Contacts of the strand formed by residues 106 - 111 (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 LEU 106 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F LYS* 4.1 26.9 - - + +
95F LEU* 4.0 45.4 + - + +
96F GLN* 4.1 16.7 - - + +
104F VAL 3.9 2.4 + - - -
105F LYS* 1.3 74.7 - - - +
107F GLU* 1.3 63.3 + - - +
108F PHE 3.4 24.7 - - - +
109F SER* 4.4 9.0 - - - +
118F MET* 3.7 26.9 - - + -
119F VAL 3.5 9.2 - - - +
120F MET* 4.3 5.4 - - + +
351F G96 5.0 0.7 - - + -
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Residues in contact with GLU 107 (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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37F THR* 4.3 3.3 + - - +
69F TYR* 3.5 34.4 + - + -
105F LYS* 4.0 18.8 - - - +
106F LEU* 1.3 78.4 - - - +
108F PHE* 1.3 90.4 + - + +
119F VAL 2.7 16.5 + - - +
120F MET 4.1 3.4 - - - -
121F GLU* 3.7 19.8 - - - +
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Residues in contact with PHE 108 (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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37F THR* 3.2 35.0 - - - +
38F ALA* 3.7 19.5 - - + -
43F PHE* 3.8 18.4 - + - -
62F HIS* 4.2 18.8 - + - -
69F TYR* 4.2 22.9 - + - -
106F LEU* 3.4 10.6 - - - +
107F GLU* 1.3 99.4 - - + +
109F SER* 1.3 59.3 + - - +
110F PHE* 4.7 0.4 - - + -
119F VAL* 2.8 46.6 + - + +
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Residues in contact with SER 109 (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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34F ALA* 4.1 12.3 + - - +
35F GLN* 4.7 2.3 - - - -
36F ASN* 3.2 4.7 - - - -
37F THR* 3.0 32.1 + - - +
92F LYS* 3.8 35.6 + - - +
96F GLN* 6.0 0.2 - - - +
106F LEU* 4.4 9.3 - - - +
108F PHE* 1.3 76.4 - - - +
110F PHE* 1.3 66.5 + - - +
117F TYR 3.3 12.1 - - - -
118F MET* 4.5 2.2 - - - -
350F PHE* 4.5 4.4 + - - -
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Residues in contact with PHE 110 (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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36F ASN* 3.8 21.3 - - - +
38F ALA* 3.2 34.8 - - + +
39F HIS* 3.7 4.5 - + - -
40F LEU* 3.4 37.9 - - + -
43F PHE* 3.8 19.5 - + - -
71F MET* 4.0 13.2 - - + -
109F SER* 1.3 81.6 - - - +
111F LYS* 1.3 63.2 + - - +
112F ASP* 6.1 0.4 - - + -
117F TYR* 2.7 71.2 + + + +
119F VAL* 3.9 13.7 - - + -
350F PHE* 3.4 11.3 - - - -
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Residues in contact with LYS 111 (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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194E ARG* 5.9 2.0 - - - +
35F GLN* 5.7 0.2 + - - -
36F ASN* 3.8 23.0 + - - +
76F LYS* 5.0 6.1 - - - +
110F PHE* 1.3 80.3 - - - +
112F ASP* 1.3 67.9 + - - +
115F ASN 3.4 13.5 - - - +
116F LEU* 3.8 15.9 - - + -
117F TYR* 4.1 4.7 - - - -
341F GLU* 5.7 4.3 - - - -
347F PHE* 2.6 30.9 + - + +
348F SER* 3.1 16.8 + - - +
350F PHE* 2.7 32.7 + - + +
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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