Contacts of the helix formed by residues 32 - 44 (chain F) in PDB entry 5XRZ
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 THR 32 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208D CYS* 4.4 2.2 - - - -
203E ALA 4.7 0.3 + - - -
207E SER* 3.3 34.9 + - - +
30F GLN 3.6 4.5 + - - +
31F TYR* 1.3 77.6 - - - +
33F ALA* 1.3 59.7 + - - +
34F GLU* 3.6 18.8 + - - +
35F GLU* 3.4 21.3 + - - +
36F TYR* 2.9 29.9 + - - +
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Residues in contact with ALA 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D TYR* 3.9 27.9 - - + +
208D CYS* 3.6 34.4 - - + +
32F THR* 1.3 74.1 - - - +
34F GLU* 1.3 67.9 + - + +
36F TYR* 3.3 3.7 + - - +
37F GLN* 2.9 31.5 + - - +
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Residues in contact with GLU 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D TYR* 5.2 6.1 - - - +
203E ALA* 3.6 25.0 - - + +
206E ASN* 5.3 8.7 - - - +
207E SER* 5.4 0.9 - - - -
32F THR* 3.6 18.1 + - - +
33F ALA* 1.3 89.2 + - + +
35F GLU* 1.3 62.5 + - - +
37F GLN* 3.9 4.8 - - - +
38F ALA* 2.9 26.2 + - - +
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Residues in contact with GLU 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E VAL* 5.1 2.2 - - + -
203E ALA* 3.5 13.7 - - + +
204E ARG* 3.2 33.8 + - + +
207E SER* 3.2 22.7 + - - -
30F GLN 5.5 0.2 - - - +
31F TYR* 3.3 26.5 - - + -
32F THR* 3.4 17.2 + - - +
34F GLU* 1.3 77.4 - - - +
36F TYR* 1.3 64.6 + - - +
38F ALA* 3.8 2.3 - - - +
39F ILE* 2.9 45.4 + - + +
79F PHE 4.5 0.3 - - - +
116F LYS* 3.2 26.5 + - - -
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Residues in contact with TYR 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D GLU* 3.6 29.1 + - - -
204D ARG* 2.8 48.0 + - + -
205D TYR* 4.3 21.8 - + + -
208D CYS* 4.9 11.7 - - - -
80E GLY* 4.8 2.0 - - - -
81E TYR* 3.4 35.0 - + - -
82E ASN* 3.8 12.6 - - - -
31F TYR* 4.6 10.4 - - + +
32F THR 2.9 19.8 + - - +
33F ALA* 3.6 6.7 - - - +
35F GLU* 1.3 78.1 - - - +
37F GLN* 1.3 71.5 + - + +
39F ILE* 3.8 1.6 - - - +
40F GLN* 2.9 35.8 + - + +
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Residues in contact with GLN 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D GLU* 4.4 16.1 + - - +
205D TYR* 3.2 45.1 + - + +
33F ALA 2.9 16.5 + - - +
34F GLU* 4.0 4.4 - - - +
36F TYR* 1.3 81.8 - - - +
38F ALA* 1.3 63.5 + - - +
40F GLN* 3.3 5.3 + - + +
41F LYS* 2.9 64.5 + - + +
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Residues in contact with ALA 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E SER* 3.8 17.2 - - - +
200E VAL* 3.5 33.1 - - + +
203E ALA* 4.7 1.6 - - + -
34F GLU 2.9 19.2 + - - +
35F GLU* 3.8 4.5 - - - +
37F GLN* 1.3 77.0 - - - +
39F ILE* 1.3 56.5 + - - +
41F LYS* 3.4 5.6 + - - +
42F ALA* 2.9 31.4 + - - +
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Residues in contact with ILE 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E TYR* 3.4 42.6 - - + +
200E VAL* 3.6 10.1 - - + -
31F TYR* 3.8 13.2 - - + +
35F GLU* 2.9 40.1 + - + +
36F TYR 3.8 2.7 - - - +
38F ALA* 1.3 74.8 - - - +
40F GLN* 1.3 57.8 + - - +
42F ALA 3.4 0.2 + - - -
43F LEU* 2.8 39.8 + - + +
78F MET* 3.5 43.3 - - + +
79F PHE* 4.1 8.3 - - + -
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Residues in contact with GLN 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D GLU* 3.7 10.8 + - - +
204D ARG* 3.7 20.2 - - - +
76E ASN* 3.5 22.2 + - - +
77E GLU* 3.9 9.8 + - - +
80E GLY* 4.3 0.4 - - - -
81E TYR* 4.0 24.0 + - + +
36F TYR* 2.9 30.2 + - + +
37F GLN* 3.6 7.2 - - + +
39F ILE* 1.3 76.7 - - - +
41F LYS* 1.3 62.6 + - - +
43F LEU* 3.1 8.7 + - - +
44F ARG* 3.0 58.6 + - - +
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Residues in contact with LYS 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D GLU* 5.4 4.2 - - - +
37F GLN* 2.9 56.0 + - + +
38F ALA* 4.0 4.5 - - - +
40F GLN* 1.3 75.5 - - - +
42F ALA* 1.3 63.3 + - - +
44F ARG* 3.4 41.8 + - - +
45F GLN* 3.7 12.8 + - - +
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Residues in contact with ALA 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E LYS* 5.0 0.5 - - - +
197E GLU* 3.3 26.9 - - - +
200E VAL* 4.0 4.5 - - + -
38F ALA 2.9 18.1 + - - +
41F LYS* 1.3 76.3 - - - +
43F LEU* 1.3 60.9 + - - +
45F GLN* 3.3 23.8 - - - +
78F MET* 3.6 26.2 - - + +
161F ALA* 3.3 17.5 - - - +
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Residues in contact with LEU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E TYR* 3.7 25.6 - - + -
39F ILE* 2.8 35.9 + - + +
40F GLN* 3.1 8.0 + - - +
42F ALA* 1.3 73.4 - - - +
44F ARG* 1.3 65.0 + - - +
45F GLN 3.1 2.0 - - - -
78F MET* 3.6 16.2 - - + -
79F PHE* 4.5 3.8 - - + -
158F PHE* 3.5 30.1 - - + +
159F GLY* 3.8 3.3 - - - -
160F ASN* 3.2 10.6 + - - -
161F ALA* 3.2 28.8 + - + -
162F LEU* 3.8 34.8 - - + +
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Residues in contact with ARG 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D LEU* 3.4 27.8 - - - +
201D GLU* 3.8 12.3 + - - +
77E GLU* 3.0 42.7 + - - +
40F GLN* 3.0 46.8 + - - +
41F LYS* 3.4 43.6 + - - +
42F ALA 3.3 0.8 - - - -
43F LEU* 1.3 74.1 - - - +
45F GLN* 1.3 64.2 + - - +
46F ARG* 3.8 7.6 + - - +
160F ASN* 3.8 18.0 + - - +
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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