Contacts of the helix formed by residues 25 - 33 (chain J) in PDB entry 5U07
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 PRO 25 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24J GLU* 1.4 82.5 - - + +
26J ALA* 1.3 74.0 + - + +
27J ALA 3.4 0.4 - - - -
28J ARG* 3.5 3.9 + - + +
29J ALA* 3.1 28.8 + - - +
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Residues in contact with ALA 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F LEU* 5.6 1.6 - - - +
25J PRO* 1.3 87.0 - - + +
27J ALA* 1.3 58.6 + - - +
29J ALA* 3.5 4.9 + - - +
30J ALA* 2.9 28.9 + - - +
49J ARG* 5.3 3.1 - - - +
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Residues in contact with ALA 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J LEU* 4.5 7.9 - - + +
24J GLU* 4.0 19.4 - - + +
25J PRO 3.4 1.4 - - - -
26J ALA* 1.3 75.8 - - - +
28J ARG* 1.3 59.8 + - - +
30J ALA* 3.2 3.6 + - - +
31J LEU* 2.9 35.5 + - + +
49J ARG* 4.1 22.8 - - - +
50J VAL* 4.5 16.9 - - + +
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Residues in contact with ARG 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J LEU 5.2 0.6 + - - -
21J ILE* 4.3 16.6 - - + +
24J GLU 3.2 24.0 + - - +
25J PRO* 3.6 6.1 - - + +
27J ALA* 1.3 79.3 - - - +
29J ALA* 1.3 57.3 + - - +
31J LEU* 3.1 24.8 - - - +
32J ARG* 3.1 22.1 + - - +
89J ALA* 4.6 7.4 - - - +
96J ARG* 5.3 6.7 - - - +
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Residues in contact with ALA 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ASP* 3.8 10.1 - - + +
22F LEU* 5.2 4.5 - - + -
25J PRO 3.1 17.4 + - - +
26J ALA* 3.9 5.2 - - - +
28J ARG* 1.3 77.9 - - - +
30J ALA* 1.3 57.7 + - - +
32J ARG* 3.3 22.2 - - - +
33J ARG* 3.0 23.6 - - - +
27K C 6.1 2.9 - - - +
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Residues in contact with ALA 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F LEU* 4.4 11.2 - - + +
26J ALA 2.9 19.2 + - - +
27J ALA* 3.2 7.2 + - - +
29J ALA* 1.3 78.6 - - - +
31J LEU* 1.3 57.3 + - - +
33J ARG* 3.3 21.5 + - - +
34J GLY 5.2 0.3 + - - -
43J ARG 5.3 0.9 - - - +
44J MET* 5.3 1.4 - - - +
46J ALA* 4.0 36.8 - - + +
47J ALA* 4.1 5.7 + - - +
49J ARG* 5.3 4.9 - - - +
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Residues in contact with LEU 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J VAL* 3.9 28.0 - - + -
21J ILE* 5.8 2.9 - - + -
27J ALA* 2.9 28.8 + - + +
28J ARG* 3.1 27.8 - - - +
30J ALA* 1.3 75.0 - - - +
32J ARG* 1.3 64.1 + - - +
33J ARG 3.2 3.5 + - - -
34J GLY* 3.4 6.6 + - - -
47J ALA* 4.0 24.4 - - + +
50J VAL* 4.8 12.1 - - + -
51J VAL* 4.6 17.0 - - + -
85J ALA* 4.2 8.3 - - + +
86J ALA* 3.4 20.9 - - + +
89J ALA* 3.4 25.1 - - + -
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Residues in contact with ARG 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ASP* 5.3 2.0 - - - +
220G HIS* 3.2 39.1 + - - -
28J ARG 3.1 12.3 + - - +
29J ALA* 3.3 30.8 - - - +
31J LEU* 1.3 74.8 - - - +
33J ARG* 1.3 61.3 + - + +
34J GLY 3.0 10.4 + - - -
35J VAL* 3.7 19.3 + - - +
86J ALA 4.2 11.0 - - - -
89J ALA 4.1 5.6 + - - +
90J ALA* 3.8 44.0 + - + +
91J GLN 5.3 3.4 + - - -
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Residues in contact with ARG 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ASP* 4.4 15.4 + - - +
21F ASP* 2.7 39.6 + - - +
22F LEU* 3.5 34.6 - - - +
24F SER* 5.1 3.4 + - - -
201G VAL* 5.6 5.2 - - - +
29J ALA 3.0 20.0 - - - +
30J ALA 3.3 15.7 - - - +
31J LEU 3.2 0.2 - - - -
32J ARG* 1.3 75.3 - - - +
34J GLY* 1.3 55.5 + - - +
35J VAL* 3.7 2.0 - - - -
37J LEU* 4.1 12.8 - - - +
43J ARG* 2.5 50.7 + - - +
44J MET* 6.4 0.2 - - - -
46J ALA* 4.9 4.4 - - - +
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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