Contacts of the helix formed by residues 38 - 46 (chain B) in PDB entry 1UR6
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 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B CYS* 3.3 5.6 - - - -
20B PRO 4.4 2.0 - - - +
21B LEU* 3.4 28.1 - - + +
22B GLU 5.1 0.2 - - - +
25B ASP* 3.1 17.9 - - - +
37B ILE* 1.3 75.6 - - - +
39B ARG* 1.3 67.6 + - - +
40B PHE* 3.8 15.0 - - + +
41B CYS* 3.0 34.5 + - - +
42B TRP* 3.3 5.0 + - - +
79B ZN 2.4 37.9 - - - -
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Residues in contact with ARG 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLU* 5.3 0.2 - - - +
24B ASP* 2.7 39.2 + - - -
25B ASP* 2.7 45.2 + - - +
28B PHE* 3.6 38.5 - - + +
37B ILE 3.7 0.6 + - - -
38B CYS* 1.3 70.5 - - - +
40B PHE* 1.3 69.1 + - + +
41B CYS 2.8 6.8 + - - -
42B TRP* 4.4 9.8 - - + +
43B HIS* 3.3 27.4 + - - +
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Residues in contact with PHE 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.2 38.0 - - + +
22B GLU* 5.8 7.9 - - + -
25B ASP* 5.7 1.6 - - - -
38B CYS* 3.1 12.4 - - + -
39B ARG* 1.3 82.2 - - + +
41B CYS* 1.3 67.2 + - - +
43B HIS* 5.1 3.1 - - + -
44B ARG* 5.3 1.7 - - - +
79B ZN 3.8 1.9 - - - -
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Residues in contact with CYS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE* 3.9 2.3 - - - -
14B CYS* 3.3 7.2 - - - -
16B LEU* 3.5 29.8 - - + +
17B CYS* 3.1 18.2 - - - -
37B ILE* 4.4 5.2 - - + -
38B CYS* 3.1 13.2 - - - +
39B ARG 2.8 1.6 + - - -
40B PHE* 1.3 78.8 - - - +
42B TRP* 1.3 66.7 + - - +
43B HIS 3.2 0.9 - - - -
44B ARG* 3.2 17.7 + - - +
45B ILE* 3.1 16.8 + - - +
79B ZN 2.4 37.9 - - - -
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Residues in contact with TRP 42 (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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16B LEU* 4.4 0.2 - - - +
28B PHE* 3.7 37.0 - + + -
30B PRO* 3.7 21.3 - - + +
37B ILE* 4.2 12.5 - - + +
38B CYS 3.3 3.9 + - - +
39B ARG* 3.5 13.7 + - + +
41B CYS* 1.3 78.8 - - - +
43B HIS* 1.3 90.5 + + + +
45B ILE* 3.1 25.0 + - + +
46B ARG* 3.3 28.3 + - + +
51B GLY* 6.4 0.2 - - - -
60B TYR* 3.8 20.8 - + - +
62B GLU* 3.7 32.7 - - + +
63B ASP* 3.2 29.1 - - + -
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Residues in contact with HIS 43 (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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39B ARG 3.3 15.7 + - - +
40B PHE* 5.3 2.9 - - + -
41B CYS 3.2 1.0 - - - +
42B TRP* 1.3 101.9 - + + +
44B ARG* 1.3 55.2 + - - +
46B ARG* 3.1 42.2 + - - +
47B THR* 2.7 30.3 + - - -
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Residues in contact with ARG 44 (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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1A MET* 4.3 24.5 - - + -
2A ALA* 4.9 13.5 - - - +
58A THR* 3.3 22.8 + - - +
59A ASP* 2.7 31.3 + - - +
61A PRO* 6.0 1.0 - - - +
62A PHE* 3.3 28.0 - - + -
41B CYS* 3.2 15.7 + - - +
42B TRP 3.2 0.8 - - - -
43B HIS* 1.3 77.1 - - - +
45B ILE* 1.3 59.1 + - - +
47B THR* 2.9 29.3 + - - +
48B ASP* 2.6 48.2 + - - +
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Residues in contact with ILE 45 (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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62A PHE* 3.4 18.8 - - + -
95A PRO* 3.9 13.0 - - + -
16B LEU* 3.5 20.2 - - + -
37B ILE* 3.8 5.4 - - + -
41B CYS 3.1 13.7 - - - +
42B TRP* 3.1 18.6 + - + +
44B ARG* 1.3 75.8 - - - +
46B ARG* 1.3 56.6 + - - +
47B THR 3.2 0.4 - - - -
49B GLU* 2.9 43.7 + - + +
51B GLY* 3.1 8.7 + - - -
52B LEU 3.6 30.5 - - - +
54B PRO* 4.9 4.3 - - + -
60B TYR* 3.7 25.1 - - + +
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Residues in contact with ARG 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TRP* 3.3 24.6 + - - +
43B HIS* 3.1 42.5 + - - +
44B ARG 3.1 0.8 - - - -
45B ILE* 1.3 77.3 - - - +
47B THR* 1.3 58.9 + - - +
49B GLU 4.2 5.8 - - - -
50B ASN 5.9 1.1 - - - -
51B GLY* 4.4 10.3 - - - -
63B ASP* 2.7 63.3 + - - -
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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