Contacts of the strand formed by residues 70 - 79 (chain F) in PDB entry 3OF6
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 TRP 70 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64E PRO* 4.0 18.3 - - + +
70E TRP* 3.3 37.1 - + - -
35F ASP 3.5 2.6 + - - -
36F VAL* 2.7 53.2 + - + +
37F ALA 4.2 1.3 - - - +
38F PRO* 3.8 36.4 - - + +
39F PRO* 4.9 5.4 - - + -
62F PRO* 3.5 29.8 - - + -
63F SER* 3.3 31.4 - - - -
64F PRO* 3.7 14.4 - - + +
65F ALA* 4.4 0.7 - - - -
68F GLY 4.0 9.4 + - - -
69F THR* 1.3 94.5 + - - +
71F THR* 1.3 70.7 + - - +
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Residues in contact with THR 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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174C SER* 5.8 0.5 - - - -
196C ARG* 3.2 29.0 + - - -
32F LEU* 3.9 11.4 - - - -
33F VAL 3.4 8.3 - - - -
34F LEU* 3.6 32.5 - - + -
35F ASP 4.4 1.6 - - - +
36F VAL* 3.7 2.2 - - - -
61F GLY 4.0 1.9 - - - +
62F PRO* 3.3 3.3 - - - +
63F SER* 3.0 30.3 + - - -
64F PRO 5.6 0.3 + - - -
65F ALA* 4.9 12.2 - - + +
69F THR* 5.0 2.0 - - - +
70F TRP* 1.3 84.5 - - - +
72F ASN* 1.3 60.9 + - - +
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Residues in contact with ASN 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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32F LEU* 3.3 5.1 - - - +
33F VAL* 3.1 47.4 + - + +
36F VAL* 3.9 6.3 - - + +
42F ASP* 3.7 16.5 + - - +
43F SER 2.9 24.5 + - - +
44F PRO* 4.2 5.5 - - - +
45F ILE* 3.5 10.7 - - - +
59F THR* 4.8 5.8 - - - +
61F GLY* 3.1 24.2 + - - -
62F PRO* 3.8 19.6 - - + +
71F THR* 1.3 73.3 - - - +
73F LEU* 1.3 71.3 + - - +
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Residues in contact with LEU 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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147C VAL* 3.5 31.6 - - + -
149C LEU* 3.9 7.2 - - + -
194C SER* 3.5 27.6 - - - +
196C ARG* 4.1 14.6 - - - +
30F VAL* 3.5 19.1 - - + -
31F CYS 3.4 15.9 - - - +
32F LEU* 3.6 25.8 - - + -
45F ILE* 3.8 2.8 - - - +
59F THR* 3.5 2.1 - - - -
60F TYR* 2.9 35.3 + - + -
61F GLY 4.3 3.4 + - - +
71F THR 4.3 0.8 + - - -
72F ASN* 1.3 84.0 + - - +
74F ALA* 1.3 70.9 + - - +
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Residues in contact with ALA 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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30F VAL* 3.2 5.0 - - - +
31F CYS 2.8 30.8 + - - -
45F ILE* 3.7 33.2 - - + +
47F PHE* 3.6 9.8 - - + -
57F ALA* 5.1 0.9 - - + -
58F PHE 3.6 8.3 - - - +
59F THR* 3.8 16.2 - - + -
60F TYR* 4.2 3.4 - - - -
73F LEU* 1.3 81.8 - - - +
75F HIS* 1.3 61.4 + - - +
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Residues in contact with HIS 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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149C LEU* 3.9 21.8 - - + -
151C THR* 4.8 11.0 - - + +
192C CYS* 5.7 0.4 - - + -
28F VAL* 4.7 10.1 - - + -
29F VAL 3.2 12.6 - - - +
30F VAL* 4.1 2.5 - - + +
47F PHE* 4.4 2.7 - - - -
57F ALA* 3.4 19.9 - - - +
58F PHE* 3.4 45.2 + + + +
60F TYR* 3.0 35.1 + - + -
74F ALA* 1.3 74.6 - - - +
76F LEU* 1.3 69.6 + - - +
77F SER* 4.5 8.3 - - - -
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Residues in contact with LEU 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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27F MET* 3.6 2.1 - - - +
28F VAL* 3.2 8.5 - - - +
29F VAL* 2.8 43.6 + - + +
47F PHE* 3.9 29.2 - - + -
55F LEU* 3.7 36.1 - - + -
56F ASP 3.4 26.2 - - - +
57F ALA* 4.6 2.9 - - + +
75F HIS* 1.3 76.2 - - - +
77F SER* 1.3 72.8 + - - +
78F LEU* 4.8 9.9 - - + -
89F LEU* 3.9 19.5 - - + -
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Residues in contact with SER 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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26F GLN* 2.8 35.4 + - - +
27F MET 3.7 2.9 - - - -
28F VAL* 4.2 9.1 - - - +
75F HIS* 4.4 10.0 - - - -
76F LEU* 1.3 83.3 - - - +
78F LEU* 1.3 64.6 + - - +
79F PRO* 4.4 1.4 - - - +
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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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26F GLN* 3.1 5.4 - - - +
27F MET* 2.7 54.4 + - + +
55F LEU* 4.4 22.0 - - + -
76F LEU* 4.8 12.1 - - + -
77F SER* 1.3 76.6 - - - +
79F PRO* 1.3 82.2 - - + +
82F GLU* 3.8 8.3 - - - +
83F LEU* 4.5 12.1 - - + -
86F TRP* 3.4 48.0 - - + +
89F LEU* 5.5 4.5 - - + -
109F LEU* 5.7 4.0 - - + -
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Residues in contact with PRO 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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24F LYS* 6.4 1.8 - - + -
25F GLN 4.2 1.1 - - - +
26F GLN* 3.1 25.3 - - - +
77F SER 4.4 1.8 - - - +
78F LEU* 1.3 102.3 - - + +
80F SER* 1.3 57.6 + - - +
81F GLU* 2.9 22.0 + - + +
82F GLU* 3.1 37.4 + - + +
83F LEU* 3.3 9.7 + - - +
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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