Contacts of the helix formed by residues 22 - 31 (chain A) in PDB entry 1U0O
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 ASN 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A MET* 1.3 78.8 - - - +
23A TRP* 1.3 66.1 + - - +
24A ALA* 3.6 7.8 + - - +
25A ASP* 2.9 51.9 + - - +
26A ALA* 3.0 21.0 + - - +
68A TRP* 3.7 2.5 - - - -
120A CYS 3.5 9.2 - - - +
121A ALA* 3.8 12.8 - - - +
122A GLN 2.9 16.6 - - - +
123A LYS* 4.2 14.2 - - + +
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Residues in contact with TRP 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ASN* 1.3 76.0 - - - +
24A ALA* 1.3 83.8 + - + +
26A ALA* 3.2 2.9 + - - +
27A GLU* 3.0 25.2 + - + +
39A LEU* 3.3 21.3 - - + +
68A TRP* 3.7 27.2 - + + +
69A ILE 2.8 22.4 + - - -
70A GLY 4.0 13.5 - - - -
71A LEU 4.1 5.5 + - - -
72A ARG* 3.7 51.4 - - + -
103A CYS* 3.3 39.5 - - + -
104A PHE 4.5 0.4 - - - -
120A CYS* 3.2 14.2 + - + +
278B GLU 5.8 0.2 - - - -
279B TRP 6.1 0.2 - - - -
280B THR* 3.4 28.7 - - + -
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ASN* 3.6 5.8 + - - +
23A TRP* 1.3 92.8 - - + +
25A ASP* 1.3 59.7 + - - +
27A GLU* 3.2 7.1 + - - +
28A ARG* 2.9 29.5 + - - +
72A ARG* 5.7 3.4 - - - +
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Residues in contact with ASP 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A MET* 3.0 31.9 - - + +
22A ASN* 2.9 47.1 + - - +
24A ALA* 1.3 76.6 - - - +
26A ALA* 1.3 65.3 + - - +
28A ARG* 3.6 10.3 + - - +
29A PHE 3.1 14.4 + - - -
123A LYS* 5.2 4.2 + - - -
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A MET* 4.0 12.1 - - + +
22A ASN 3.0 18.4 + - - +
23A TRP 3.7 1.6 - - - +
25A ASP* 1.3 76.7 - - - +
27A GLU* 1.3 63.6 + - - +
29A PHE* 3.6 2.8 + - - +
30A CYS* 3.1 28.2 + - - -
39A LEU* 3.6 17.5 - - + -
68A TRP* 4.4 5.6 - - + -
126A PHE* 3.5 32.8 - - + -
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Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TRP* 3.0 17.0 + - + +
24A ALA* 3.4 13.0 - - - +
26A ALA* 1.3 75.8 - - - +
28A ARG* 1.3 69.4 + - - +
30A CYS* 3.0 10.5 + - - +
31A SER* 3.1 14.3 + - - +
38A HIS* 2.9 45.1 + - - +
39A LEU* 3.0 23.3 + - + +
280B THR* 3.2 25.8 - - + +
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Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ALA 2.9 16.7 + - - +
25A ASP* 3.9 10.7 + - - +
27A GLU* 1.3 75.8 - - - +
29A PHE* 1.3 59.8 + - - +
31A SER* 2.8 32.4 + - - +
32A GLU* 3.2 41.1 + - - +
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Residues in contact with PHE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 3.2 23.3 - + - -
19A GLN* 3.4 33.4 - - - -
21A MET* 3.8 13.5 - - + -
25A ASP 3.1 17.0 + - - +
26A ALA 3.7 4.9 - - - +
28A ARG* 1.3 79.1 - - - +
30A CYS* 1.3 52.6 + - - +
32A GLU* 3.7 12.8 + - + +
33A GLN* 2.7 75.6 + - + +
126A PHE* 3.9 15.7 - + - -
128A CYS* 4.4 1.1 - - - -
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Residues in contact with CYS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A TRP* 5.2 1.6 - - - -
26A ALA 3.1 21.9 + - - -
27A GLU 3.0 5.2 + - - +
29A PHE* 1.3 73.4 - - - +
31A SER* 1.3 58.6 + - - +
32A GLU 2.9 10.4 + - - -
33A GLN* 3.3 11.3 + - - +
34A ALA* 3.8 5.9 + - - +
37A GLY* 3.3 14.7 - - - +
38A HIS* 3.3 35.9 - - - +
39A LEU* 3.7 6.5 - - - -
126A PHE* 4.3 4.5 - - - -
128A CYS* 2.0 53.2 - - + -
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Residues in contact with SER 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLU* 3.1 13.7 + - - +
28A ARG* 2.8 19.2 + - - +
30A CYS* 1.3 73.6 - - - +
32A GLU* 1.3 66.2 + - - +
34A ALA 4.4 8.7 - - - -
37A GLY 3.0 18.1 + - - +
38A HIS* 4.8 9.4 - - - -
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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