Contacts of the helix formed by residues 47 - 56 (chain B) 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 SER 47 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B TYR* 3.7 9.0 - - - -
45B PHE* 3.4 4.2 - - - +
46B LYS* 1.3 81.8 - - - +
48B ALA* 1.3 64.0 + - - +
49B GLU* 3.6 14.5 + - - +
50B ASP* 3.3 23.6 + - - +
51B CYS* 3.2 19.9 + - - +
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Residues in contact with ALA 48 (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 TYR* 3.7 37.8 - - + +
30B CYS* 4.4 6.2 - - + +
47B SER* 1.3 74.1 - - - +
49B GLU* 1.3 62.6 + - + +
51B CYS* 3.3 5.8 + - - +
52B MET* 2.9 36.1 + - + +
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Residues in contact with GLU 49 (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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47B SER* 3.6 12.8 - - - +
48B ALA* 1.3 89.0 + - + +
50B ASP* 1.3 57.2 + - - +
52B MET* 3.3 6.6 + - - +
53B ARG* 3.0 29.2 + - - +
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Residues in contact with ASP 50 (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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45B PHE* 3.8 18.5 - - + +
46B LYS 5.5 1.3 + - - +
47B SER* 3.3 21.2 + - - +
49B GLU* 1.3 77.5 - - - +
51B CYS* 1.3 63.0 + - - +
53B ARG* 2.9 35.3 + - - +
54B THR* 3.0 30.7 + - - -
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Residues in contact with CYS 51 (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 TYR* 4.2 2.9 - - + -
22B PHE* 3.7 4.3 - - - -
23B TYR* 3.6 17.5 - - - -
30B CYS* 2.0 47.8 - - + -
45B PHE* 3.4 40.1 - - + -
47B SER 3.2 11.8 + - - +
48B ALA 3.5 6.1 - - - +
50B ASP* 1.3 78.1 - - - +
52B MET* 1.3 56.2 + - - +
54B THR* 3.9 0.5 - - - -
55B CYS* 2.9 29.8 + - - +
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Residues in contact with MET 52 (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 TYR* 4.5 1.1 - - - -
28B GLY 4.0 15.9 - - - +
29B LEU* 3.9 11.0 - - + -
30B CYS* 3.6 33.9 - - + -
48B ALA* 2.9 22.2 + - + +
49B GLU* 3.3 5.6 + - - +
51B CYS* 1.3 76.0 - - - +
53B ARG* 1.3 59.3 + - - +
56B GLY* 2.7 45.1 + - - +
57B GLY 4.2 0.9 + - - -
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Residues in contact with ARG 53 (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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45B PHE* 5.7 0.2 - - - -
49B GLU 3.0 17.1 + - - +
50B ASP* 2.9 31.8 + - - +
51B CYS 3.3 0.4 - - - -
52B MET* 1.3 77.6 - - - +
54B THR* 1.3 88.4 + - - +
56B GLY 4.7 0.3 + - - -
57B GLY 5.2 0.5 + - - -
58B ALA* 4.2 11.4 + - - +
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Residues in contact with THR 54 (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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2B PRO* 3.6 10.2 - - + +
4B PHE* 3.9 24.9 - - + -
45B PHE* 3.4 30.7 - - + -
50B ASP 3.0 18.0 + - - -
53B ARG* 1.3 107.7 + - - +
55B CYS* 1.3 57.1 + - - +
56B GLY 3.8 0.2 - - - -
58B ALA* 3.1 23.5 - - - +
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Residues in contact with CYS 55 (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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1B ARG* 2.7 34.2 + - - +
4B PHE* 4.2 2.0 - - - -
5B CYS* 2.0 50.9 - - - -
23B TYR* 3.6 33.3 - - + -
43B ASN* 4.4 0.4 - - - -
45B PHE* 3.9 25.1 - - - -
51B CYS 2.9 9.7 + - - +
54B THR* 1.3 78.7 - - - +
56B GLY* 1.3 59.9 + - - +
57B GLY 3.4 2.7 - - - -
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Residues in contact with GLY 56 (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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1B ARG* 3.0 18.0 + - - -
23B TYR* 4.1 14.0 + - - -
28B GLY 5.6 0.5 - - - +
51B CYS 3.9 0.6 + - - -
52B MET* 2.7 43.5 + - - +
55B CYS* 1.3 72.4 - - - +
57B GLY* 1.3 56.0 + - - +
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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