Contacts of the strand formed by residues 68 - 75 (chain F) in PDB entry 3E8C
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 HIS 68 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F ILE* 3.6 31.7 - - + +
59F LEU* 4.0 10.9 - - + +
60F VAL 3.3 8.6 + - - +
61F LYS* 4.1 17.1 - - + +
66F GLY 3.8 13.0 + - - -
67F ASN* 1.3 75.4 - - - +
69F TYR* 1.3 72.1 + - - +
122F TYR* 4.3 10.3 + - + +
321F PRO* 4.0 29.7 - - + +
322F GLY* 3.9 31.5 + - - -
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Residues in contact with TYR 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F PHE* 4.4 4.0 - + - -
59F LEU* 3.5 5.9 - - - +
60F VAL* 2.9 37.2 + - + +
62F HIS* 3.7 28.9 - + + -
65F THR* 5.0 0.7 - - - +
67F ASN* 3.5 39.1 + - + -
68F HIS* 1.3 76.6 - - - +
70F ALA* 1.3 60.4 + - - +
107F GLU* 3.5 34.7 + - + -
108F PHE* 4.2 19.2 - + - -
119F VAL* 3.5 25.1 - - + -
120F MET 3.4 17.0 - - - +
121F GLU* 4.6 3.6 - - - -
122F TYR* 3.8 9.9 - - - -
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Residues in contact with ALA 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F LEU* 4.4 6.7 - - + -
57F VAL* 4.4 5.8 - - + -
58F MET 3.4 6.5 - - - +
69F TYR* 1.3 74.1 - - - +
71F MET* 1.3 60.1 + - - +
119F VAL* 3.4 4.7 - - - +
120F MET* 2.8 57.7 + - + +
121F GLU 4.0 1.6 - - - +
122F TYR* 3.8 4.9 - - - +
351F G96 3.8 29.8 - - + +
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Residues in contact with MET 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F LEU* 4.1 11.9 - - + -
43F PHE* 3.7 35.4 - - + -
45F ARG* 5.6 3.4 - - - -
56F ARG 3.8 0.3 - - - +
57F VAL* 3.4 2.7 - - - -
58F MET* 2.8 36.9 + - + +
60F VAL* 3.6 25.1 - - + -
70F ALA* 1.3 75.3 - - - +
72F LYS* 1.3 65.8 + - - +
73F ILE* 3.6 21.1 + - + +
110F PHE* 4.0 9.6 - - + -
117F TYR* 3.9 20.6 - - + -
118F MET 3.4 8.3 - - - +
119F VAL* 3.3 28.3 - - + -
120F MET* 3.7 0.9 - - - -
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Residues in contact with LYS 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F PHE* 5.4 3.7 - - - -
56F ARG 3.6 3.1 - - - -
57F VAL* 4.2 8.5 - - + +
71F MET* 1.3 72.8 - - - +
73F ILE* 1.3 62.4 + - - +
74F LEU* 3.8 30.8 - - + +
91F GLU* 2.9 34.6 + - - +
116F LEU 3.7 0.9 - - - +
117F TYR* 3.5 5.9 - - - -
118F MET* 2.9 43.9 + - + +
120F MET* 3.1 16.1 - - + +
184F ASP* 4.1 4.8 + - - -
186F GLY* 4.8 2.2 - - - -
351F G96 3.3 66.8 + - + +
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Residues in contact with ILE 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F LEU* 5.9 0.7 - - + -
45F ARG* 5.0 3.6 - - - -
55F GLY* 3.2 6.6 - - - -
56F ARG* 2.8 40.2 + - + +
58F MET* 4.1 26.0 - - + -
71F MET* 4.0 25.4 - - + +
72F LYS* 1.3 75.1 - - - +
74F LEU* 1.3 65.1 + - - +
115F ASN* 3.9 21.3 - - + +
116F LEU 3.5 2.5 - - - -
117F TYR* 3.6 27.6 - - + -
335F ILE* 3.6 36.1 - - + -
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Residues in contact with LEU 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F PHE* 3.6 22.2 - - + -
72F LYS* 3.8 26.0 - - + +
73F ILE* 1.3 75.6 - - - +
75F ASP* 1.3 62.0 + - - +
76F LYS 3.3 0.5 + - - -
79F VAL* 4.0 14.6 - - + -
88F THR* 4.9 4.0 - - + -
91F GLU* 5.6 0.9 - - - +
115F ASN* 3.1 8.1 - - - -
116F LEU* 2.8 65.4 + - + +
117F TYR 4.8 0.4 - - - +
118F MET* 3.8 28.3 - - + -
351F G96 3.5 29.8 - - + -
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Residues in contact with ASP 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F PHE 2.9 16.4 + - - +
55F GLY* 4.5 2.4 - - - -
73F ILE* 4.1 1.8 + - - +
74F LEU* 1.3 68.7 - - - +
76F LYS* 1.3 58.4 + - - +
77F GLN* 3.0 27.3 + - - +
78F LYS* 3.1 37.2 + - + +
79F VAL* 2.9 29.4 + - - +
114F SER* 4.3 5.4 - - - +
115F ASN* 3.4 15.9 + - - +
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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