Contacts of the strand formed by residues 46 - 52 (chain F) in PDB entry 2PGW
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 VAL 46 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F ARG* 4.2 9.6 - - - +
38F GLU* 4.0 22.0 - - + -
39F ILE 3.3 9.0 - - - +
40F GLU* 3.8 19.5 - - + +
44F GLY 3.4 16.1 + - - +
45F THR* 1.3 77.3 - - - +
47F GLY* 1.3 72.9 + - - +
48F ILE* 4.1 12.3 - - + +
116F LEU* 4.4 1.1 - - - -
119F LYS* 2.8 32.1 + - - +
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Residues in contact with GLY 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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37F ILE 3.8 0.7 - - - +
38F GLU* 3.4 3.8 - - - -
39F ILE* 2.7 37.3 + - - -
46F VAL* 1.3 74.5 - - - +
48F ILE* 1.3 61.5 + - - +
112F ALA* 3.4 23.2 - - - +
115F ASP* 3.4 7.4 - - - -
116F LEU* 3.8 14.6 - - - +
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Residues in contact with ILE 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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36F LEU* 5.0 4.3 - - + -
37F ILE 3.5 5.6 - - - +
38F GLU* 4.3 20.0 - - + +
46F VAL* 4.1 18.2 - - + +
47F GLY* 1.3 79.8 - - - +
49F GLY* 1.3 66.3 + - - +
112F ALA* 3.7 8.1 - - - -
115F ASP* 2.8 12.4 + - - +
119F LYS* 4.6 7.9 - - - +
305F ILE* 3.9 25.3 - - + +
356F LEU* 3.7 14.9 - - - +
358F PHE* 3.6 28.0 - - + -
360F LEU* 3.7 28.9 - - + -
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Residues in contact with GLY 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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36F LEU* 3.5 3.8 - - - +
37F ILE* 2.9 33.9 + - - -
48F ILE* 1.3 80.0 - - - +
50F GLU* 1.3 63.1 + - - +
108F GLY 3.8 16.2 - - - -
111F MSE 4.0 8.5 - - - -
112F ALA* 3.6 1.6 - - - +
305F ILE* 3.9 9.9 - - - -
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Residues in contact with GLU 50 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34F VAL* 3.9 8.4 - - + +
35F ASN 3.4 8.1 - - - +
36F LEU* 3.8 19.7 - - + +
37F ILE* 4.3 1.3 - - - -
49F GLY* 1.3 74.4 - - - +
51F CYS* 1.3 60.0 + - - +
107F SER* 4.9 1.2 + - - -
108F GLY* 3.3 20.4 + - - -
111F MSE 3.8 14.2 - - - +
302F THR* 3.2 8.5 - - + +
303F THR* 2.8 52.4 + - - +
305F ILE* 3.5 14.9 - - + +
306F THR* 2.5 36.5 + - - +
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Residues in contact with CYS 51 (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 VAL* 3.5 8.6 - - - +
35F ASN* 3.0 34.6 + - + +
37F ILE* 5.0 0.2 - - - -
50F GLU* 1.3 73.7 - - - +
52F THR* 1.3 69.9 + - - +
53F VAL* 4.0 0.2 - - - +
64F LEU* 3.8 28.3 - - + -
104F GLN 3.7 11.7 - - - +
105F ILE* 3.1 37.5 - - + -
107F SER* 5.8 0.4 - - - -
108F GLY* 3.6 16.2 - - - -
302F THR* 5.1 3.6 - - - -
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Residues in contact with THR 52 (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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94B HIS 5.6 2.0 - - - +
33F ALA 4.8 4.7 - - - -
35F ASN* 4.7 0.9 + - - -
51F CYS* 1.3 85.3 - - - +
53F VAL* 1.3 61.3 + - - +
54F ALA* 5.0 2.0 - - - -
60F THR* 4.4 3.8 + - - -
104F GLN* 3.2 39.8 + - - +
105F ILE* 5.1 0.9 - - - +
273F ARG* 3.5 41.5 + - + +
300F SER* 4.0 6.1 - - - +
301F PHE* 4.8 5.6 - - + +
302F THR* 3.7 25.6 - - + -
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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