Contacts of the helix formed by residues 73 - 78 (chain E) in PDB entry 1FV1
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 ALA 73 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69E GLU 3.2 7.9 + - - +
70E ASP* 2.8 12.0 + - - +
72E ARG* 1.3 78.4 - - - +
74E ALA* 1.3 58.0 + - - +
75E VAL* 3.3 4.0 - - - -
76E ASP* 3.0 11.1 + - + +
77E THR* 2.8 44.6 + - + +
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Residues in contact with ALA 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E PHE* 3.7 33.7 - - + -
70E ASP* 3.3 6.7 + - - +
71E ARG* 3.5 18.2 - - - +
72E ARG 3.4 1.0 - - - -
73E ALA* 1.3 71.5 - - - +
75E VAL* 1.3 62.8 + - - +
76E ASP 2.9 5.2 - - - -
77E THR* 3.4 9.2 - - - -
78E TYR* 2.7 33.5 + - + +
79E CYS* 2.9 8.6 + - - -
95F ILE* 4.2 7.2 - - + -
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Residues in contact with VAL 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E VAL* 3.9 17.1 - - + +
26E PHE* 3.5 28.7 - - + +
42E SER* 3.6 19.5 - - - +
71E ARG 4.9 0.6 + - - +
72E ARG 3.8 19.1 - - - +
73E ALA 4.4 0.7 - - - -
74E ALA* 1.3 78.1 - - - +
76E ASP* 1.3 74.0 + - - +
79E CYS* 3.3 13.7 - - - +
80E ARG* 3.1 38.4 + - - +
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Residues in contact with ASP 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E ALA* 3.0 10.5 + - + +
74E ALA 2.8 1.4 + - - -
75E VAL* 1.3 86.6 - - - +
77E THR* 1.3 67.7 + - + +
78E TYR 3.2 1.8 + - - -
80E ARG* 2.8 41.9 + - - +
81E HIS* 3.4 21.1 + - - +
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Residues in contact with THR 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E ASP* 4.9 5.4 + - - -
73E ALA* 2.8 43.2 + - + +
74E ALA* 3.4 4.7 + - - -
76E ASP* 1.3 75.5 - - + +
78E TYR* 1.3 59.3 + - - +
81E HIS* 3.4 19.1 - - - +
93F LYS* 4.3 12.3 + - - +
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Residues in contact with TYR 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ILE* 5.5 2.1 + - + +
9D GLN* 2.8 45.0 + - - +
24D PHE* 3.8 5.4 - + - -
13E TYR* 3.6 11.1 + - + +
15E CYS* 3.3 33.4 - - - -
26E PHE* 3.6 23.1 - + - -
74E ALA* 2.7 19.3 + - - +
77E THR* 1.3 76.2 + - - +
79E CYS* 1.3 64.0 + - - +
80E ARG 3.6 0.2 - - - -
81E HIS* 3.4 1.4 + - - +
82E ASN* 3.0 41.7 + - - +
93F LYS* 2.9 36.6 - - + -
94F ASN 4.3 0.7 - - - -
95F ILE* 3.5 33.0 - - + -
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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