Contacts of the helix formed by residues 87 - 97 (chain E) in PDB entry 4KYI
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 ASP 87 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85E GLY 3.4 4.3 + - - -
86E MET* 1.3 73.2 - - - +
88E ILE* 1.3 68.1 + - - +
89E LYS* 3.0 33.8 + - - +
90E ASP* 2.7 40.7 + - - +
91E ILE 3.0 8.5 + - - -
129E GLN* 4.3 5.5 + - - +
132E LYS* 5.8 3.4 - - - +
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Residues in contact with ILE 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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51E LEU* 6.3 2.5 - - + -
54E ILE* 4.2 19.5 - - + +
55E GLN* 4.2 24.5 - - + -
58E GLN* 3.5 54.1 - - + +
63E ILE* 5.2 3.4 - - + -
86E MET 3.3 3.0 + - - -
87E ASP* 1.3 80.5 + - - +
89E LYS* 1.3 63.6 + - + +
90E ASP 3.2 0.2 - - - -
91E ILE* 3.7 16.2 - - + -
92E LYS* 3.2 21.8 + - - +
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Residues in contact with LYS 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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60A ARG* 5.2 1.8 - - - +
407A ASP* 3.4 35.3 + - - +
410A LYS* 3.6 25.8 - - - +
87E ASP* 3.0 22.3 + - - +
88E ILE* 1.3 85.9 - - + +
90E ASP* 1.3 66.0 + - - +
92E LYS* 3.6 16.9 - - - +
93E LYS* 3.7 31.2 + - - +
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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
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86E MET* 3.8 10.5 - - + -
87E ASP* 2.7 31.1 + - - +
89E LYS* 1.3 77.9 - - - +
91E ILE* 1.3 59.5 + - - +
92E LYS 3.2 0.4 - - - -
93E LYS* 3.4 23.9 + - - +
94E LEU* 2.8 30.8 + - - +
128E MET* 5.1 1.0 - - - +
129E GLN* 4.6 5.4 - - - +
132E LYS* 4.2 15.8 + - - -
172E ASN* 5.3 2.1 - - - +
173E VAL* 3.6 32.9 - - + +
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Residues in contact with ILE 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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51E LEU* 4.7 5.2 - - + -
54E ILE* 4.1 21.1 - - + -
63E ILE* 6.4 0.2 - - + -
81E ILE* 3.8 31.9 - - + +
82E LEU* 4.0 22.4 - - + -
86E MET* 3.4 36.6 - - + +
87E ASP 3.0 11.3 + - - +
88E ILE* 3.7 19.7 - - + +
89E LYS 3.4 0.2 - - - -
90E ASP* 1.3 77.2 - - - +
92E LYS* 1.3 53.9 + - - +
94E LEU* 3.7 2.6 - - - +
95E ILE* 2.8 48.8 + - + +
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Residues in contact with LYS 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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27A GLN* 2.7 32.8 + - - +
412A THR* 5.1 2.4 - - - +
548A LEU* 4.6 10.0 - - - +
51E LEU* 3.9 18.8 - - + +
55E GLN* 4.5 22.7 - - - +
88E ILE 3.2 10.5 + - - +
89E LYS* 3.6 12.8 - - - +
91E ILE* 1.3 79.0 - - - +
93E LYS* 1.3 60.8 + - + +
95E ILE* 3.8 0.5 - - - +
96E GLU* 2.7 73.2 + - + +
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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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60A ARG* 5.7 0.6 - - - +
410A LYS* 3.7 21.6 - - + +
89E LYS* 3.7 28.1 + - - +
90E ASP* 3.4 28.5 + - - +
92E LYS* 1.3 82.8 - - + +
94E LEU* 1.3 61.7 + - - +
96E GLU* 4.8 4.9 - - - -
97E GLY* 3.1 19.4 + - - -
172E ASN* 5.6 0.7 - - - -
173E VAL* 4.4 7.4 - - + -
174E ASP* 3.3 34.1 - - - +
177E ILE* 3.3 23.8 - - + +
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Residues in contact with LEU 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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77E MET* 3.8 13.9 - - + +
81E ILE* 4.4 16.4 - - + -
86E MET* 4.4 13.5 - - - -
90E ASP 2.8 19.7 + - - +
91E ILE* 3.7 7.4 - - - +
93E LYS* 1.3 76.6 - - - +
95E ILE* 1.3 60.5 + - - +
98E LEU* 3.1 45.2 - - + +
125E ILE* 3.7 39.9 - - + -
173E VAL* 3.8 22.2 - - + +
176E ILE* 5.1 6.5 - - + -
177E ILE* 4.4 9.4 - - + +
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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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47E GLY* 3.3 35.5 - - - +
48E ILE* 4.0 18.0 - - + +
51E LEU* 3.7 31.0 - - + +
54E ILE* 5.5 0.4 - - + -
77E MET* 5.0 10.8 - - - -
78E THR* 4.2 22.2 - - + +
81E ILE* 4.4 14.6 - - + -
91E ILE* 2.8 37.9 + - + +
92E LYS 3.8 2.2 - - - +
94E LEU* 1.3 74.4 - - - +
96E GLU* 1.3 67.7 + - - +
97E GLY 3.5 0.3 + - - -
98E LEU 3.8 10.2 + - - +
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Residues in contact with GLU 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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23A THR* 5.0 5.9 + - - -
24A GLU* 4.0 11.4 - - + +
25A ALA* 3.6 30.2 - - + +
27A GLN* 3.9 9.0 + - - +
48E ILE* 5.0 3.4 - - + -
51E LEU* 4.0 19.0 - - + +
92E LYS* 2.7 61.7 + - + +
93E LYS* 4.4 3.6 - - - +
95E ILE* 1.3 77.0 - - + +
97E GLY* 1.3 58.5 + - - +
98E LEU 3.5 2.5 + - - -
99E ASP* 3.9 2.9 - - - +
391E ARG* 3.0 26.7 + - - +
395E VAL* 5.4 1.8 - - + +
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Residues in contact with GLY 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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24A GLU* 4.0 20.6 - - - -
93E LYS 3.1 18.4 + - - -
96E GLU* 1.3 78.5 - - - +
98E LEU* 1.3 64.0 + - - +
99E ASP* 4.1 0.7 - - - -
102E LYS* 5.9 3.3 - - - -
177E ILE* 3.4 28.1 - - - +
180E THR* 4.8 2.1 + - - -
181E LYS* 5.6 1.1 + - - -
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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