Contacts of the helix formed by residues 24 - 29 (chain I) in PDB entry 3EO1
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 PHE 24 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22I ILE 3.7 1.4 + - - -
23I ASP* 1.3 74.6 + - - +
25I ARG* 1.3 67.0 + - + +
28I LEU* 2.8 30.2 + - + +
29I GLY 3.1 5.4 + - - -
30I TRP* 3.5 44.5 + + + +
33I VAL* 3.6 30.3 - - + -
36I PRO* 3.3 41.5 - - + -
37I LYS 3.0 7.6 + - - +
38I GLY 3.7 9.6 - - - -
39I TYR* 3.5 37.7 - + - -
86I LEU* 3.9 18.4 - - + -
88I ILE* 4.8 3.8 - - + -
101I LEU* 5.9 0.7 - - + -
104I MET* 4.7 2.2 - - + -
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Residues in contact with ARG 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I ASP* 2.7 12.7 + - - +
24I PHE* 1.3 72.2 - - + +
26I GLN* 1.3 71.7 + - - +
29I GLY* 2.8 30.8 + - - +
30I TRP 4.1 8.3 - - - +
31I LYS* 3.8 50.1 + - - +
33I VAL 5.4 5.3 + - - -
37I LYS* 5.1 12.3 - - + +
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Residues in contact with GLN 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I ASP* 2.8 29.1 + - + +
25I ARG* 1.3 85.0 - - - +
27I ASP* 1.3 65.7 + - - +
68L LEU* 6.0 0.9 - - - +
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Residues in contact with ASP 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I TYR* 4.0 5.2 - - - +
22I ILE* 3.5 20.4 - - + -
23I ASP* 2.6 44.9 + - - +
26I GLN* 1.3 83.6 - - - +
28I LEU* 1.3 68.1 + - + +
29I GLY 3.8 0.2 - - - -
64L LEU* 4.8 6.2 - - - +
65L TYR* 4.4 25.6 - - + -
68L LEU* 4.7 14.9 - - - +
69L ASN* 5.3 4.2 + - - +
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Residues in contact with LEU 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H SER 4.3 0.9 - - - +
31H SER* 3.1 12.4 + - - -
22I ILE* 3.9 24.0 - - + -
23I ASP 4.3 0.2 - - - +
24I PHE* 2.8 21.2 + - + +
27I ASP* 1.3 90.6 - - + +
29I GLY* 1.3 60.7 + - - +
30I TRP* 2.9 68.4 + - + +
39I TYR* 5.1 1.3 - - + -
61L VAL* 3.9 28.3 - - + +
64L LEU* 4.2 25.6 - - + +
65L TYR* 5.1 3.8 - - + -
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Residues in contact with GLY 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H SER* 3.3 14.0 - - - +
24I PHE 3.1 0.2 + - - -
25I ARG* 2.8 20.5 + - - -
26I GLN 4.8 0.2 - - - -
27I ASP 3.8 0.2 - - - -
28I LEU* 1.3 77.4 - - - +
30I TRP* 1.3 59.2 + - - +
31I LYS* 2.8 38.1 + - - +
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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