Contacts of the helix formed by residues 55 - 60 (chain E) in PDB entry 2FIF
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 THR 55 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B TRP* 3.7 9.4 - - + -
36B SER* 3.7 19.5 - - - -
19E PRO 3.7 8.1 - - - -
20E SER 3.3 19.5 - - - +
21E ASP 3.2 10.3 - - - +
22E THR* 4.4 5.6 - - - -
23E ILE* 4.6 2.0 - - - -
53E GLY 5.3 1.6 - - - +
54E ARG* 1.3 77.5 - - - +
56E LEU* 1.3 65.5 + - - +
57E SER* 2.9 22.2 + - - -
58E ASP* 2.8 37.4 + - - +
59E TYR* 3.4 10.3 - - - -
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Residues in contact with LEU 56 (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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1E MET* 4.1 3.6 - - + -
3E ILE* 4.3 8.3 - - + -
17E VAL* 3.6 29.4 - - + -
18E GLU 3.5 19.7 - - - +
19E PRO* 3.6 10.3 - - + +
21E ASP* 3.1 13.0 + - + +
23E ILE* 3.8 21.7 - - + +
26E VAL* 3.8 24.0 - - + -
55E THR* 1.3 69.8 - - - +
57E SER* 1.3 58.5 + - - +
59E TYR* 2.9 21.4 + - - +
61E ILE* 3.2 54.3 + - + +
67E LEU* 4.8 3.8 - - + -
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Residues in contact with SER 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TYR* 3.5 15.8 - - - +
27B GLY 4.5 3.7 - - - +
28B ASN* 3.2 35.0 + - - +
31B TRP* 3.5 8.5 - - - -
19E PRO* 2.9 26.4 + - - +
55E THR* 2.9 20.4 + - - -
56E LEU* 1.3 74.9 - - - +
58E ASP* 1.3 61.3 + - - +
60E ASN* 3.2 14.9 + - - +
61E ILE 4.8 3.1 - - - +
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Residues in contact with ASP 58 (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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25B TYR* 3.8 14.7 - - + +
26B TYR* 3.0 31.9 + - - +
35B CYS* 3.2 10.4 - - - +
36B SER* 2.5 45.3 + - - -
54E ARG* 3.2 26.4 - - - +
55E THR* 2.8 36.6 + - - +
57E SER* 1.3 78.7 + - - +
59E TYR* 1.3 61.4 + - + +
60E ASN 3.4 0.4 - - - -
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Residues in contact with TYR 59 (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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25B TYR* 4.0 19.5 + + - -
26B TYR* 4.0 8.4 - - - -
23E ILE* 4.1 13.0 - - + -
45E PHE* 3.4 20.3 - - + -
46E ALA* 5.5 1.0 - - - +
48E LYS* 5.4 9.9 - - + -
49E GLN 4.4 4.8 + - - -
50E LEU* 3.7 29.6 - - + -
51E GLU* 2.8 33.2 + - - +
54E ARG* 3.4 33.3 - - + +
55E THR 3.4 13.5 - - - -
56E LEU 2.9 7.5 + - - +
58E ASP* 1.3 80.3 - - + +
60E ASN* 1.3 70.4 + - - +
61E ILE* 3.1 17.9 + - + -
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Residues in contact with ASN 60 (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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15B SER* 4.1 15.7 + - - -
17B LEU* 5.7 6.1 - - - +
26B TYR* 3.6 36.0 - - + +
45E PHE* 4.5 6.9 - - + -
57E SER* 3.2 16.5 + - - +
58E ASP 3.4 1.0 + - - -
59E TYR* 1.3 79.3 - - - +
61E ILE* 1.3 58.7 + - - +
62E GLN* 2.9 41.2 + - - +
65E SER* 4.7 0.3 + - - -
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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