Contacts of the helix formed by residues 20 - 29 (chain E) in PDB entry 4O9U
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 VAL 20 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17E VAL* 4.5 2.5 - - + -
19E LEU* 1.3 75.9 - - - +
21E PRO* 1.4 69.1 - - + +
22E GLU* 3.0 10.7 + - + +
23E VAL* 3.2 19.1 + - + +
24E VAL* 2.9 27.5 + - - +
46E HIS* 3.7 28.3 - - + +
51E TYR* 3.5 4.0 - - - -
323E SER* 4.0 13.7 - - - -
324E GLU* 4.0 36.8 - - + +
327E ALA* 3.7 17.8 - - + +
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Residues in contact with PRO 21 (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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20E VAL* 1.4 88.3 - - + +
22E GLU* 1.3 56.1 + - - +
24E VAL* 4.1 2.2 - - + -
25E ALA* 2.9 28.6 + - - +
46E HIS* 3.6 24.2 - - + +
50E ALA* 3.2 48.9 - - + +
51E TYR* 3.4 30.9 - - + -
54E ALA* 3.3 8.3 - - + +
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Residues in contact with GLU 22 (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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20E VAL* 3.0 9.7 + - + +
21E PRO* 1.3 77.9 - - - +
23E VAL* 1.3 72.8 + - - +
25E ALA* 3.1 19.8 + - + +
26E ARG* 3.2 31.9 + - - +
46E HIS* 6.5 0.9 - - + -
324E GLU* 5.7 6.6 - - + +
328E LYS* 3.7 24.6 + - - -
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Residues in contact with VAL 23 (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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19E LEU* 4.2 7.2 - - + -
20E VAL* 3.2 10.7 + - + +
22E GLU* 1.3 83.2 - - - +
24E VAL* 1.3 65.2 + - - +
26E ARG* 3.3 9.0 + - - +
27E LEU* 3.2 30.6 + - + +
324E GLU* 5.0 1.3 - - + +
327E ALA* 3.6 40.4 - - + +
328E LYS* 3.6 29.8 - - + +
331E TYR* 3.7 23.0 - - + -
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Residues in contact with VAL 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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6E VAL* 5.2 0.7 - - + -
19E LEU* 3.8 25.8 - - + -
20E VAL 2.9 22.8 + - - +
21E PRO* 3.8 5.8 - - + +
23E VAL* 1.3 77.6 - - - +
25E ALA* 1.3 62.5 + - - +
27E LEU* 3.2 8.7 + - - +
28E VAL* 3.2 25.6 + - + +
34E VAL* 4.0 22.2 - - + -
51E TYR* 4.0 13.7 - - + +
54E ALA* 3.8 13.7 - - + -
56E ALA* 3.8 28.3 - - + -
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Residues in contact with ALA 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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21E PRO 2.9 19.8 + - - +
22E GLU* 3.1 10.5 + - + +
24E VAL* 1.3 77.6 - - - +
26E ARG* 1.3 55.7 + - - +
28E VAL* 3.8 2.9 + - - +
29E LYS* 3.0 42.3 + - - +
54E ALA* 3.8 24.0 - - + +
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Residues in contact with ARG 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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359B GLU* 4.9 15.4 + - - -
22E GLU* 3.2 30.5 + - - +
23E VAL* 3.3 9.1 + - - +
24E VAL 3.3 0.4 - - - -
25E ALA* 1.3 77.0 - - - +
27E LEU* 1.3 60.0 + - - +
29E LYS* 3.4 21.8 - - + +
30E GLY* 2.8 20.3 + - - -
328E LYS* 3.1 31.2 - - - +
331E TYR* 3.6 45.3 + - + +
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Residues in contact with LEU 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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4E VAL* 5.3 7.4 - - + -
19E LEU* 4.8 17.7 - - + -
23E VAL* 3.2 26.7 + - + +
24E VAL* 3.2 8.0 + - - +
26E ARG* 1.3 75.3 - - - +
28E VAL* 1.3 60.2 + - - +
29E LYS 3.2 0.9 - - - -
30E GLY* 3.0 5.2 + - - +
31E GLY 2.8 21.1 + - - -
32E ALA* 3.2 14.0 + - + +
34E VAL* 4.8 9.2 - - + -
72E PHE* 5.4 3.8 - - + -
331E TYR* 3.6 33.7 - - + -
334E SER* 3.7 17.7 - - - +
338E ILE* 3.7 28.4 - - + +
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Residues in contact with VAL 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 VAL* 3.2 17.1 + - + +
25E ALA 4.2 0.7 - - - +
27E LEU* 1.3 72.9 - - - +
29E LYS* 1.3 60.2 + - - +
30E GLY 3.2 0.4 - - - -
31E GLY* 3.4 11.1 + - - -
32E ALA 3.6 24.2 - - - +
33E ARG* 5.7 5.6 - - - +
34E VAL* 3.8 17.5 - - + +
54E ALA 4.1 10.5 - - - +
55E GLY* 3.8 35.9 - - - +
56E ALA 4.4 0.7 - - - +
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Residues in contact with LYS 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 ALA* 3.0 36.7 + - - +
26E ARG* 3.4 26.7 - - + +
27E LEU 3.2 0.2 - - - -
28E VAL* 1.3 76.5 - - - +
30E GLY* 1.3 60.6 + - - +
31E GLY* 4.8 0.2 - - - -
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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