Contacts of the helix formed by residues 37 - 46 (chain B) in PDB entry 2OY0
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 ARG 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B VAL* 3.6 13.1 + - - +
36B ASP* 1.3 71.0 - - - +
38B SER* 1.3 66.5 + - - +
39B ALA 3.2 0.2 - - - -
40B ALA* 2.8 38.9 + - + +
41B LYS* 3.1 17.3 + - + +
44B ARG* 4.7 12.6 - - - +
54B PRO* 3.1 25.1 + - - +
55B VAL* 3.2 4.8 + - - +
56B SER* 3.0 42.4 + - - +
57B ARG* 3.7 49.6 - - + +
84B ARG* 5.4 0.2 - - - +
257B ASP* 3.1 25.2 + - - -
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Residues in contact with SER 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASP* 2.3 39.2 + - - -
37B ARG* 1.3 75.2 - - - +
39B ALA* 1.3 66.7 + - - +
41B LYS* 3.3 5.8 + - - +
42B HIS* 3.1 35.0 + - - -
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASP* 4.3 6.9 + - - +
37B ARG 2.8 4.2 + - - -
38B SER* 1.3 80.2 + - - +
40B ALA* 1.3 63.3 + - - +
42B HIS* 3.1 7.6 + - - +
43B ALA* 3.0 23.0 + - - +
53B HIS* 3.9 23.3 + - + +
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Residues in contact with ALA 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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36B ASP 5.3 0.2 + - - -
37B ARG* 2.8 50.6 + - + +
39B ALA* 1.3 74.4 - - - +
41B LYS* 1.3 62.1 - - - +
43B ALA* 2.9 13.8 + - - +
44B ARG* 3.1 22.0 + - - +
53B HIS* 4.1 22.0 + - + +
54B PRO 4.1 7.6 - - - +
257B ASP* 4.6 4.2 + - - +
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Residues in contact with LYS 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 ARG* 3.1 13.4 + - + +
38B SER* 3.5 12.8 - - - +
39B ALA 3.2 0.2 - - - -
40B ALA* 1.3 79.7 - - - +
42B HIS* 1.3 69.5 + - + +
44B ARG* 2.8 55.1 + - - +
45B LYS* 3.8 4.7 + - - +
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Residues in contact with HIS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B SER* 3.1 20.6 + - - +
39B ALA* 3.1 9.4 + - - +
41B LYS* 1.3 83.9 - - + +
43B ALA* 1.3 61.2 + - - +
44B ARG 3.2 1.8 - - - -
45B LYS* 3.2 52.7 + - + +
46B GLU* 3.6 8.5 + - - +
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Residues in contact with ALA 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 ALA 3.0 11.5 + - - +
40B ALA* 2.9 11.3 + - - +
42B HIS* 1.3 77.3 - - - +
44B ARG* 1.3 63.8 + - - +
46B GLU* 3.6 2.3 + - - -
47B GLY 3.4 1.9 + - - -
48B ASN* 2.8 52.8 + - + +
53B HIS* 3.7 29.4 - - + +
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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
----------------------------------------------------------
37B ARG* 4.7 11.7 - - - +
40B ALA* 3.1 33.1 + - - +
41B LYS* 2.8 51.8 - - - +
42B HIS 3.2 0.2 - - - -
43B ALA* 1.3 79.8 - - - +
45B LYS* 1.3 62.9 + - - +
47B GLY* 3.1 13.3 + - - -
48B ASN 5.0 0.9 - - - +
54B PRO 5.4 1.2 + - - -
55B VAL* 5.5 2.0 + - - +
84B ARG* 3.2 42.8 - - - +
114B GLN* 4.4 11.9 - - + -
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Residues in contact with LYS 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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41B LYS 3.8 4.4 + - - +
42B HIS* 3.2 52.9 + - + +
44B ARG* 1.3 76.4 - - - +
46B GLU* 1.3 80.8 + - - +
47B GLY* 2.7 16.4 + - - -
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Residues in contact with GLU 46 (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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42B HIS 3.6 16.1 + - - +
43B ALA* 3.6 6.0 + - - +
44B ARG 3.4 0.6 - - - -
45B LYS* 1.3 96.4 - - + +
47B GLY* 1.3 61.0 + - - +
48B ASN* 2.9 14.9 + - + +
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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