Contacts of the helix formed by residues 23 - 33 (chain B) in PDB entry 1A4Y
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 23 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A TYR* 5.8 3.1 - - + -
22B ASP* 1.3 76.2 - - + +
24B ARG* 1.3 56.2 + - - +
26B CYS* 3.3 2.6 + - - +
27B GLU* 3.0 38.4 + - - +
94B TYR 3.6 16.4 - - - +
95B ARG* 3.0 32.9 + - - +
96B ALA* 2.7 28.5 + - - +
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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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64A SER* 5.2 7.3 + - - -
66A GLU* 5.2 10.4 + - - +
93A ASN* 3.4 37.2 + - - +
19B GLN 5.5 5.1 + - - -
22B ASP* 3.1 17.1 + - - +
23B ASP* 1.3 77.7 - - - +
25B TYR* 1.3 68.0 + - - +
27B GLU* 3.6 7.2 + - - +
28B SER* 3.2 49.4 + - - -
32B ARG* 5.8 2.2 - - - +
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Residues in contact with TYR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASP* 2.4 35.3 + - - +
18B PRO 3.3 18.4 - - - -
19B GLN 4.3 3.4 - - - +
20B GLY* 3.1 31.9 - - - -
21B ARG* 4.0 7.6 - - - -
22B ASP* 2.8 24.9 + - - +
24B ARG* 1.3 79.5 - - - +
26B CYS* 1.3 61.6 + - - +
28B SER* 3.2 6.4 + - - -
29B ILE* 2.8 56.0 + - + +
45B PHE* 4.0 11.1 - + - +
47B HIS* 3.2 18.7 - + - -
79B THR* 3.9 28.5 - - + -
81B CYS* 4.9 0.7 - - - -
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Residues in contact with CYS 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 ASP 3.1 5.9 + - - +
23B ASP 3.3 9.6 + - - +
25B TYR* 1.3 77.9 - - - +
27B GLU* 1.3 64.4 + - - +
28B SER 3.1 0.2 + - - -
29B ILE* 3.9 2.5 - - - -
30B MET* 2.9 32.3 + - - +
79B THR* 4.4 6.3 - - - -
80B THR 4.1 0.9 - - - -
81B CYS* 2.0 53.8 - - - -
94B TYR* 3.7 16.2 - - + +
96B ALA* 3.3 30.1 - - + -
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Residues in contact with GLU 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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121A ASP* 5.7 0.9 - - - +
150A TYR* 4.5 12.6 + - - -
23B ASP* 3.0 17.5 + - - +
24B ARG* 3.8 7.1 - - - +
26B CYS* 1.3 78.0 - - - +
28B SER* 1.3 61.4 + - - +
30B MET* 4.2 1.6 - - - +
31B ARG* 3.4 30.3 + - - +
92B CYS 3.7 19.3 - - - +
93B GLN* 3.8 16.6 - - + +
94B TYR* 2.7 50.8 + - - +
95B ARG* 4.3 2.5 + - - -
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Residues in contact with SER 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASP* 4.4 4.2 + - - +
64A SER* 5.7 2.3 + - - -
93A ASN* 5.7 0.3 + - - -
24B ARG* 3.2 41.9 + - - -
25B TYR* 3.5 5.2 - - - -
26B CYS 3.1 0.6 - - - -
27B GLU* 1.3 79.0 - - - +
29B ILE* 1.3 63.8 + - - +
31B ARG* 3.3 8.5 + - - +
32B ARG* 2.9 49.8 + - - +
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Residues in contact with ILE 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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15B ASP* 3.7 23.1 - - - +
25B TYR* 2.8 41.3 + - + +
26B CYS* 3.5 12.1 - - - +
28B SER* 1.3 71.1 - - - +
30B MET* 1.3 67.8 + - - +
32B ARG* 3.3 10.9 + - + +
33B ARG* 3.0 58.1 + - + +
45B PHE* 3.3 41.3 - - + -
81B CYS* 4.5 0.4 - - - -
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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 CYS 2.9 21.8 + - - +
27B GLU 4.2 2.2 - - - +
29B ILE* 1.3 76.7 - - - +
31B ARG* 1.3 62.3 + - - +
33B ARG* 3.4 3.0 + - - +
34B GLY 3.1 3.8 + - - -
35B LEU* 3.1 43.9 + - + -
36B THR* 4.6 7.0 - - - +
40B LYS* 4.0 17.3 - - + +
43B ASN* 3.5 34.3 - - + +
45B PHE* 4.0 12.3 - - - -
81B CYS* 4.3 7.2 - - + -
94B TYR* 3.4 59.5 - - + +
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Residues in contact with ARG 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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10A GLN* 3.3 26.1 + - - +
11A CYS* 4.0 19.4 - - - -
33A ARG* 3.7 7.1 - - - +
35A ASP* 2.5 45.5 + - - -
36A ASP* 4.3 6.9 + - - +
63A ARG* 4.2 22.5 - - - +
64A SER* 4.5 4.2 + - - -
27B GLU* 3.4 17.4 + - - +
28B SER* 3.3 10.1 + - - +
29B ILE 3.2 0.4 - - - -
30B MET* 1.3 76.7 - - - +
32B ARG* 1.3 66.3 + - - +
34B GLY* 3.0 15.1 + - - -
36B THR* 4.2 29.8 - - + +
92B CYS 6.1 0.9 - - - +
1D SER* 4.2 6.1 + - - -
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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
----------------------------------------------------------
11A CYS* 3.9 24.6 - - + +
36A ASP* 2.5 55.0 + - - +
24B ARG* 5.8 2.0 - - - +
28B SER* 2.9 33.2 + - - +
29B ILE* 3.8 13.9 - - + +
31B ARG* 1.3 76.2 - - - +
33B ARG* 1.3 67.8 + - + +
34B GLY 3.7 0.3 + - - -
1D SER* 4.5 12.0 + - - -
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Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU 3.4 6.7 + - - -
11B THR* 2.7 62.6 + - - +
14B TYR 3.0 29.5 + - - -
15B ASP* 3.6 18.2 + - - +
29B ILE* 3.0 43.5 + - + +
30B MET 3.9 0.2 - - - +
32B ARG* 1.3 82.6 - - - +
34B GLY* 1.3 61.7 + - - +
35B LEU* 3.7 25.0 + - + +
45B PHE* 4.1 10.9 - - + -
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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