Contacts of the helix formed by residues 74 - 84 (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 ALA 74 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45E ALA* 3.3 30.3 - - + +
46E LYS* 4.2 13.2 - - - -
47E GLY* 4.3 4.4 - - - +
50E TYR* 4.2 7.8 + - + +
73E SER* 1.3 78.6 - - - +
75E GLY* 1.3 56.7 + - - +
76E ALA 3.1 3.2 + - - -
77E MET* 3.5 10.0 + - - +
78E THR* 3.1 23.2 + - - -
269E GLY* 5.7 0.7 - - - -
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Residues in contact with GLY 75 (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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40E LEU* 3.7 24.9 - - - +
50E TYR* 4.0 16.4 + - - -
71E GLY* 3.5 8.8 - - - -
72E ALA 2.9 12.4 + - - -
74E ALA* 1.3 78.7 - - - +
76E ALA* 1.3 57.7 + - - +
77E MET 3.3 0.4 - - - -
78E THR* 3.8 2.0 - - - -
79E ALA* 3.0 28.9 + - - +
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Residues in contact with ALA 76 (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 GLY* 3.7 16.6 - - - +
72E ALA 3.4 1.8 + - - -
73E SER 3.3 8.7 + - - +
74E ALA 3.1 0.6 - - - -
75E GLY* 1.3 79.3 - - - +
77E MET* 1.3 59.3 + - - +
79E ALA* 4.0 2.6 - - - +
80E SER* 3.3 24.1 + - - -
238E VAL* 4.2 12.5 - - + +
265E VAL* 3.4 16.7 - - + +
268E SER* 3.4 34.1 - - - +
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Residues in contact with MET 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E GLY* 6.3 2.5 - - - -
73E SER 4.3 1.7 + - - +
74E ALA* 3.5 10.8 + - - +
76E ALA* 1.3 76.1 - - - +
78E THR* 1.3 66.4 + - - +
80E SER* 2.7 20.7 + - - +
81E ILE* 3.3 16.6 - - + +
94E LEU* 3.8 19.7 - - + +
95E ILE* 5.0 12.3 - - - -
98E LEU* 3.7 36.6 - - + +
100E ILE* 6.0 1.3 - - + -
118E PHE* 4.1 25.8 - - + -
122E LEU* 3.7 25.8 - - + -
125E ILE* 4.5 1.1 - - + -
265E VAL* 3.5 12.7 - - + +
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Residues in contact with THR 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E LEU* 3.8 18.2 - - + -
47E GLY* 4.7 2.9 + - - -
50E TYR* 3.7 29.1 - - + -
54E ILE* 3.6 27.8 - - + -
74E ALA 3.1 16.6 + - - -
75E GLY* 4.1 0.4 - - - -
76E ALA 3.4 0.2 - - - -
77E MET* 1.3 79.5 - - - +
79E ALA* 1.3 62.7 + - - +
81E ILE* 3.5 10.1 - - + +
82E LEU* 3.3 24.3 + - + +
95E ILE* 4.2 17.4 - - + +
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Residues in contact with ALA 79 (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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40E LEU* 4.2 3.3 - - + +
69E VAL* 3.6 30.5 - - + +
70E SER 4.0 13.7 - - - +
71E GLY* 4.3 1.1 - - - +
75E GLY 3.0 20.2 + - - +
76E ALA* 4.3 2.2 - - - +
78E THR* 1.3 77.1 - - - +
80E SER* 1.3 57.6 + - - +
82E LEU* 3.3 6.2 + - - +
83E ALA* 2.8 30.0 + - - +
236E LEU* 3.9 14.6 - - + -
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Residues in contact with SER 80 (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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76E ALA 3.3 14.1 + - - -
77E MET* 2.7 26.9 + - - +
79E ALA* 1.3 80.7 - - - +
81E ILE* 1.3 57.2 + - - +
82E LEU 3.2 0.7 - - - -
83E ALA* 3.4 2.8 + - - +
84E VAL* 3.2 26.9 + - - +
126E TYR* 2.8 36.9 + - - -
218E LEU* 5.8 0.9 - - - +
236E LEU* 3.7 26.1 - - - +
261E ILE* 5.8 0.2 - - - +
265E VAL* 3.9 1.6 - - - -
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Residues in contact with ILE 81 (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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54E ILE* 5.8 0.2 - - + -
77E MET* 3.3 19.9 + - + +
78E THR* 3.5 13.5 - - + +
80E SER* 1.3 78.0 + - - +
82E LEU* 1.3 63.6 + - + +
84E VAL* 3.6 8.8 - - - +
86E MET* 3.3 38.8 + - + +
91E ILE* 3.8 39.0 - - + +
94E LEU* 4.4 21.8 - - + -
95E ILE* 4.4 17.0 - - + -
122E LEU* 5.8 0.7 - - + -
125E ILE* 4.2 24.5 - - + -
126E TYR* 4.6 4.7 - - + -
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Residues in contact with LEU 82 (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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38E LEU* 3.9 28.7 - - + -
40E LEU* 5.1 2.5 - - + -
53E MET* 5.4 0.2 - - + -
54E ILE* 4.1 35.0 - - + -
57E LEU* 6.3 0.2 - - + -
63E ILE* 4.6 19.7 - - + +
66E LEU* 6.0 2.0 - - + -
69E VAL* 4.5 11.9 - - + -
78E THR* 3.3 20.8 + - + +
79E ALA* 3.5 10.1 - - - +
80E SER 3.2 0.2 - - - -
81E ILE* 1.3 78.7 - - - +
83E ALA* 1.3 63.1 + - - +
84E VAL 3.2 0.2 - - - -
85E GLY* 3.3 13.2 + - - -
86E MET 5.3 0.2 - - - +
91E ILE* 4.0 20.2 - - + -
232E LEU 3.9 1.0 - - - +
234E LYS* 3.7 15.8 - - + +
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Residues in contact with ALA 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E VAL* 3.8 9.9 - - + -
79E ALA 2.8 17.7 + - - +
80E SER 3.4 5.4 + - - +
82E LEU* 1.3 76.2 - - - +
84E VAL* 1.3 56.5 + - - +
85E GLY 3.2 1.6 - - - -
218E LEU* 4.4 6.3 - - + +
233E ILE* 3.3 15.6 - - - +
234E LYS* 3.0 38.1 + - + +
236E LEU* 3.6 29.4 - - + -
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Residues in contact with VAL 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E SER 3.2 11.5 + - - +
81E ILE* 3.6 23.8 - - + +
82E LEU 3.2 0.8 - - - -
83E ALA* 1.3 76.8 - - - +
85E GLY* 1.3 58.9 + - - +
86E MET* 3.6 14.4 - - + +
125E ILE* 5.5 0.9 - - + +
126E TYR* 4.4 16.4 - - + +
129E GLN* 3.5 22.3 - - + +
130E MET* 3.5 35.0 - - + -
133E HIS* 3.1 22.3 + - - -
218E LEU* 4.5 10.5 - - + -
233E ILE* 3.4 8.9 - - + +
261E ILE* 6.1 0.9 - - + -
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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