Contacts of the helix formed by residues 73 - 83 (chain F) in PDB entry 1WRL
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 73 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C LYS* 6.0 0.3 + - - -
24F PHE* 3.9 8.1 - - - -
35F SER* 4.5 8.7 - - - +
67F ASP* 3.8 18.5 - - - +
71F THR 4.2 0.2 + - - -
72F VAL* 1.3 76.5 - - - +
74F PHE* 1.3 64.2 + - - +
75F ASP* 3.6 15.6 - - - +
76F GLU* 2.6 54.8 + - - +
77F PHE* 2.9 17.2 + - - +
106F CA 4.3 0.4 - - - -
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Residues in contact with PHE 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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33C ASP 5.9 4.5 - - - -
17F LYS* 3.4 28.7 - - + -
20F PHE* 3.9 3.4 - - + -
21F LYS* 3.5 51.1 - - + -
24F PHE* 3.8 30.4 - - + -
73F ASP* 1.3 74.6 - - - +
75F ASP* 1.3 66.9 + - - +
77F PHE* 3.6 9.8 - + - +
78F LEU* 3.3 56.2 + - + +
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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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21C LYS* 3.9 20.4 + - - -
24C PHE* 6.2 0.2 - - - -
74C PHE* 6.1 0.3 - - - +
9F VAL* 6.0 0.2 - - - +
73F ASP* 3.0 16.5 + - - +
74F PHE* 1.3 87.6 - - - +
76F GLU* 1.3 67.0 + - + +
78F LEU* 3.5 15.4 + - - +
79F VAL* 3.6 15.9 + - - +
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Residues in contact with GLU 76 (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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64F VAL* 3.4 26.4 - - + +
65F ASP* 2.9 24.4 - - - +
66F GLU* 3.1 7.9 + - + +
67F ASP* 3.1 8.4 + - - +
71F THR 3.1 0.5 - - - +
72F VAL* 2.9 20.7 - - + -
73F ASP* 2.6 47.6 + - - +
75F ASP* 1.3 74.1 - - + +
77F PHE* 1.3 57.1 + - - +
79F VAL* 3.0 13.1 + - - +
80F MET* 2.9 26.3 + - - +
106F CA 2.5 29.9 - - - -
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Residues in contact with PHE 77 (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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20F PHE* 3.6 35.7 - + + -
23F ALA* 4.6 0.7 - - + -
24F PHE* 4.2 8.3 - + + -
27F PHE* 4.1 19.3 - + - -
36F ILE* 3.9 26.2 - - + -
72F VAL* 3.5 9.6 - - + +
73F ASP 2.9 16.9 + - - +
74F PHE* 3.6 21.5 - + - +
75F ASP 3.2 0.2 - - - -
76F GLU* 1.3 76.4 - - - +
78F LEU* 1.3 57.9 + - - +
80F MET* 3.0 15.2 + - - +
81F MET* 2.8 69.2 + - + +
209F TFP 5.1 2.0 - - - -
211F TFP 3.7 16.8 - - - -
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Residues in contact with LEU 78 (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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9F VAL* 4.2 22.9 - - + -
12F LEU* 4.4 10.4 - - + +
17F LYS* 4.1 26.2 - - + -
20F PHE* 3.9 27.4 - - + -
74F PHE* 3.3 53.0 + - + +
75F ASP* 3.8 12.3 - - - +
76F GLU 3.3 0.4 - - - -
77F PHE* 1.3 77.9 - - + +
79F VAL* 1.3 58.9 + - - +
81F MET* 3.2 6.2 + - + +
82F VAL* 2.9 33.4 + - - +
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Residues in contact with VAL 79 (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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5F TYR* 4.0 17.5 - - + -
6F LYS* 5.7 2.2 - - - +
9F VAL* 4.3 14.8 - - + -
64F VAL* 4.1 9.0 - - + -
75F ASP 3.6 14.6 + - - +
76F GLU* 3.0 12.2 + - - +
78F LEU* 1.3 76.2 - - - +
80F MET* 1.3 52.7 + - - +
82F VAL* 2.9 7.0 + - - +
83F ARG* 2.5 65.6 + - + +
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Residues in contact with MET 80 (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 ILE* 6.3 0.9 - - - -
41F LEU* 5.3 9.9 - - + -
60F MET* 3.0 37.5 - - + +
61F ILE* 4.4 6.3 - - + -
64F VAL* 3.8 24.9 - - + +
72F VAL* 4.6 10.8 - - + -
76F GLU 2.9 11.0 + - - +
77F PHE* 3.2 20.4 - - - +
79F VAL* 1.3 77.7 - - - +
81F MET* 1.3 62.4 + - - +
83F ARG* 4.5 5.4 - - - +
84F SER* 3.3 27.2 + - - +
209F TFP 3.1 37.7 - - - -
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Residues in contact with MET 81 (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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12F LEU* 6.0 0.9 - - + -
20F PHE* 3.3 39.0 - - + -
77F PHE* 2.8 46.2 + - + +
78F LEU* 3.5 10.1 - - + +
80F MET* 1.3 76.8 - - + +
82F VAL* 1.3 63.3 + - + +
84F SER 3.3 6.9 - - - +
209F TFP 3.2 39.7 - - - -
211F TFP 3.1 74.3 + - - -
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Residues in contact with VAL 82 (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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5F TYR* 3.9 23.4 - - + +
8F ALA* 3.3 28.9 - - + -
9F VAL* 3.4 30.3 - - + +
12F LEU* 4.5 12.8 - - + -
78F LEU 2.9 23.0 + - - +
79F VAL* 3.3 8.7 - - - +
81F MET* 1.3 79.1 - - + +
83F ARG* 1.3 71.2 + - - +
84F SER 4.2 0.9 - - - +
211F TFP 5.1 6.4 + - - -
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Residues in contact with ARG 83 (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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5F TYR* 3.1 63.8 + - + +
63F GLU* 2.7 60.4 + - - +
64F VAL* 3.6 10.6 - - - +
79F VAL* 2.5 39.1 + - + +
80F MET* 4.3 2.5 - - - +
82F VAL* 1.3 79.2 - - - +
84F SER* 1.3 65.9 + - - +
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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