Contacts of the strand formed by residues 70 - 76 (chain E) in PDB entry 5LF4
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 ILE 70 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66E VAL* 3.1 27.7 + - + -
67E ASP* 2.9 31.2 + - + +
68E ASN 3.6 0.6 - - - -
69E HIS* 1.3 115.7 - - + +
71E GLY* 1.3 64.2 + - - +
88E MET* 4.6 1.3 - - + -
92E CYS* 4.0 4.9 - - - -
103E LEU 4.2 4.0 - - - +
105E VAL* 4.0 22.9 - - + -
108E LEU* 3.6 26.2 - - + -
134E ILE* 4.0 21.1 - - + -
135E ALA 3.3 8.7 - - - +
136E GLY* 4.5 0.7 - - - -
221E PHE* 4.0 8.4 - - - +
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Residues in contact with GLY 71 (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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46E LEU* 3.8 8.0 - - - +
64E LEU 3.3 11.7 - - - -
66E VAL* 4.3 1.8 - - - -
70E ILE* 1.3 75.4 - - - +
72E ILE* 1.3 68.5 + - - +
134E ILE* 3.7 0.3 - - - -
135E ALA 2.9 32.2 + - - +
221E PHE* 3.5 22.2 - - - -
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Residues in contact with ILE 72 (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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46E LEU* 3.6 4.9 - - - +
62E LYS 3.8 0.3 - - - +
63E ILE* 3.1 6.4 - - - +
64E LEU* 2.8 53.3 + - + +
66E VAL* 3.9 7.2 - - + -
70E ILE* 4.8 0.2 - - + -
71E GLY* 1.3 80.8 - - - +
73E SER* 1.3 62.3 + - - +
74E ILE* 4.2 9.9 - - + -
81E ALA 4.9 0.4 - - - +
85E CYS* 3.8 37.0 - - + +
88E MET* 3.5 28.9 - - + -
132E LEU* 4.0 24.7 - - + -
133E LEU 3.2 5.8 - - - +
134E ILE* 3.9 15.0 - - + -
221E PHE* 4.3 0.2 - - - -
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Residues in contact with SER 73 (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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35E THR* 2.7 36.4 + - - +
46E LEU* 3.6 16.3 - - - +
48E ALA* 3.8 4.0 - - - +
62E LYS* 3.2 10.5 + - - +
63E ILE* 3.7 12.4 - - - +
72E ILE* 1.3 73.5 - - - +
74E ILE* 1.3 63.6 + - - +
132E LEU* 3.3 7.4 - - - +
133E LEU* 2.8 38.1 + - - -
161E ILE* 5.1 0.2 - - - +
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Residues in contact with ILE 74 (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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35E THR* 4.3 5.1 - - - +
61E LYS* 4.0 21.5 - - + +
62E LYS* 2.8 62.2 + - - +
64E LEU* 4.1 23.3 - - + -
72E ILE* 4.2 6.7 - - + -
73E SER* 1.3 79.6 - - - +
75E ALA* 1.3 56.2 + - - +
76E GLY 5.7 1.8 - - - +
78E THR* 4.6 20.4 - - + +
81E ALA* 3.7 31.6 - - + -
130E VAL* 4.4 0.7 - - + -
131E GLY 3.7 4.0 - - - -
132E LEU* 3.7 18.8 - - + -
161E ILE* 5.1 0.2 - - - -
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Residues in contact with ALA 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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29E VAL* 3.5 24.3 - - + +
32E GLY* 4.6 2.5 - - - -
33E SER 4.3 7.6 - - - +
35E THR* 4.8 0.9 - - + -
62E LYS* 4.0 13.0 - - - +
74E ILE* 1.3 78.4 - - - +
76E GLY* 1.3 58.4 + - - +
130E VAL* 3.4 3.4 - - - -
131E GLY 2.9 33.9 + - - -
161E ILE* 4.0 23.8 - - + -
162E GLY* 4.7 1.6 - - - -
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Residues in contact with GLY 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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28E ALA* 3.6 24.4 + - - -
32E GLY* 4.4 8.3 - - - -
74E ILE* 5.7 2.0 - - - +
75E ALA* 1.3 75.6 - - - +
77E LEU* 1.3 68.3 + - - -
78E THR* 3.2 10.9 + - - +
129E GLY 3.5 7.9 - - - -
130E VAL* 4.8 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