Contacts of the strand formed by residues 33 - 38 (chain A) in PDB entry 1D0D
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 CYS 33 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A TYR* 4.4 4.3 - - + -
26A PHE 3.1 7.9 - - - +
27A ARG* 4.1 2.7 - - - +
28A ASN* 3.8 3.0 + - - +
32A GLY* 1.3 81.0 - - - -
34A ASP* 1.3 71.5 + - - +
52A TYR* 3.2 36.7 + - + -
55A CYS* 2.0 65.5 - - + -
56A PHE* 3.6 7.4 - - - -
59A CYS* 4.8 0.4 - - - -
60A ILE* 4.4 4.0 - - - -
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Residues in contact with ASP 34 (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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25A TYR* 3.4 6.7 - - - -
26A PHE* 2.9 32.2 + - - +
28A ASN* 3.1 31.3 + - + +
33A CYS* 1.3 79.9 - - - +
35A SER* 1.3 67.9 + - - +
36A PHE* 4.0 0.5 + - - +
52A TYR* 5.5 0.2 - - - -
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Residues in contact with SER 35 (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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14A GLU* 4.5 4.0 - - - +
23A ARG* 4.1 15.7 - - - -
24A ALA 3.3 7.9 - - - -
25A TYR* 3.7 29.0 - - - -
34A ASP* 1.3 80.2 - - - +
36A PHE* 1.3 62.9 + - - +
37A TRP* 5.0 6.9 + - - -
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Residues in contact with PHE 36 (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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7A LYS* 3.9 26.5 - - + -
11A TRP* 3.9 44.6 - + + -
12A ILE 4.3 8.1 - - - -
13A ASP 3.5 22.7 - - - -
14A GLU* 3.5 25.6 - - + -
23A ARG* 3.6 0.6 - - - -
24A ALA* 2.8 31.5 + - - +
26A PHE* 4.0 21.1 - + + -
34A ASP 5.0 0.2 - - - +
35A SER* 1.3 77.5 - - - +
37A TRP* 1.3 79.9 + - - +
38A ILE* 3.5 17.0 + - + -
39A CYS 5.2 0.4 - - - -
42A ASP* 5.8 0.9 - - - -
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Residues in contact with TRP 37 (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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14A GLU* 2.9 34.5 + - + +
15A CYS 3.1 41.4 + - - +
16A ASP* 5.3 2.2 - - - -
17A SER* 3.7 25.4 - - - -
21A GLY 3.7 25.6 - - - -
22A GLU* 3.6 2.9 - - - -
23A ARG* 3.7 57.6 - - + +
35A SER* 5.0 6.6 + - - -
36A PHE* 1.3 77.2 - - - +
38A ILE* 1.3 60.9 + - - +
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Residues in contact with ILE 38 (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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11A TRP* 3.7 42.2 - - + -
15A CYS* 4.5 0.2 - - - -
20A GLY 4.2 0.7 - - - +
21A GLY* 3.2 7.9 - - - -
22A GLU* 2.9 34.4 + - - +
24A ALA* 3.7 23.8 - - + -
36A PHE* 3.9 17.5 - - + +
37A TRP* 1.3 71.9 - - - +
39A CYS* 1.3 74.4 + - - +
40A PRO 3.7 0.7 - - - -
42A ASP* 4.4 3.8 - - + -
43A HIS* 3.9 32.0 + - + +
48A TYR* 3.7 20.6 - - + -
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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