Contacts of the helix formed by residues 44 - 53 (chain A) in PDB entry 4CQM
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 ASP 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ASP* 2.6 22.3 + - - +
43A LEU* 1.3 71.3 - - - +
45A ARG* 1.3 66.4 + - - +
46A ALA* 3.3 13.3 + - - +
47A ALA* 2.7 46.9 + - + +
48A ALA 3.0 9.4 + - - -
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Residues in contact with ARG 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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42A ASP 4.5 0.7 - - - -
43A LEU 3.4 5.5 + - - -
44A ASP* 1.3 72.2 - - - +
46A ALA* 1.3 55.3 + - - +
48A ALA* 3.0 9.8 + - + +
49A GLN* 2.8 64.3 + - + +
71A ALA* 5.7 2.5 - - + +
72A PHE 5.5 1.6 - - - -
73A GLN* 3.7 31.8 - - + +
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Residues in contact with ALA 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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44A ASP* 3.2 10.9 + - - +
45A ARG* 1.3 82.2 - - - +
47A ALA* 1.3 57.1 + - - +
49A GLN* 3.6 13.6 + - - +
50A GLU* 3.0 27.3 + - - +
53A ARG* 5.1 2.1 + - - -
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Residues in contact with ALA 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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20A GLY* 3.3 24.6 - - - +
21A SER* 5.7 1.1 - - - -
25A ARG* 3.3 7.0 + - - +
42A ASP* 4.3 1.8 - - - +
44A ASP* 2.7 33.8 + - + +
46A ALA* 1.3 72.0 - - - +
48A ALA* 1.3 63.0 + - - +
50A GLU* 3.4 8.5 + - - +
51A THR* 2.9 26.9 + - - -
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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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20A GLY* 4.0 8.5 - - - +
40A ALA* 3.7 23.5 - - - +
42A ASP* 3.7 21.3 - - + -
44A ASP 3.0 6.5 + - - +
45A ARG* 3.4 9.0 - - - +
47A ALA* 1.3 76.0 - - - +
49A GLN* 1.3 63.9 + - - +
51A THR* 3.2 7.5 + - - -
52A VAL* 3.2 25.3 + - - +
71A ALA* 3.9 6.7 - - + -
72A PHE 3.8 11.0 - - - +
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Residues in contact with GLN 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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45A ARG* 2.8 49.3 + - + +
46A ALA* 3.8 13.9 - - - +
48A ALA* 1.3 69.3 - - - +
50A GLU* 1.3 66.2 + - - +
52A VAL* 3.3 5.2 + - - +
53A ARG* 3.3 34.4 + - - +
71A ALA* 3.7 22.6 - - + +
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Residues in contact with GLU 50 (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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25A ARG* 3.0 30.8 + - - +
46A ALA 3.0 18.8 + - - +
47A ALA* 3.6 6.8 - - - +
48A ALA 3.2 0.2 - - - -
49A GLN* 1.3 77.6 - - - +
51A THR* 1.3 61.0 + - - +
53A ARG* 3.3 43.2 + - - +
54A LEU* 3.5 13.0 - - + +
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Residues in contact with THR 51 (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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19A ALA 2.6 29.8 + - - +
20A GLY* 3.4 0.2 - - - -
25A ARG* 3.0 31.5 + - + +
28A SER* 3.8 26.9 - - - +
29A VAL* 5.5 0.4 - - + -
40A ALA* 4.6 6.5 - - + -
47A ALA 2.9 13.3 + - - -
48A ALA* 3.2 10.5 + - - -
49A GLN 3.2 0.4 - - - -
50A GLU* 1.3 76.7 - - - +
52A VAL* 1.3 63.9 + - - +
54A LEU* 3.1 19.8 + - + +
55A LEU* 3.3 10.9 - - + +
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Residues in contact with VAL 52 (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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40A ALA* 4.0 9.4 - - + +
48A ALA 3.2 15.4 + - - +
49A GLN* 3.3 8.7 + - - +
51A THR* 1.3 77.2 - - - +
53A ARG* 1.3 57.5 + - - +
54A LEU 3.1 0.2 - - - -
55A LEU* 3.0 32.4 + - + +
69A HIS* 3.9 32.4 - - + +
70A ALA* 3.7 16.6 - - - +
71A ALA* 3.6 22.4 - - + +
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Residues in contact with ARG 53 (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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46A ALA 5.1 1.6 + - - -
49A GLN* 3.3 15.9 + - - +
50A GLU* 3.3 57.9 + - + +
52A VAL* 1.3 79.7 - - - +
54A LEU* 1.3 63.9 + - + +
55A LEU 3.7 6.1 - - - +
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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