Contacts of the helix formed by residues 87 - 95 (chain E) in PDB entry 1Q57
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 87 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80E ALA* 3.6 3.4 - - - -
86E ILE* 1.3 78.9 - - - +
88E LYS* 1.3 66.2 + - - +
89E GLU* 4.2 8.4 - - - +
90E THR* 3.1 23.0 + - - -
91E CYS* 3.3 13.0 + - - -
167E GLU* 2.8 30.5 + - - -
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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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78E TYR* 2.9 33.0 - - + +
79E SER* 4.1 7.0 - - - -
80E ALA* 3.0 30.6 - - + +
87E SER* 1.3 73.4 - - - +
89E GLU* 1.3 66.7 + - - +
90E THR 3.2 0.7 + - - -
91E CYS* 3.4 4.2 + - - +
92E GLN* 3.2 22.6 + - + +
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Residues in contact with GLU 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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127D ASP* 5.5 3.8 - - - +
128D LYS 4.7 2.1 - - - +
129D ASN* 2.4 50.0 + - - +
87E SER* 3.3 7.1 - - - +
88E LYS* 1.3 80.9 - - - +
90E THR* 1.3 58.3 + - - +
92E GLN* 3.3 13.8 - - + +
93E LYS* 3.0 53.9 + - - +
170E ASP* 5.1 6.9 - - - +
171E CYS* 5.2 3.8 - - - -
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Residues in contact with THR 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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86E ILE* 3.3 22.9 - - + -
87E SER* 3.1 26.8 + - - -
88E LYS 3.1 1.0 - - - -
89E GLU* 1.3 75.0 + - - +
91E CYS* 1.3 68.7 + - - +
92E GLN 2.9 1.3 - - - -
93E LYS* 2.8 17.2 + - - +
94E ALA* 3.4 8.5 + - - +
163E LEU* 3.5 26.5 - - + +
166E MET* 4.4 10.4 - - + +
167E GLU* 3.2 15.8 + - + +
171E CYS* 3.5 20.9 - - - -
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Residues in contact with CYS 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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78E TYR* 4.3 2.8 - - + -
79E SER 3.8 16.8 - - - +
81E LEU* 3.3 43.7 - - - -
86E ILE* 3.8 5.6 - - - -
87E SER 3.3 7.9 + - - -
88E LYS 3.8 7.0 - - - +
90E THR* 1.3 79.1 - - - +
92E GLN* 1.3 61.8 + - - +
94E ALA 3.6 0.4 + - - +
95E GLY* 3.0 5.2 + - - -
96E TYR* 2.8 50.3 + - - +
163E LEU* 3.5 17.3 - - - -
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Residues in contact with GLN 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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78E TYR* 3.2 54.9 + - + -
88E LYS* 3.2 13.6 + - + +
89E GLU* 3.3 18.2 - - + +
90E THR 2.9 1.0 + - - -
91E CYS* 1.3 80.2 - - - +
93E LYS* 1.3 63.8 + - + +
95E GLY* 3.9 4.5 + - - -
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Residues in contact with LYS 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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128D LYS 4.7 9.3 + - - -
129D ASN* 4.5 5.9 + - - +
89E GLU* 3.0 50.8 + - - +
90E THR 2.8 12.7 + - - +
92E GLN* 1.3 75.2 - - + +
94E ALA* 1.3 61.7 + - - +
95E GLY 3.5 0.5 + - - -
145E HIS* 4.7 2.4 - - - -
146E LEU* 3.6 22.2 - - + +
166E MET* 4.6 10.8 - - + -
170E ASP* 5.1 4.0 + - - -
171E CYS* 4.1 25.6 - - + +
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Residues in contact with ALA 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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90E THR 3.4 7.9 + - - +
91E CYS 4.6 1.1 - - - +
93E LYS* 1.3 78.7 - - - +
95E GLY* 1.3 58.9 + - - +
96E TYR 4.9 0.4 - - - +
110E ASP 4.1 5.4 - - - +
142E PHE* 3.2 25.9 - - + -
143E GLY* 5.1 1.0 - - - -
145E HIS* 4.2 11.7 + - - -
146E LEU* 4.1 9.3 - - - +
162E MET* 3.4 31.8 - - + +
163E LEU* 3.9 13.2 - - + -
166E MET* 4.2 9.6 - - - -
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Residues in contact with GLY 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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78E TYR* 4.4 12.8 - - - -
91E CYS 3.0 5.8 + - - -
92E GLN 3.9 5.3 + - - -
93E LYS 3.3 3.6 - - - -
94E ALA* 1.3 79.8 - - - +
96E TYR* 1.3 60.5 + - - +
97E TRP* 3.7 3.6 - - - -
108E VAL 3.6 2.1 - - - +
109E ALA* 3.8 1.0 - - - -
110E ASP* 3.0 42.3 + - - +
112E ARG* 5.9 3.6 - - - -
142E PHE* 3.9 1.8 - - - -
145E HIS* 5.9 0.2 - - - -
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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