Contacts of the helix formed by residues 22 - 33 (chain B) in PDB entry 1OUQ
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 GLU 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B SER* 3.9 5.4 + - - +
21B ASP* 1.3 72.7 - - + +
23B VAL* 1.3 57.4 + - + +
24B ARG 2.7 4.6 + - - -
25B LYS* 2.3 46.3 + - + +
26B ASN* 3.0 13.3 + - - +
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B SER* 3.8 30.1 - - - +
21B ASP 3.4 0.2 - - - -
22B GLU* 1.3 75.7 - - + +
24B ARG* 1.3 58.4 + - + +
25B LYS 3.2 0.2 - - - -
26B ASN* 4.5 1.8 - - - -
27B LEU* 3.2 27.4 + - + +
64B PHE* 4.1 21.5 - - + -
102B SER* 3.6 42.0 - - - +
103B GLY 5.4 1.1 - - - +
104B LEU* 4.3 22.0 - - + -
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Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B SER 3.3 31.4 + - - +
21B ASP* 3.3 17.2 + - - +
22B GLU 2.7 3.0 + - - -
23B VAL* 1.3 75.9 - - + +
25B LYS* 1.3 60.9 + - - +
27B LEU* 4.3 3.7 - - - +
28B MET* 3.0 31.7 + - - +
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Residues in contact with LYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ASP 3.7 2.6 + - - +
22B GLU* 2.3 37.7 + - + +
24B ARG* 1.3 65.4 - - - +
26B ASN* 1.3 60.6 + - - +
27B LEU 3.1 1.1 - - - -
28B MET* 2.5 29.0 + - + +
29B ASP* 2.7 35.4 + - - +
69E GLU* 5.1 9.6 + - - -
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Residues in contact with ASN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLU* 3.0 19.5 + - - +
23B VAL* 4.3 1.3 - - - +
25B LYS* 1.3 82.1 - - - +
27B LEU* 1.3 63.4 + - - +
29B ASP* 3.5 9.8 + - - +
30B MET* 3.0 26.3 + - - +
101B ARG 3.8 9.6 + - - +
102B SER* 3.5 37.9 + - - +
103B GLY* 3.8 8.5 - - - +
111E ASN* 4.9 13.9 + - - +
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B VAL* 3.2 16.7 + - + +
24B ARG* 4.3 4.7 - - - +
25B LYS 3.1 0.8 - - - -
26B ASN* 1.3 78.6 - - - +
28B MET* 1.3 64.2 + - + +
30B MET* 3.3 19.1 - - + +
31B PHE* 3.0 25.0 + - + +
42B TRP* 6.1 2.9 - - + -
64B PHE* 4.8 6.7 - - + -
98B LEU* 3.7 30.1 - - + +
101B ARG 5.2 0.4 - - - -
102B SER* 3.2 33.0 - - - +
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Residues in contact with MET 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ARG 3.0 17.9 - - - +
25B LYS* 2.5 18.9 + - + +
27B LEU* 1.3 71.7 - - + +
29B ASP* 1.3 71.0 + - - +
30B MET 2.7 2.7 + - - -
31B PHE* 2.7 19.0 + - + +
32B ARG* 2.6 24.7 + - - +
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Residues in contact with ASP 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LYS* 2.7 41.5 + - - +
26B ASN* 3.8 9.5 - - - +
28B MET* 1.3 72.1 - - - +
30B MET* 1.3 59.7 + - - +
32B ARG* 2.9 55.0 + - - +
33B ASP* 3.1 14.2 + - - +
69E GLU* 4.9 1.0 - - - +
111E ASN* 3.6 24.6 + - - +
112E ALA* 4.5 8.5 + - + +
115E LEU* 4.6 9.1 - - + +
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Residues in contact with MET 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASN 3.0 14.0 + - - +
27B LEU* 3.3 27.6 - - + +
28B MET 2.7 3.0 + - - -
29B ASP* 1.3 73.7 - - - +
31B PHE* 1.3 67.0 + - - +
32B ARG 3.0 1.0 + - - -
33B ASP 3.4 2.3 + - - -
34B ARG* 3.1 19.4 + - - -
37B PHE* 4.0 25.9 - - + -
42B TRP* 4.7 15.6 + - + +
45B LEU* 4.7 20.6 - - + -
97B MET* 5.4 6.5 - - - +
98B LEU* 5.1 8.5 - - + -
101B ARG* 3.3 46.2 - - + +
115E LEU* 4.9 14.6 - - + +
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Residues in contact with PHE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 3.0 11.7 + - + +
28B MET* 2.7 23.5 + - + +
30B MET* 1.3 75.9 - - - +
32B ARG* 1.3 66.9 + - - +
34B ARG* 3.0 49.6 - - - +
42B TRP* 3.1 42.7 - + + -
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Residues in contact with ARG 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B MET 2.6 16.5 + - - +
29B ASP* 2.9 48.3 + - - +
30B MET 3.0 0.8 - - - -
31B PHE* 1.3 79.0 - - - +
33B ASP* 1.3 59.4 + - - +
34B ARG* 3.2 4.2 + - - +
35B GLN 5.0 0.3 + - - -
69E GLU* 3.2 38.4 + - - -
72E ARG* 3.3 43.7 + - - +
112E ALA* 3.9 15.4 - - - +
119E ARG* 5.0 3.3 + - - -
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Residues in contact with ASP 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ASP* 3.1 9.1 + - - +
30B MET 3.6 3.4 - - - -
32B ARG* 1.3 81.2 + - - +
34B ARG* 1.3 49.9 + - - +
35B GLN* 2.6 17.9 + - - -
36B ALA* 2.7 20.8 + - - +
37B PHE* 4.5 0.7 - - - -
72E ARG* 2.7 40.7 + - - -
112E ALA* 4.2 1.6 - - - +
115E LEU* 4.0 35.0 - - + +
116E VAL* 3.1 22.3 + - - +
119E ARG* 3.1 21.3 + - - +
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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