Contacts of the helix formed by residues 43 - 49 (chain A) in PDB entry 3M5B
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 HIS 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ALA* 3.5 29.5 + - + +
24A LEU* 4.8 6.3 - - + -
25A ARG* 4.0 2.6 + - - +
27A ALA 3.0 27.6 + - - -
28A LEU* 3.5 21.3 + - + +
29A CYS* 3.6 19.3 + - - -
30A ASP* 3.6 5.6 - - - +
42A ALA* 1.3 70.2 - - - +
44A SER* 1.3 66.1 + - - +
45A LEU* 3.1 4.0 - - + +
46A VAL* 3.1 25.6 + - + +
47A LEU* 3.2 15.0 + - - +
79A TYR* 2.8 43.0 + + - +
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Residues in contact with SER 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASP* 2.7 35.8 + - - -
31A THR* 3.4 19.5 + - - -
43A HIS* 1.3 70.9 - - - +
45A LEU* 1.3 58.6 + - - +
47A LEU* 3.4 9.8 + - - +
48A ALA* 3.0 30.0 + - - +
55A GLY* 3.8 3.9 - - - -
56A ARG* 3.8 22.7 - - - +
57A ARG* 4.2 3.1 - - - +
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 4.6 19.7 - - + -
43A HIS* 3.1 4.1 - - + +
44A SER* 1.3 80.6 + - - +
46A VAL* 1.3 69.3 + - + +
48A ALA* 3.4 9.8 + - + +
49A GLY* 3.2 17.8 + - - -
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 5.1 1.6 - - + +
18A VAL* 4.7 20.2 - - + -
21A ALA* 3.7 29.6 - - + -
43A HIS* 3.1 21.3 + - + +
45A LEU* 1.3 80.1 - - + +
47A LEU* 1.3 63.0 + - + +
49A GLY* 3.1 15.8 + - - -
50A VAL* 3.7 9.8 + - + +
78A VAL* 4.1 28.0 - - + +
79A TYR* 4.1 21.8 - - + +
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A THR* 4.3 11.4 - - + -
33A ILE* 4.1 19.5 - - + -
42A ALA* 4.0 20.0 - - + -
43A HIS 3.2 13.2 + - - +
44A SER* 3.5 10.1 - - - +
46A VAL* 1.3 76.3 - - + +
48A ALA* 1.3 63.4 + - - +
50A VAL* 3.0 6.0 + - - +
51A SER* 3.0 26.8 + - - +
54A LEU* 3.5 44.1 - - + +
55A GLY 4.3 0.4 - - - -
71A PHE* 6.1 0.4 - - + -
74A LEU* 6.2 0.2 - - + -
75A LEU* 4.1 25.8 - - + -
78A VAL* 4.3 15.9 - - + -
79A TYR* 5.6 1.3 - - + -
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A SER 3.0 17.2 + - - +
45A LEU* 3.7 14.4 - - + +
47A LEU* 1.3 76.2 - - - +
49A GLY* 1.3 61.8 + - - +
50A VAL 3.3 1.0 + - - -
51A SER 3.7 18.6 + - - -
52A GLN* 4.3 5.1 + - - +
55A GLY* 3.8 13.8 - - - +
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TYR* 5.1 4.9 + - - -
45A LEU 3.2 8.9 + - - -
46A VAL* 3.1 11.2 + - - -
48A ALA* 1.3 77.2 - - - +
50A VAL* 1.3 63.4 + - - +
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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