Contacts of the strand formed by residues 46 - 52 (chain A) in PDB entry 2FV7
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 LYS 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A VAL 3.7 0.5 - - - +
30A SER* 3.4 3.5 - - - -
31A LEU* 2.9 43.3 + - + +
44A GLY* 3.8 1.5 - - - -
45A HIS* 1.3 91.9 + - - +
47A PHE* 1.3 68.4 + - - +
48A PHE* 3.8 34.8 - - + +
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Residues in contact with PHE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 3.9 43.1 - - + -
29A VAL 3.1 13.5 - - - -
30A SER* 3.7 16.4 - - - +
46A LYS* 1.3 82.1 + - - +
48A PHE* 1.3 70.2 + - - +
49A ILE* 3.8 27.8 - - + -
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Residues in contact with PHE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASP 3.7 0.2 - - - +
28A LEU* 3.8 1.7 - - - -
29A VAL* 2.8 74.6 + - + +
31A LEU* 4.2 22.2 - - + -
46A LYS* 3.8 30.5 - - + +
47A PHE* 1.3 84.4 - - - +
49A ILE* 1.3 75.1 + - - +
50A GLY* 5.2 1.1 - - - -
512A UNX 4.4 14.6 - - - -
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Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR* 3.6 22.7 - - + -
27A ASP 3.2 2.5 - - - -
28A LEU* 4.0 10.8 - - + -
47A PHE* 3.8 22.9 - - + -
48A PHE* 1.3 85.1 - - - +
50A GLY* 1.3 65.8 + - - +
51A PHE* 4.9 16.0 - - + -
80A PHE* 4.3 24.7 - - + -
83A ASP* 5.5 7.6 - - + +
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Residues in contact with GLY 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR* 3.8 2.9 - - - -
27A ASP* 2.8 40.7 + - - +
48A PHE* 4.3 4.3 + - - -
49A ILE* 1.3 80.3 - - - +
51A PHE* 1.3 68.3 + - - -
512A UNX 4.6 13.0 - - - -
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Residues in contact with PHE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A MET 3.9 1.6 - - - -
26A THR* 5.3 4.7 - - + -
27A ASP* 3.8 4.4 - - - +
49A ILE* 4.9 14.8 - - + -
50A GLY* 1.3 80.0 - - - -
52A GLY* 1.3 58.4 + - - +
57A ASN* 4.1 0.7 - - - +
80A PHE 5.2 1.1 - - - -
83A ASP* 3.9 38.4 - - + -
84A TYR* 3.7 27.6 - + - +
87A ASN* 3.5 45.3 - - + +
306A GLY 5.5 0.7 - - - +
307A THR* 4.9 4.7 - - - +
308A GLN* 3.7 25.6 + - + +
508A UNX 4.4 13.0 - - - -
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Residues in contact with GLY 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A CYS* 3.7 1.6 - - - -
25A MET 2.7 29.4 + - - -
27A ASP* 3.6 14.6 + - - -
51A PHE* 1.3 73.2 - - - +
53A GLY* 1.3 63.8 + - - +
57A ASN* 3.8 11.9 - - - -
84A TYR* 2.5 23.8 + - - -
307A THR* 5.5 2.2 - - - -
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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