Contacts of the helix formed by residues 88 - 98 (chain E) in PDB entry 3KZ1
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 88 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85E SER* 3.2 11.9 + - - +
86E ILE 3.0 2.4 - - - -
87E ASP* 1.3 89.0 + - - +
89E PRO* 1.3 57.7 - - - +
90E ASP* 2.9 13.5 + - - +
91E SER* 2.7 48.9 + - - -
92E LEU 3.5 1.0 + - - -
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Residues in contact with PRO 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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86E ILE 3.8 4.2 - - - +
87E ASP 3.6 8.7 - - - +
88E SER* 1.3 84.5 - - - +
90E ASP* 1.3 64.3 + - - +
92E LEU* 3.2 18.7 + - + +
93E GLU* 3.4 8.3 + - - +
131E LEU* 4.1 13.7 - - + -
136E GLN* 4.4 20.9 - - + +
137E GLU 3.4 28.0 - - - +
139E VAL* 3.9 21.5 - - + +
143E GLU* 5.3 6.1 - - - +
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Residues in contact with ASP 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E SER* 2.8 9.5 + - - +
89E PRO* 1.3 78.7 - - - +
91E SER* 1.3 62.2 + - - +
93E GLU* 3.2 17.2 + - - +
94E ASN* 3.3 20.6 + - - +
136E GLN* 2.6 36.9 + - - +
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Residues in contact with SER 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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13E ASP* 3.3 35.4 + - - -
16E CYS* 4.9 2.2 - - - -
83E CYS 5.1 0.3 - - - +
84E PHE* 3.7 6.8 - - - +
85E SER 2.9 31.2 + - - -
88E SER* 2.7 38.9 + - - -
90E ASP* 1.3 68.8 - - - +
92E LEU* 1.3 63.2 + - - +
94E ASN* 3.3 11.0 + - - +
95E ILE* 3.6 14.6 + - - +
99E TRP* 5.1 0.7 - - - -
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Residues in contact with LEU 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E PHE* 4.0 38.3 - - + +
88E SER 3.5 0.8 + - - -
89E PRO* 3.2 16.7 + - + +
91E SER* 1.3 81.3 + - - +
93E GLU* 1.3 60.2 + - - +
94E ASN 3.1 0.2 - - - -
95E ILE* 3.2 23.2 + - + +
96E PRO* 3.3 4.5 - - - +
139E VAL* 3.9 22.0 - - + -
143E GLU* 3.8 35.7 - - + +
144E GLY* 5.5 0.4 - - - -
147E MET* 3.7 40.2 - - + +
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Residues in contact with GLU 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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89E PRO 3.4 6.8 + - - +
90E ASP* 3.2 12.5 + - - +
92E LEU* 1.3 77.5 - - - +
94E ASN* 1.3 58.1 + - - +
95E ILE 3.3 0.7 - - - -
96E PRO* 3.2 27.2 - - - +
97E GLU* 3.3 30.6 - - - +
147E MET* 5.1 4.8 - - + +
150E ARG* 4.6 11.1 + - - -
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Residues in contact with ASN 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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13E ASP* 2.6 39.9 + - - +
90E ASP* 3.3 16.6 + - - +
91E SER 3.7 6.3 - - - +
92E LEU 3.1 1.2 - - - -
93E GLU* 1.3 78.5 - - - +
95E ILE* 1.3 59.9 + - - +
96E PRO 3.5 0.2 - - - -
97E GLU* 3.8 10.6 - - - +
98E LYS* 2.9 33.6 + - + +
99E TRP* 3.1 15.9 + - - +
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Residues in contact with ILE 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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82E MET* 3.6 28.7 - - + -
83E CYS 3.4 27.8 - - - +
84E PHE* 4.2 8.5 - - + -
91E SER 3.6 8.1 - - - +
92E LEU* 3.3 19.7 - - + +
94E ASN* 1.3 79.2 - - - +
96E PRO* 1.4 59.8 - - + +
99E TRP* 4.1 10.5 - - + -
100E THR* 2.6 46.0 + - - +
114E LEU* 3.7 25.1 - - + -
147E MET* 4.0 13.9 - - + -
151E ILE* 4.1 6.5 - - + -
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Residues in contact with PRO 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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92E LEU 3.3 8.1 - - - +
93E GLU* 3.2 31.6 - - - +
95E ILE* 1.4 99.6 - - + +
97E GLU* 1.3 60.3 + - + +
100E THR* 4.0 9.0 - - - +
101E PRO* 3.4 17.8 - - - +
147E MET* 3.9 18.8 - - + -
150E ARG* 3.9 25.6 - - - +
151E ILE* 4.6 4.7 - - + -
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Residues in contact with GLU 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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93E GLU* 3.3 32.5 - - - +
94E ASN* 3.6 9.6 + - - +
95E ILE 3.3 0.4 - - - -
96E PRO* 1.3 85.0 - - - +
98E LYS* 1.3 61.0 + - + +
101E PRO* 3.9 10.2 - - - +
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Residues in contact with LYS 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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13E ASP* 5.3 2.9 - - - +
62E GLY 5.5 2.2 - - - -
64E GLU* 4.1 15.8 - - + +
67E ASP* 2.8 34.6 + - - -
70E ARG* 3.7 6.2 - - - +
94E ASN* 2.9 23.9 + - - +
97E GLU* 1.3 79.6 - - + +
99E TRP* 1.3 100.6 + - + +
101E PRO* 3.3 6.6 - - - +
102E GLU* 3.3 32.5 + - - +
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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