Contacts of the helix formed by residues 23 - 28 (chain E) in PDB entry 4QAE
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 GLN 23 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E ASN* 2.8 39.4 + - - +
22E PHE* 1.3 79.8 + - - +
24E ASP* 1.3 67.5 + - - +
25E ASN* 3.1 11.3 + - - +
26E GLN* 2.9 45.0 + - + +
27E PHE* 3.2 9.5 + - - +
115E TYR* 2.9 27.2 + - + +
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Residues in contact with ASP 24 (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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22E PHE* 3.5 20.4 + - + -
23E GLN* 1.3 72.4 - - - +
25E ASN* 1.3 76.8 + - - +
27E PHE 3.4 6.2 + - - -
28E HIS* 3.5 4.9 + - - +
58E LEU* 3.8 13.5 - - + +
62E LYS* 2.9 48.3 + - - +
64E TYR* 2.5 40.5 + - + +
92E PHE* 5.5 2.7 - - + -
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Residues in contact with ASN 25 (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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23E GLN* 4.2 12.9 + - - +
24E ASP* 1.3 89.7 + - - +
26E GLN* 1.3 71.2 + - - +
28E HIS* 2.8 30.0 + - + +
58E LEU* 3.8 17.7 - - + -
62E LYS* 4.9 5.9 - - - +
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Residues in contact with GLN 26 (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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23E GLN* 2.9 35.6 + - + +
25E ASN* 1.3 87.9 + - - +
27E PHE* 1.3 60.0 + - - +
28E HIS* 3.3 5.6 - - - +
115E TYR* 3.5 43.7 - - + +
140E ARG* 3.2 18.0 + - - -
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Residues in contact with PHE 27 (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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22E PHE* 3.5 31.0 - + + -
23E GLN 3.2 4.7 + - - +
24E ASP 3.4 0.6 + - - -
26E GLN* 1.3 76.1 - - - +
28E HIS* 1.3 64.1 + - - +
31E TRP* 2.9 51.9 + + - -
56E TYR* 3.9 35.2 - + - +
64E TYR* 3.5 18.8 - + - +
110E VAL* 4.1 16.6 - - + -
113E THR* 3.8 16.6 - - + -
115E TYR* 3.9 2.7 - + + -
119E ALA* 3.6 32.1 - - + -
121E VAL* 3.9 16.2 - - + -
138E TYR* 4.1 2.9 - + - -
140E ARG* 3.7 2.2 - - - +
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Residues in contact with HIS 28 (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 ASP 3.5 9.8 + - - +
25E ASN* 2.8 36.0 + - + -
26E GLN* 3.3 3.5 - - - +
27E PHE* 1.3 79.6 - - - +
29E GLY* 1.3 66.7 + - - +
56E TYR* 3.5 18.6 - - - +
57E GLU* 5.1 0.2 - - - -
58E LEU* 4.4 13.4 - - + +
64E TYR* 4.2 7.6 - - + -
140E ARG* 2.9 23.0 + - - -
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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