Contacts of the helix formed by residues 33 - 41 (chain B) in PDB entry 1RIO
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 33 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B TYR* 3.2 11.2 - - - -
32B LEU* 1.3 74.7 - - - +
34B GLN* 1.3 65.2 + - - +
35B GLU* 3.4 12.5 + - - +
36B SER* 2.8 42.5 + - - -
37B VAL* 3.0 15.1 + - - +
7T C 4.3 26.6 + - - -
8T A 3.6 10.3 - - - -
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Residues in contact with GLN 34 (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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20B LYS* 5.0 2.6 - - - +
23B TYR* 3.0 18.4 + - + +
24B GLU* 5.1 0.6 + - - -
33B SER* 1.3 70.6 - - - +
35B GLU* 1.3 61.9 + - - +
37B VAL* 3.6 4.8 + - - +
38B ALA* 3.1 24.3 + - - +
45B GLN* 3.0 32.9 + - + +
48B VAL* 3.9 14.7 - - + +
49B GLY* 3.4 15.4 - - - -
52B PHE* 3.6 35.1 - - + +
8T A 2.8 35.9 + - - +
9T A 2.6 28.7 + - - +
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Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B SER* 3.4 9.1 + - - +
34B GLN* 1.3 80.5 - - - +
36B SER* 1.3 62.2 + - - +
38B ALA* 3.3 4.0 + - - +
39B ASP* 3.2 20.3 + - - +
45B GLN* 3.9 26.1 - - + +
413H ARG* 2.9 37.9 + - - +
414H GLN* 4.3 13.0 - - - +
417H ASN* 3.3 31.2 - - + +
421H ARG* 4.8 7.7 + - - +
7T C 4.0 10.2 + - + -
8T A 4.4 0.8 + - - -
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Residues in contact with SER 36 (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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31B GLY 4.2 3.5 + - - -
32B LEU* 3.5 15.7 - - - +
33B SER* 2.8 40.4 + - - -
35B GLU* 1.3 70.9 - - - +
37B VAL* 1.3 67.1 + - - +
39B ASP* 3.4 4.6 + - - +
40B LYS* 3.3 29.7 + - - +
421H ARG* 4.1 29.2 + - - +
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Residues in contact with VAL 37 (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* 4.3 12.1 - - + -
32B LEU* 4.0 30.7 - - + -
33B SER 3.0 17.6 + - - +
34B GLN* 3.7 6.7 - - - +
36B SER* 1.3 74.1 + - - +
38B ALA* 1.3 66.5 + - - +
40B LYS* 3.0 18.1 + - - +
41B MSE 3.2 20.7 + - + +
48B VAL* 4.3 9.2 - - + -
52B PHE* 4.7 2.5 - - + -
66B LEU* 3.8 28.9 - - + -
69B ILE* 4.4 15.7 - - + -
70B LEU* 5.6 2.2 - - + -
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Residues in contact with ALA 38 (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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34B GLN 3.1 15.4 + - - +
35B GLU 3.5 5.6 - - - +
36B SER 3.3 0.2 - - - -
37B VAL* 1.3 78.7 - - - +
39B ASP* 1.3 58.8 + - - +
41B MSE 2.8 18.6 + - - +
42B GLY 3.0 0.2 + - - -
43B MSE 3.0 35.2 + - - +
44B GLY 3.3 26.7 - - - +
45B GLN* 3.8 1.6 - - - +
48B VAL* 3.5 15.9 - - + -
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Residues in contact with ASP 39 (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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35B GLU 3.2 10.5 + - - +
36B SER 3.5 9.9 - - - +
37B VAL 3.2 0.2 - - - -
38B ALA* 1.3 80.2 - - - +
40B LYS* 1.3 65.4 + - + +
41B MSE 3.1 0.7 + - - -
42B GLY* 3.3 10.0 + - - +
43B MSE 3.6 6.7 + - - +
418H LYS* 2.3 39.6 + - + +
421H ARG* 3.1 41.6 + - - +
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Residues in contact with LYS 40 (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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32B LEU* 4.4 17.3 - - + +
36B SER* 3.3 19.7 + - - +
37B VAL* 3.0 6.4 + - - +
39B ASP* 1.3 81.9 - - + +
41B MSE 1.3 59.4 + - - +
42B GLY 3.5 0.4 + - - -
65B LEU* 5.0 5.5 - - - +
69B ILE* 3.3 40.0 - - + +
421H ARG* 5.9 3.6 - - - +
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Residues in contact with MSE 41 (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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37B VAL* 3.4 13.0 - - + +
38B ALA* 2.8 8.6 + - - +
40B LYS* 1.3 81.1 - - - +
42B GLY* 1.3 59.4 + - - +
43B MSE 3.6 21.7 + - + +
48B VAL* 3.7 19.1 - - - -
51B LEU* 4.1 7.9 - - + -
61B TYR* 5.8 0.7 - - - -
62B ASN* 3.6 42.9 - - + +
65B LEU* 4.2 30.2 - - + +
66B LEU* 3.6 36.8 - - + -
69B ILE* 4.7 7.0 - - + -
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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