Contacts of the helix formed by residues 38 - 50 (chain F) in PDB entry 3FZ7
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 ARG 38 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37F MET* 1.3 75.3 - - - +
39F ASP* 1.3 66.3 + - - +
40F ASP* 4.0 26.7 + - - +
41F VAL* 2.9 37.0 + - + +
42F ALA* 3.1 10.0 + - - +
44F GLN* 5.7 1.8 - - - +
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Residues in contact with ASP 39 (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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69A ASP* 4.5 4.2 - - - +
71A ASN* 3.6 6.6 + - - +
329A TYR* 3.5 22.5 + - - +
333A ARG* 3.0 51.1 + - - +
17B ARG 5.7 0.5 - - - +
37F MET 3.2 3.4 + - - +
38F ARG* 1.3 70.9 - - - +
40F ASP* 1.3 62.3 + - - +
42F ALA 3.3 1.4 + - - -
43F PHE 2.9 22.9 + - - -
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Residues in contact with ASP 40 (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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71A ASN* 2.9 29.6 + - - +
38F ARG* 3.1 22.3 + - - +
39F ASP* 1.3 76.7 - - - +
41F VAL* 1.3 60.0 + - - +
43F PHE* 3.7 5.8 - - + +
44F GLN* 3.0 44.0 + - - +
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Residues in contact with VAL 41 (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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18F PHE* 3.9 42.0 - - + -
22F SER* 5.4 1.8 - - - +
37F MET* 4.0 12.6 - - + -
38F ARG* 2.9 36.6 + - + +
40F ASP* 1.3 77.3 - - - +
42F ALA* 1.3 67.3 + - - +
44F GLN* 3.2 7.6 + - - +
45F ILE* 2.8 35.6 + - + +
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Residues in contact with ALA 42 (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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329A TYR* 4.2 8.5 - - + -
332A LEU* 4.1 11.9 - - + -
333A ARG* 3.9 29.2 - - + +
37F MET* 3.7 22.4 - - - -
38F ARG 3.1 6.3 + - - +
39F ASP 3.7 7.0 - - - +
41F VAL* 1.3 78.9 - - - +
43F PHE* 1.3 63.2 + - - +
45F ILE* 3.7 1.4 - - - +
46F ILE* 3.1 29.6 + - - +
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Residues in contact with PHE 43 (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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71A ASN* 3.8 31.4 - - + +
74A LYS* 3.7 46.4 - - + -
75A LEU* 3.5 33.7 - - + -
78A LEU* 4.5 4.0 - - + -
329A TYR* 3.9 6.8 - - - -
39F ASP 2.9 16.9 + - - +
40F ASP* 3.7 6.7 - - + +
41F VAL 3.2 0.2 - - - -
42F ALA* 1.3 76.8 - - - +
44F GLN* 1.3 71.3 + - + +
46F ILE* 3.1 3.8 + - - +
47F ASN* 2.8 54.7 + - + +
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Residues in contact with GLN 44 (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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67E TRP* 3.7 28.0 - - + -
68E ASP 5.0 1.7 - - - +
69E ASP* 5.8 1.9 - - - -
17F ARG* 4.7 0.2 - - - -
18F PHE* 4.0 26.5 - - + -
38F ARG* 5.7 1.6 - - - +
40F ASP* 3.0 34.8 + - - +
41F VAL* 3.2 5.9 + - - +
43F PHE* 1.3 89.3 - - + +
45F ILE* 1.3 63.8 + - - +
47F ASN* 3.6 6.4 - - + +
48F ASP* 2.8 36.3 + - - +
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Residues in contact with ILE 45 (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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332A LEU* 4.3 9.2 - - + -
432E ASP* 5.7 0.7 - - - +
433E PHE* 5.4 0.2 - - - -
17F ARG* 4.2 17.7 + - - +
18F PHE* 3.8 15.9 - - + -
22F SER* 4.3 16.4 - - - +
23F ILE* 4.7 7.9 - - + +
25F THR* 3.6 28.7 - - + -
37F MET* 4.0 20.9 - - + -
41F VAL* 2.8 35.5 + - + +
42F ALA 3.7 4.7 - - - +
44F GLN* 1.3 77.6 - - - +
46F ILE* 1.3 64.6 + - + +
48F ASP* 3.5 2.6 + - - +
49F GLU* 3.1 28.9 + - + +
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Residues in contact with ILE 46 (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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75A LEU* 4.1 7.0 - - + -
96A ILE* 4.3 10.8 - - + -
325A ILE* 3.7 28.9 - - + +
328A TYR* 3.7 28.0 - - + -
329A TYR* 3.4 39.9 - - + +
332A LEU* 4.0 12.1 - - + -
42F ALA 3.1 19.4 + - - +
43F PHE 3.9 2.0 - - - +
45F ILE* 1.3 75.8 - - + +
47F ASN* 1.3 66.8 + - - +
49F GLU* 2.9 18.5 + - + +
50F LEU* 2.9 21.8 + - + +
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Residues in contact with ASN 47 (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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75A LEU* 4.6 2.6 - - - +
78A LEU* 3.3 28.5 - - + +
57E ARG* 5.7 0.4 - - - +
68E ASP* 6.2 1.8 - - - +
43F PHE* 2.8 43.1 + - + +
44F GLN* 3.6 7.2 + - - +
46F ILE* 1.3 77.9 - - - +
48F ASP* 1.3 67.8 + - - +
50F LEU* 3.3 20.1 + - - +
51F TYR* 3.3 33.0 + - - -
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Residues in contact with ASP 48 (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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57E ARG* 2.9 26.0 + - - +
67E TRP* 2.9 30.4 + - - -
68E ASP 5.5 0.7 - - - +
428E GLY 5.9 1.3 - - - +
433E PHE* 3.8 18.6 - - + -
17F ARG* 2.8 35.0 + - - +
44F GLN* 2.8 22.9 + - - +
45F ILE 3.9 0.7 - - - +
47F ASN* 1.3 80.7 + - - +
49F GLU* 1.3 64.3 + - - +
51F TYR* 3.3 22.8 + - - +
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Residues in contact with GLU 49 (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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92A GLN* 3.0 42.5 + - + +
96A ILE* 3.5 14.0 - - + +
99A ARG* 2.8 24.2 + - - -
328A TYR* 5.1 1.8 - - - -
432E ASP* 4.8 4.7 - - - +
433E PHE* 4.1 17.9 - - + -
25F THR* 2.8 35.5 + - - +
45F ILE* 3.1 21.9 + - + +
46F ILE* 2.9 10.3 + - - +
48F ASP* 1.3 77.6 - - - +
50F LEU* 1.3 57.7 + - - +
51F TYR 3.1 0.2 - - - -
52F LEU* 2.9 21.9 + - + +
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Residues in contact with LEU 50 (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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75A LEU* 4.4 11.0 - - + -
78A LEU* 4.8 10.1 - - + -
79A SER* 4.4 4.7 - - - +
82A LYS* 3.5 21.5 + - - +
92A GLN* 4.6 1.8 - - - -
93A SER* 3.9 5.2 - - - +
96A ILE* 4.0 18.6 - - + -
325A ILE* 3.8 40.8 - - + -
46F ILE* 2.9 22.2 + - + +
47F ASN* 3.6 11.2 - - - +
48F ASP 3.2 0.8 - - - -
49F GLU* 1.3 76.9 - - - +
51F TYR* 1.3 60.0 + - - +
52F LEU 3.1 0.2 - - - -
53F ASP* 3.1 40.8 + - - +
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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