +
83E VAL* 3.5 25.6 - - + +
85E GLY* 3.6 22.4 - - - -
89E VAL* 3.9 17.3 - - + -
93E GLY 2.9 18.3 + - - +
94E ILE* 3.5 5.4 - - + +
96E ILE* 1.3 76.8 - - - +
98E LEU* 1.3 61.7 + - + +
99E ALA 3.2 4.0 + - - -
100E ALA* 3.5 3.8 + - - +
105E ARG* 3.4 31.8 - - + +
106E PHE 2.7 39.4 + - - -
113E TYR* 4.0 7.9 - + - -
178E ILE* 3.3 42.4 - - + -
179E VAL* 3.5 12.8 - - - +
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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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71E HIS* 4.5 4.4 + - - -
75E LYS* 4.9 3.6 + - - -
94E ILE* 2.9 38.3 + - + +
95E THR 3.9 5.6 - - - +
96E ILE 3.2 0.6 - - - -
97E TYR* 1.3 75.8 - - + +
99E ALA* 1.3 62.0 + - - +
100E ALA 3.2 9.4 - - - +
105E ARG* 3.6 35.4 - - - +
146E LEU* 4.7 6.2 - - + +
147E ILE* 3.8 37.9 - - + -
150E ALA* 3.8 20.3 - - + +
151E THR* 4.0 16.4 - - + -
178E ILE* 4.2 17.5 - - + -
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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