Contacts of the helix formed by residues 26 - 36 (chain E) in PDB entry 6D6U
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 ASP 26 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E GLY* 1.3 74.0 - - - +
27E VAL* 1.3 61.1 + - + +
28E THR 3.2 2.2 - - - -
29E VAL* 3.0 16.5 + - + +
30E ILE* 2.9 36.7 + - + +
93E ILE* 5.2 8.7 - - + -
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Residues in contact with VAL 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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30D LEU* 3.7 31.4 - - + -
34D LEU* 3.6 24.2 - - + -
25E GLY 3.4 3.0 - - - +
26E ASP* 1.3 78.4 - - + +
28E THR* 1.3 57.3 + - - +
30E ILE* 3.2 10.8 + - + +
31E LEU* 2.9 36.1 + - + +
93E ILE* 4.6 27.4 - - + -
96E LEU* 4.5 20.0 - - + -
98E LEU* 6.3 0.7 - - + -
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Residues in contact with THR 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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27D ASP* 2.7 40.2 + - + +
29D ARG* 5.2 1.6 - - - +
30D LEU* 4.1 9.6 - - - +
25E GLY* 3.8 12.9 + - - -
26E ASP 3.2 0.4 - - - -
27E VAL* 1.3 79.4 - - - +
29E VAL* 1.3 57.8 + - + +
31E LEU* 3.4 5.0 + - - +
32E ASN* 2.9 51.8 + - - +
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Residues in contact with VAL 29 (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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25E GLY 4.0 13.7 - - - +
26E ASP* 3.0 17.8 + - + +
28E THR* 1.3 79.8 - - + +
30E ILE* 1.3 63.7 + - + +
32E ASN* 3.3 7.3 + - - +
33E ASN* 2.9 45.6 + - - +
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Residues in contact with ILE 30 (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 ASP* 2.9 23.0 + - + +
27E VAL* 3.2 15.2 + - + +
29E VAL* 1.3 77.7 - - + +
31E LEU* 1.3 56.5 + - + +
33E ASN* 3.3 9.0 + - - +
34E LEU* 2.9 34.4 + - + +
89E PHE* 3.6 36.1 - - + -
90E ASN 5.8 0.4 - - - +
91E SER* 3.5 32.8 - - - +
93E ILE* 4.1 19.1 - - + -
96E LEU* 5.4 8.1 - - + -
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Residues in contact with LEU 31 (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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27D ASP* 4.5 1.6 - - - +
29D ARG* 3.4 41.1 - - - +
30D LEU* 4.0 21.8 - - + -
27E VAL* 2.9 23.4 + - + +
28E THR 3.8 3.8 - - - +
30E ILE* 1.3 76.1 - - + +
32E ASN* 1.3 63.5 + - - +
34E LEU* 3.1 14.8 + - + -
35E LEU* 3.0 37.3 + - + +
96E LEU* 3.8 25.6 - - + -
98E LEU* 4.5 19.5 - - + -
102E MET* 5.3 5.2 - - + -
133E ILE* 5.7 1.8 - - + -
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Residues in contact with ASN 32 (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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29D ARG* 4.4 12.2 + - - -
28E THR* 2.9 42.7 + - - +
29E VAL* 3.9 6.7 - - - +
31E LEU* 1.3 76.6 - - - +
33E ASN* 1.3 62.8 + - - +
35E LEU* 4.1 4.5 - - - +
36E GLU* 3.3 24.6 + - - +
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Residues in contact with ASN 33 (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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29E VAL* 2.9 42.5 + - - +
30E ILE* 3.6 8.1 - - - +
32E ASN* 1.3 77.3 - - - +
34E LEU* 1.3 66.9 + - + +
35E LEU 3.4 0.2 + - - -
36E GLU* 3.6 25.7 + - - +
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Residues in contact with LEU 34 (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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30E ILE* 2.9 25.0 + - + +
31E LEU* 3.1 21.1 + - + +
33E ASN* 1.3 79.7 - - + +
35E LEU* 1.3 70.9 + - + +
36E GLU 3.6 3.3 + - - +
38E TYR* 3.7 17.7 - - - +
86E ARG 4.1 9.7 - - - +
87E LEU* 4.0 36.7 - - + +
88E LYS 4.1 1.6 - - - +
89E PHE* 4.0 46.4 - - + +
96E LEU* 5.5 2.2 - - + -
133E ILE* 5.4 6.3 - - + -
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Residues in contact with LEU 35 (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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31E LEU* 3.0 27.8 + - + +
32E ASN* 3.6 4.7 + - - +
34E LEU* 1.3 85.1 - - + +
36E GLU* 1.3 63.9 + - - +
37E GLY 3.5 2.1 + - - -
38E TYR* 3.5 33.5 + - + +
40E ASN* 5.3 1.3 - - - +
102E MET* 3.5 32.8 - - + -
105E LYS* 4.1 24.2 - - + -
106E ILE* 5.1 5.4 - - + -
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Residues in contact with GLU 36 (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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32E ASN 3.3 18.3 + - - +
33E ASN* 3.8 21.8 - - - +
34E LEU 3.4 4.6 - - - +
35E LEU* 1.3 75.0 - - - +
37E GLY* 1.3 70.4 + - - +
38E TYR 3.4 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