Contacts of the strand formed by residues 49 - 55 (chain F) in PDB entry 6PI7
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 GLU 49 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E PHE* 5.0 0.2 - - - -
40F VAL* 3.9 3.5 - - - +
41F ARG* 2.8 79.6 + - + +
47F GLY 5.0 1.8 - - - +
48F LEU* 1.3 72.8 - - - +
50F TRP* 1.3 73.2 + - - +
51F VAL* 3.6 0.6 + - - -
64F ALA* 5.2 1.4 - - - +
66F SER* 3.2 25.8 + - - -
67F VAL* 5.5 0.2 - - - +
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Residues in contact with TRP 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E ASP* 4.9 4.7 - - + -
96E PRO* 3.5 35.7 - - + -
97E ILE* 3.8 50.9 + - + +
99E PHE* 4.4 6.4 - - + -
38F HIS* 3.6 6.4 + - + -
39F TRP 4.0 7.2 - - - -
40F VAL* 4.2 18.8 - - + +
48F LEU 4.3 0.4 - - - -
49F GLU* 1.3 82.5 - - - +
51F VAL* 1.3 61.1 + - - +
52F ALA* 3.3 15.6 + - - -
53F SER* 2.8 29.5 + - - -
62F SER* 3.1 39.5 - - - -
63F TYR 3.5 15.5 - - - -
64F ALA* 3.3 39.0 - - + +
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Residues in contact with VAL 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F TRP* 2.9 30.5 + - + +
40F VAL* 4.7 1.1 - - - +
41F ARG* 4.9 14.8 - - - +
49F GLU* 3.6 4.5 + - - +
50F TRP* 1.3 76.1 - - - +
52F ALA* 1.3 62.8 + - + +
63F TYR* 3.6 0.2 - - - -
64F ALA* 3.0 29.4 + - - -
67F VAL* 3.5 23.0 - - + +
71F PHE* 5.2 2.0 - - + -
84F LEU* 5.2 4.9 - - + -
97F TYR* 5.2 7.2 - - + -
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Residues in contact with ALA 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F HIS* 3.3 4.0 - - - -
39F TRP* 2.9 28.5 + - + -
50F TRP* 3.3 10.2 + - - -
51F VAL* 1.3 83.0 - - + +
53F SER* 1.3 62.2 + - - +
62F SER 3.2 14.6 - - - +
63F TYR* 3.8 20.9 - - + -
67F VAL* 5.4 0.9 - - + -
73F ILE* 4.2 15.3 - - + -
84F LEU* 4.5 12.6 - - + -
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Residues in contact with SER 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E ASP* 4.9 4.5 + - - -
97E ILE* 4.5 1.7 - - - +
36F TYR* 4.9 9.6 - - - -
37F ILE 3.3 6.7 - - - -
38F HIS* 2.7 34.6 + - - -
50F TRP* 2.8 23.6 + - - -
52F ALA* 1.3 69.6 - - - +
54F ILE* 1.3 59.5 + - - +
60F SER 4.6 0.2 - - - -
61F THR* 3.2 5.4 - - - -
62F SER* 3.0 34.5 + - - -
73F ILE* 3.4 12.1 - - - +
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Residues in contact with ILE 54 (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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35F TYR 3.7 1.2 - - - +
36F TYR* 3.3 9.0 - - - -
37F ILE* 2.9 52.8 + - + +
53F SER* 1.3 75.6 - - - +
55F TYR* 1.3 62.9 + - - +
56F PRO* 4.0 26.0 - - + -
59F GLY* 5.4 1.6 - - - -
60F SER 3.4 14.1 - - - +
61F THR* 3.8 14.1 - - + -
73F ILE* 4.1 20.6 - - + -
74F SER* 4.7 18.8 - - - +
75F ALA* 4.8 3.8 - - + +
82F ALA* 5.1 0.9 - - + -
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Residues in contact with TYR 55 (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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311D TYR* 5.0 1.7 + - - -
448D TRP 4.2 8.8 + - - -
34F TYR* 3.3 39.4 + - - +
35F TYR* 3.4 19.7 - - - -
36F TYR* 3.5 30.2 - + + -
54F ILE* 1.3 72.1 - - - +
56F PRO* 1.4 69.1 - - - +
57F TYR* 3.1 20.3 + + + -
58F TYR* 3.2 36.5 + + + -
59F GLY 3.1 15.4 + - - -
60F SER* 3.0 21.4 + - - +
104F TYR* 3.3 42.9 - + + +
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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
------------------------------------------------------------
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